From 4f67d128505409f619fdc7da35aaf196e5a5b16a Mon Sep 17 00:00:00 2001
From: Jason Wood <jasonwood8123@gmail.com>
Date: Tue, 5 Aug 2025 13:05:04 +0100
Subject: [PATCH 01/13] adding get_values to CategoricalVariable and making a
 new function for IntegerVariable

---
 R/RcppExports.R                    | 1006 ++++-----
 R/categorical_variable.R           |    9 +
 R/integer_variable.R               |    9 +
 inst/include/CategoricalVariable.h |   23 +-
 inst/include/IntegerVariable.h     |   18 +
 inst/include/individual_types.h    |    1 +
 src/RcppExports.cpp                | 3251 ++++++++++++++--------------
 src/categorical_variable.cpp       |   11 +
 src/integer_variable.cpp           |    9 +
 9 files changed, 2225 insertions(+), 2112 deletions(-)

diff --git a/R/RcppExports.R b/R/RcppExports.R
index e8f2962..6967dfe 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -1,499 +1,507 @@
-# Generated by using Rcpp::compileAttributes() -> do not edit by hand
-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-create_bitset <- function(size) {
-    .Call(`_individual_create_bitset`, size)
-}
-
-bitset_copy <- function(b) {
-    .Call(`_individual_bitset_copy`, b)
-}
-
-bitset_insert <- function(b, v) {
-    invisible(.Call(`_individual_bitset_insert`, b, v))
-}
-
-bitset_remove <- function(b, v) {
-    invisible(.Call(`_individual_bitset_remove`, b, v))
-}
-
-bitset_clear <- function(b) {
-    invisible(.Call(`_individual_bitset_clear`, b))
-}
-
-bitset_size <- function(b) {
-    .Call(`_individual_bitset_size`, b)
-}
-
-bitset_max_size <- function(b) {
-    .Call(`_individual_bitset_max_size`, b)
-}
-
-bitset_and <- function(a, b) {
-    invisible(.Call(`_individual_bitset_and`, a, b))
-}
-
-bitset_not <- function(b, inplace) {
-    .Call(`_individual_bitset_not`, b, inplace)
-}
-
-bitset_or <- function(a, b) {
-    invisible(.Call(`_individual_bitset_or`, a, b))
-}
-
-bitset_copy_from <- function(a, b) {
-    invisible(.Call(`_individual_bitset_copy_from`, a, b))
-}
-
-bitset_xor <- function(a, b) {
-    invisible(.Call(`_individual_bitset_xor`, a, b))
-}
-
-bitset_set_difference <- function(a, b) {
-    invisible(.Call(`_individual_bitset_set_difference`, a, b))
-}
-
-bitset_sample <- function(b, rate) {
-    invisible(.Call(`_individual_bitset_sample`, b, rate))
-}
-
-bitset_sample_vector <- function(b, rate) {
-    invisible(.Call(`_individual_bitset_sample_vector`, b, rate))
-}
-
-bitset_to_vector <- function(b) {
-    .Call(`_individual_bitset_to_vector`, b)
-}
-
-filter_bitset_integer <- function(b, other) {
-    .Call(`_individual_filter_bitset_integer`, b, other)
-}
-
-filter_bitset_bitset <- function(b, other) {
-    .Call(`_individual_filter_bitset_bitset`, b, other)
-}
-
-filter_bitset_logical <- function(bitset, other) {
-    .Call(`_individual_filter_bitset_logical`, bitset, other)
-}
-
-bitset_choose <- function(b, k) {
-    invisible(.Call(`_individual_bitset_choose`, b, k))
-}
-
-create_categorical_variable <- function(categories, values) {
-    .Call(`_individual_create_categorical_variable`, categories, values)
-}
-
-categorical_variable_get_size <- function(variable) {
-    .Call(`_individual_categorical_variable_get_size`, variable)
-}
-
-categorical_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_update`, variable, value, index))
-}
-
-categorical_variable_get_index_of <- function(variable, values) {
-    .Call(`_individual_categorical_variable_get_index_of`, variable, values)
-}
-
-categorical_variable_get_size_of <- function(variable, values) {
-    .Call(`_individual_categorical_variable_get_size_of`, variable, values)
-}
-
-categorical_variable_get_categories <- function(variable) {
-    .Call(`_individual_categorical_variable_get_categories`, variable)
-}
-
-categorical_variable_queue_update_vector <- function(variable, value, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_update_vector`, variable, value, index))
-}
-
-categorical_variable_update <- function(variable) {
-    invisible(.Call(`_individual_categorical_variable_update`, variable))
-}
-
-categorical_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_categorical_variable_queue_extend`, variable, values))
-}
-
-categorical_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_shrink`, variable, index))
-}
-
-categorical_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_shrink_bitset`, variable, index))
-}
-
-create_double_variable <- function(values) {
-    .Call(`_individual_create_double_variable`, values)
-}
-
-double_variable_get_values <- function(variable) {
-    .Call(`_individual_double_variable_get_values`, variable)
-}
-
-double_variable_get_values_at_index <- function(variable, index) {
-    .Call(`_individual_double_variable_get_values_at_index`, variable, index)
-}
-
-double_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_double_variable_get_values_at_index_vector`, variable, index)
-}
-
-double_variable_get_index_of_range <- function(variable, a, b) {
-    .Call(`_individual_double_variable_get_index_of_range`, variable, a, b)
-}
-
-double_variable_get_size_of_range <- function(variable, a, b) {
-    .Call(`_individual_double_variable_get_size_of_range`, variable, a, b)
-}
-
-double_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_double_variable_queue_fill`, variable, value))
-}
-
-double_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_variable_queue_update`, variable, value, index))
-}
-
-double_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_variable_queue_update_bitset`, variable, value, index))
-}
-
-double_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_double_variable_queue_extend`, variable, values))
-}
-
-double_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_double_variable_queue_shrink`, variable, index))
-}
-
-double_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_double_variable_queue_shrink_bitset`, variable, index))
-}
-
-create_event <- function() {
-    .Call(`_individual_create_event`)
-}
-
-create_targeted_event <- function(size) {
-    .Call(`_individual_create_targeted_event`, size)
-}
-
-event_base_tick <- function(event) {
-    invisible(.Call(`_individual_event_base_tick`, event))
-}
-
-event_base_get_timestep <- function(event) {
-    .Call(`_individual_event_base_get_timestep`, event)
-}
-
-event_base_set_timestep <- function(event, time) {
-    invisible(.Call(`_individual_event_base_set_timestep`, event, time))
-}
-
-event_base_should_trigger <- function(event) {
-    .Call(`_individual_event_base_should_trigger`, event)
-}
-
-event_schedule <- function(event, delays) {
-    invisible(.Call(`_individual_event_schedule`, event, delays))
-}
-
-event_clear_schedule <- function(event) {
-    invisible(.Call(`_individual_event_clear_schedule`, event))
-}
-
-event_checkpoint <- function(event) {
-    .Call(`_individual_event_checkpoint`, event)
-}
-
-event_restore <- function(event, schedule) {
-    invisible(.Call(`_individual_event_restore`, event, schedule))
-}
-
-targeted_event_clear_schedule_vector <- function(event, target) {
-    invisible(.Call(`_individual_targeted_event_clear_schedule_vector`, event, target))
-}
-
-targeted_event_clear_schedule <- function(event, target) {
-    invisible(.Call(`_individual_targeted_event_clear_schedule`, event, target))
-}
-
-targeted_event_get_scheduled <- function(event) {
-    .Call(`_individual_targeted_event_get_scheduled`, event)
-}
-
-targeted_event_schedule <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule`, event, target, delay))
-}
-
-targeted_event_queue_shrink_bitset <- function(event, index) {
-    invisible(.Call(`_individual_targeted_event_queue_shrink_bitset`, event, index))
-}
-
-targeted_event_queue_shrink <- function(event, index) {
-    invisible(.Call(`_individual_targeted_event_queue_shrink`, event, index))
-}
-
-targeted_event_queue_extend <- function(event, n) {
-    invisible(.Call(`_individual_targeted_event_queue_extend`, event, n))
-}
-
-targeted_event_queue_extend_with_schedule <- function(event, delays) {
-    invisible(.Call(`_individual_targeted_event_queue_extend_with_schedule`, event, delays))
-}
-
-targeted_event_schedule_vector <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule_vector`, event, target, delay))
-}
-
-targeted_event_schedule_multi_delay <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule_multi_delay`, event, target, delay))
-}
-
-targeted_event_schedule_multi_delay_vector <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule_multi_delay_vector`, event, target, delay))
-}
-
-targeted_event_get_target <- function(event) {
-    .Call(`_individual_targeted_event_get_target`, event)
-}
-
-targeted_event_resize <- function(event) {
-    invisible(.Call(`_individual_targeted_event_resize`, event))
-}
-
-targeted_event_checkpoint <- function(event) {
-    .Call(`_individual_targeted_event_checkpoint`, event)
-}
-
-targeted_event_restore <- function(event, state) {
-    invisible(.Call(`_individual_targeted_event_restore`, event, state))
-}
-
-process_listener <- function(event, listener) {
-    invisible(.Call(`_individual_process_listener`, event, listener))
-}
-
-process_targeted_listener <- function(event, listener, target) {
-    invisible(.Call(`_individual_process_targeted_listener`, event, listener, target))
-}
-
-create_integer_variable <- function(values) {
-    .Call(`_individual_create_integer_variable`, values)
-}
-
-integer_variable_get_values <- function(variable) {
-    .Call(`_individual_integer_variable_get_values`, variable)
-}
-
-integer_variable_get_values_at_index <- function(variable, index) {
-    .Call(`_individual_integer_variable_get_values_at_index`, variable, index)
-}
-
-integer_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_integer_variable_get_values_at_index_vector`, variable, index)
-}
-
-integer_variable_get_index_of_set_vector <- function(variable, values_set) {
-    .Call(`_individual_integer_variable_get_index_of_set_vector`, variable, values_set)
-}
-
-integer_variable_get_index_of_set_scalar <- function(variable, values_set) {
-    .Call(`_individual_integer_variable_get_index_of_set_scalar`, variable, values_set)
-}
-
-integer_variable_get_index_of_range <- function(variable, a, b) {
-    .Call(`_individual_integer_variable_get_index_of_range`, variable, a, b)
-}
-
-integer_variable_get_size_of_set_vector <- function(variable, values_set) {
-    .Call(`_individual_integer_variable_get_size_of_set_vector`, variable, values_set)
-}
-
-integer_variable_get_size_of_set_scalar <- function(variable, value) {
-    .Call(`_individual_integer_variable_get_size_of_set_scalar`, variable, value)
-}
-
-integer_variable_get_size_of_range <- function(variable, a, b) {
-    .Call(`_individual_integer_variable_get_size_of_range`, variable, a, b)
-}
-
-integer_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_integer_variable_queue_fill`, variable, value))
-}
-
-integer_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_variable_queue_update`, variable, value, index))
-}
-
-integer_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_variable_queue_update_bitset`, variable, value, index))
-}
-
-integer_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_integer_variable_queue_extend`, variable, values))
-}
-
-integer_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_integer_variable_queue_shrink`, variable, index))
-}
-
-integer_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_integer_variable_queue_shrink_bitset`, variable, index))
-}
-
-fixed_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate, destination_probabilities) {
-    .Call(`_individual_fixed_probability_multinomial_process_internal`, variable, source_state, destination_states, rate, destination_probabilities)
-}
-
-multi_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate_variable, destination_probabilities) {
-    .Call(`_individual_multi_probability_multinomial_process_internal`, variable, source_state, destination_states, rate_variable, destination_probabilities)
-}
-
-multi_probability_bernoulli_process_internal <- function(variable, from, to, rate_variable) {
-    .Call(`_individual_multi_probability_bernoulli_process_internal`, variable, from, to, rate_variable)
-}
-
-infection_age_process_internal <- function(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing) {
-    .Call(`_individual_infection_age_process_internal`, state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing)
-}
-
-create_double_ragged_variable <- function(values) {
-    .Call(`_individual_create_double_ragged_variable`, values)
-}
-
-double_ragged_variable_get_values <- function(variable) {
-    .Call(`_individual_double_ragged_variable_get_values`, variable)
-}
-
-double_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_values_at_index_bitset`, variable, index)
-}
-
-double_ragged_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_values_at_index_vector`, variable, index)
-}
-
-double_ragged_variable_get_length <- function(variable) {
-    .Call(`_individual_double_ragged_variable_get_length`, variable)
-}
-
-double_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_length_at_index_bitset`, variable, index)
-}
-
-double_ragged_variable_get_length_at_index_vector <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_length_at_index_vector`, variable, index)
-}
-
-double_ragged_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_fill`, variable, value))
-}
-
-double_ragged_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_update`, variable, value, index))
-}
-
-double_ragged_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_update_bitset`, variable, value, index))
-}
-
-double_ragged_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_extend`, variable, values))
-}
-
-double_ragged_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_shrink`, variable, index))
-}
-
-double_ragged_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_shrink_bitset`, variable, index))
-}
-
-create_integer_ragged_variable <- function(values) {
-    .Call(`_individual_create_integer_ragged_variable`, values)
-}
-
-integer_ragged_variable_get_values <- function(variable) {
-    .Call(`_individual_integer_ragged_variable_get_values`, variable)
-}
-
-integer_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_values_at_index_bitset`, variable, index)
-}
-
-integer_ragged_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_values_at_index_vector`, variable, index)
-}
-
-integer_ragged_variable_get_length <- function(variable) {
-    .Call(`_individual_integer_ragged_variable_get_length`, variable)
-}
-
-integer_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_length_at_index_bitset`, variable, index)
-}
-
-integer_ragged_variable_get_length_at_index_vector <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_length_at_index_vector`, variable, index)
-}
-
-integer_ragged_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_fill`, variable, value))
-}
-
-integer_ragged_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_update`, variable, value, index))
-}
-
-integer_ragged_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_update_bitset`, variable, value, index))
-}
-
-integer_ragged_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_extend`, variable, values))
-}
-
-integer_ragged_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink`, variable, index))
-}
-
-integer_ragged_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink_bitset`, variable, index))
-}
-
-create_render_vector <- function(data) {
-    .Call(`_individual_create_render_vector`, data)
-}
-
-render_vector_update <- function(v, index, value) {
-    invisible(.Call(`_individual_render_vector_update`, v, index, value))
-}
-
-render_vector_data <- function(v) {
-    .Call(`_individual_render_vector_data`, v)
-}
-
-execute_process <- function(process, timestep) {
-    invisible(.Call(`_individual_execute_process`, process, timestep))
-}
-
-variable_get_size <- function(variable) {
-    .Call(`_individual_variable_get_size`, variable)
-}
-
-variable_update <- function(variable) {
-    invisible(.Call(`_individual_variable_update`, variable))
-}
-
-variable_resize <- function(variable) {
-    invisible(.Call(`_individual_variable_resize`, variable))
-}
-
-# Register entry points for exported C++ functions
-methods::setLoadAction(function(ns) {
-    .Call(`_individual_RcppExport_registerCCallable`)
-})
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+create_bitset <- function(size) {
+    .Call(`_individual_create_bitset`, size)
+}
+
+bitset_copy <- function(b) {
+    .Call(`_individual_bitset_copy`, b)
+}
+
+bitset_insert <- function(b, v) {
+    invisible(.Call(`_individual_bitset_insert`, b, v))
+}
+
+bitset_remove <- function(b, v) {
+    invisible(.Call(`_individual_bitset_remove`, b, v))
+}
+
+bitset_clear <- function(b) {
+    invisible(.Call(`_individual_bitset_clear`, b))
+}
+
+bitset_size <- function(b) {
+    .Call(`_individual_bitset_size`, b)
+}
+
+bitset_max_size <- function(b) {
+    .Call(`_individual_bitset_max_size`, b)
+}
+
+bitset_and <- function(a, b) {
+    invisible(.Call(`_individual_bitset_and`, a, b))
+}
+
+bitset_not <- function(b, inplace) {
+    .Call(`_individual_bitset_not`, b, inplace)
+}
+
+bitset_or <- function(a, b) {
+    invisible(.Call(`_individual_bitset_or`, a, b))
+}
+
+bitset_copy_from <- function(a, b) {
+    invisible(.Call(`_individual_bitset_copy_from`, a, b))
+}
+
+bitset_xor <- function(a, b) {
+    invisible(.Call(`_individual_bitset_xor`, a, b))
+}
+
+bitset_set_difference <- function(a, b) {
+    invisible(.Call(`_individual_bitset_set_difference`, a, b))
+}
+
+bitset_sample <- function(b, rate) {
+    invisible(.Call(`_individual_bitset_sample`, b, rate))
+}
+
+bitset_sample_vector <- function(b, rate) {
+    invisible(.Call(`_individual_bitset_sample_vector`, b, rate))
+}
+
+bitset_to_vector <- function(b) {
+    .Call(`_individual_bitset_to_vector`, b)
+}
+
+filter_bitset_integer <- function(b, other) {
+    .Call(`_individual_filter_bitset_integer`, b, other)
+}
+
+filter_bitset_bitset <- function(b, other) {
+    .Call(`_individual_filter_bitset_bitset`, b, other)
+}
+
+filter_bitset_logical <- function(bitset, other) {
+    .Call(`_individual_filter_bitset_logical`, bitset, other)
+}
+
+bitset_choose <- function(b, k) {
+    invisible(.Call(`_individual_bitset_choose`, b, k))
+}
+
+create_categorical_variable <- function(categories, values) {
+    .Call(`_individual_create_categorical_variable`, categories, values)
+}
+
+categorical_variable_get_size <- function(variable) {
+    .Call(`_individual_categorical_variable_get_size`, variable)
+}
+
+categorical_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_update`, variable, value, index))
+}
+
+categorical_variable_get_index_of <- function(variable, values) {
+    .Call(`_individual_categorical_variable_get_index_of`, variable, values)
+}
+
+categorical_variable_get_size_of <- function(variable, values) {
+    .Call(`_individual_categorical_variable_get_size_of`, variable, values)
+}
+
+categorical_variable_get_categories <- function(variable) {
+    .Call(`_individual_categorical_variable_get_categories`, variable)
+}
+
+categorical_variable_queue_update_vector <- function(variable, value, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_update_vector`, variable, value, index))
+}
+
+categorical_variable_update <- function(variable) {
+    invisible(.Call(`_individual_categorical_variable_update`, variable))
+}
+
+categorical_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_categorical_variable_queue_extend`, variable, values))
+}
+
+categorical_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_shrink`, variable, index))
+}
+
+categorical_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_shrink_bitset`, variable, index))
+}
+
+categorical_variable_get_values <- function(variable, index) {
+    .Call(`_individual_categorical_variable_get_values`, variable, index)
+}
+
+create_double_variable <- function(values) {
+    .Call(`_individual_create_double_variable`, values)
+}
+
+double_variable_get_values <- function(variable) {
+    .Call(`_individual_double_variable_get_values`, variable)
+}
+
+double_variable_get_values_at_index <- function(variable, index) {
+    .Call(`_individual_double_variable_get_values_at_index`, variable, index)
+}
+
+double_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_double_variable_get_values_at_index_vector`, variable, index)
+}
+
+double_variable_get_index_of_range <- function(variable, a, b) {
+    .Call(`_individual_double_variable_get_index_of_range`, variable, a, b)
+}
+
+double_variable_get_size_of_range <- function(variable, a, b) {
+    .Call(`_individual_double_variable_get_size_of_range`, variable, a, b)
+}
+
+double_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_double_variable_queue_fill`, variable, value))
+}
+
+double_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_variable_queue_update`, variable, value, index))
+}
+
+double_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_variable_queue_update_bitset`, variable, value, index))
+}
+
+double_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_double_variable_queue_extend`, variable, values))
+}
+
+double_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_double_variable_queue_shrink`, variable, index))
+}
+
+double_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_double_variable_queue_shrink_bitset`, variable, index))
+}
+
+create_event <- function() {
+    .Call(`_individual_create_event`)
+}
+
+create_targeted_event <- function(size) {
+    .Call(`_individual_create_targeted_event`, size)
+}
+
+event_base_tick <- function(event) {
+    invisible(.Call(`_individual_event_base_tick`, event))
+}
+
+event_base_get_timestep <- function(event) {
+    .Call(`_individual_event_base_get_timestep`, event)
+}
+
+event_base_set_timestep <- function(event, time) {
+    invisible(.Call(`_individual_event_base_set_timestep`, event, time))
+}
+
+event_base_should_trigger <- function(event) {
+    .Call(`_individual_event_base_should_trigger`, event)
+}
+
+event_schedule <- function(event, delays) {
+    invisible(.Call(`_individual_event_schedule`, event, delays))
+}
+
+event_clear_schedule <- function(event) {
+    invisible(.Call(`_individual_event_clear_schedule`, event))
+}
+
+event_checkpoint <- function(event) {
+    .Call(`_individual_event_checkpoint`, event)
+}
+
+event_restore <- function(event, schedule) {
+    invisible(.Call(`_individual_event_restore`, event, schedule))
+}
+
+targeted_event_clear_schedule_vector <- function(event, target) {
+    invisible(.Call(`_individual_targeted_event_clear_schedule_vector`, event, target))
+}
+
+targeted_event_clear_schedule <- function(event, target) {
+    invisible(.Call(`_individual_targeted_event_clear_schedule`, event, target))
+}
+
+targeted_event_get_scheduled <- function(event) {
+    .Call(`_individual_targeted_event_get_scheduled`, event)
+}
+
+targeted_event_schedule <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule`, event, target, delay))
+}
+
+targeted_event_queue_shrink_bitset <- function(event, index) {
+    invisible(.Call(`_individual_targeted_event_queue_shrink_bitset`, event, index))
+}
+
+targeted_event_queue_shrink <- function(event, index) {
+    invisible(.Call(`_individual_targeted_event_queue_shrink`, event, index))
+}
+
+targeted_event_queue_extend <- function(event, n) {
+    invisible(.Call(`_individual_targeted_event_queue_extend`, event, n))
+}
+
+targeted_event_queue_extend_with_schedule <- function(event, delays) {
+    invisible(.Call(`_individual_targeted_event_queue_extend_with_schedule`, event, delays))
+}
+
+targeted_event_schedule_vector <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule_vector`, event, target, delay))
+}
+
+targeted_event_schedule_multi_delay <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule_multi_delay`, event, target, delay))
+}
+
+targeted_event_schedule_multi_delay_vector <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule_multi_delay_vector`, event, target, delay))
+}
+
+targeted_event_get_target <- function(event) {
+    .Call(`_individual_targeted_event_get_target`, event)
+}
+
+targeted_event_resize <- function(event) {
+    invisible(.Call(`_individual_targeted_event_resize`, event))
+}
+
+targeted_event_checkpoint <- function(event) {
+    .Call(`_individual_targeted_event_checkpoint`, event)
+}
+
+targeted_event_restore <- function(event, state) {
+    invisible(.Call(`_individual_targeted_event_restore`, event, state))
+}
+
+process_listener <- function(event, listener) {
+    invisible(.Call(`_individual_process_listener`, event, listener))
+}
+
+process_targeted_listener <- function(event, listener, target) {
+    invisible(.Call(`_individual_process_targeted_listener`, event, listener, target))
+}
+
+create_integer_variable <- function(values) {
+    .Call(`_individual_create_integer_variable`, values)
+}
+
+integer_variable_get_values <- function(variable) {
+    .Call(`_individual_integer_variable_get_values`, variable)
+}
+
+integer_variable_get_modulo_differences <- function(variable, value, difference) {
+    .Call(`_individual_integer_variable_get_modulo_differences`, variable, value, difference)
+}
+
+integer_variable_get_values_at_index <- function(variable, index) {
+    .Call(`_individual_integer_variable_get_values_at_index`, variable, index)
+}
+
+integer_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_integer_variable_get_values_at_index_vector`, variable, index)
+}
+
+integer_variable_get_index_of_set_vector <- function(variable, values_set) {
+    .Call(`_individual_integer_variable_get_index_of_set_vector`, variable, values_set)
+}
+
+integer_variable_get_index_of_set_scalar <- function(variable, values_set) {
+    .Call(`_individual_integer_variable_get_index_of_set_scalar`, variable, values_set)
+}
+
+integer_variable_get_index_of_range <- function(variable, a, b) {
+    .Call(`_individual_integer_variable_get_index_of_range`, variable, a, b)
+}
+
+integer_variable_get_size_of_set_vector <- function(variable, values_set) {
+    .Call(`_individual_integer_variable_get_size_of_set_vector`, variable, values_set)
+}
+
+integer_variable_get_size_of_set_scalar <- function(variable, value) {
+    .Call(`_individual_integer_variable_get_size_of_set_scalar`, variable, value)
+}
+
+integer_variable_get_size_of_range <- function(variable, a, b) {
+    .Call(`_individual_integer_variable_get_size_of_range`, variable, a, b)
+}
+
+integer_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_integer_variable_queue_fill`, variable, value))
+}
+
+integer_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_variable_queue_update`, variable, value, index))
+}
+
+integer_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_variable_queue_update_bitset`, variable, value, index))
+}
+
+integer_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_integer_variable_queue_extend`, variable, values))
+}
+
+integer_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_integer_variable_queue_shrink`, variable, index))
+}
+
+integer_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_integer_variable_queue_shrink_bitset`, variable, index))
+}
+
+fixed_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate, destination_probabilities) {
+    .Call(`_individual_fixed_probability_multinomial_process_internal`, variable, source_state, destination_states, rate, destination_probabilities)
+}
+
+multi_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate_variable, destination_probabilities) {
+    .Call(`_individual_multi_probability_multinomial_process_internal`, variable, source_state, destination_states, rate_variable, destination_probabilities)
+}
+
+multi_probability_bernoulli_process_internal <- function(variable, from, to, rate_variable) {
+    .Call(`_individual_multi_probability_bernoulli_process_internal`, variable, from, to, rate_variable)
+}
+
+infection_age_process_internal <- function(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing) {
+    .Call(`_individual_infection_age_process_internal`, state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing)
+}
+
+create_double_ragged_variable <- function(values) {
+    .Call(`_individual_create_double_ragged_variable`, values)
+}
+
+double_ragged_variable_get_values <- function(variable) {
+    .Call(`_individual_double_ragged_variable_get_values`, variable)
+}
+
+double_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_values_at_index_bitset`, variable, index)
+}
+
+double_ragged_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_values_at_index_vector`, variable, index)
+}
+
+double_ragged_variable_get_length <- function(variable) {
+    .Call(`_individual_double_ragged_variable_get_length`, variable)
+}
+
+double_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_length_at_index_bitset`, variable, index)
+}
+
+double_ragged_variable_get_length_at_index_vector <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_length_at_index_vector`, variable, index)
+}
+
+double_ragged_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_fill`, variable, value))
+}
+
+double_ragged_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_update`, variable, value, index))
+}
+
+double_ragged_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_update_bitset`, variable, value, index))
+}
+
+double_ragged_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_extend`, variable, values))
+}
+
+double_ragged_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_shrink`, variable, index))
+}
+
+double_ragged_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_shrink_bitset`, variable, index))
+}
+
+create_integer_ragged_variable <- function(values) {
+    .Call(`_individual_create_integer_ragged_variable`, values)
+}
+
+integer_ragged_variable_get_values <- function(variable) {
+    .Call(`_individual_integer_ragged_variable_get_values`, variable)
+}
+
+integer_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_values_at_index_bitset`, variable, index)
+}
+
+integer_ragged_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_values_at_index_vector`, variable, index)
+}
+
+integer_ragged_variable_get_length <- function(variable) {
+    .Call(`_individual_integer_ragged_variable_get_length`, variable)
+}
+
+integer_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_length_at_index_bitset`, variable, index)
+}
+
+integer_ragged_variable_get_length_at_index_vector <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_length_at_index_vector`, variable, index)
+}
+
+integer_ragged_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_fill`, variable, value))
+}
+
+integer_ragged_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_update`, variable, value, index))
+}
+
+integer_ragged_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_update_bitset`, variable, value, index))
+}
+
+integer_ragged_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_extend`, variable, values))
+}
+
+integer_ragged_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink`, variable, index))
+}
+
+integer_ragged_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink_bitset`, variable, index))
+}
+
+create_render_vector <- function(data) {
+    .Call(`_individual_create_render_vector`, data)
+}
+
+render_vector_update <- function(v, index, value) {
+    invisible(.Call(`_individual_render_vector_update`, v, index, value))
+}
+
+render_vector_data <- function(v) {
+    .Call(`_individual_render_vector_data`, v)
+}
+
+execute_process <- function(process, timestep) {
+    invisible(.Call(`_individual_execute_process`, process, timestep))
+}
+
+variable_get_size <- function(variable) {
+    .Call(`_individual_variable_get_size`, variable)
+}
+
+variable_update <- function(variable) {
+    invisible(.Call(`_individual_variable_update`, variable))
+}
+
+variable_resize <- function(variable) {
+    invisible(.Call(`_individual_variable_resize`, variable))
+}
+
+# Register entry points for exported C++ functions
+methods::setLoadAction(function(ns) {
+    .Call(`_individual_RcppExport_registerCCallable`)
+})
diff --git a/R/categorical_variable.R b/R/categorical_variable.R
index 8a172b1..93e5eb9 100644
--- a/R/categorical_variable.R
+++ b/R/categorical_variable.R
@@ -43,6 +43,15 @@ CategoricalVariable <- R6Class(
       categorical_variable_get_categories(self$.variable)
     },
 
+    #' @description return the value of the variable for the given individuals
+    #' @param index the indices of individuals whose categories will be returned
+    get_values = function(index) {
+      stopifnot(is.finite(index))
+      stopifnot(index > 0)
+      results <- categorical_variable_get_values(self$.variable, index)
+      return(results)
+    },
+
     #' @description queue an update for this variable
     #' @param value the new value
     #' @param index the indices of individuals whose value will be updated
diff --git a/R/integer_variable.R b/R/integer_variable.R
index 2e3543e..adc477d 100644
--- a/R/integer_variable.R
+++ b/R/integer_variable.R
@@ -39,6 +39,15 @@ IntegerVariable <- R6Class(
 
     },
 
+    #' @description Return a vector of individuals with 0 modulo difference from input value
+    #' and the distance being compared
+    #' @param value the value to check
+    #' @param difference the difference to check, e.g. difference = 2 checks whether the
+    #' difference is even
+    get_modulo_differences = function(value, difference){
+      integer_variable_get_modulo_differences(self$.variable, value, difference)
+    },
+
     #' @description Return a \code{\link[individual]{Bitset}} for individuals with some subset of values.
     #' Either search for indices corresponding to values in \code{set}, or
     #' for indices corresponding to values in range \eqn{[a,b]}. Either \code{set}
diff --git a/inst/include/CategoricalVariable.h b/inst/include/CategoricalVariable.h
index 69a631c..66aefb0 100644
--- a/inst/include/CategoricalVariable.h
+++ b/inst/include/CategoricalVariable.h
@@ -52,6 +52,7 @@ class CategoricalVariable : public Variable {
     virtual void resize() override;
     virtual size_t size() const override;
     virtual void update() override;
+    virtual std::vector<std::string> get_values(const std::vector<size_t>&);
 };
 
 
@@ -228,5 +229,25 @@ inline size_t CategoricalVariable::size() const {
 inline const std::vector<std::string>& CategoricalVariable::get_categories() const {
     return categories;
 }
-
+//' @title get values at index given by a vector
+inline std::vector<std::string> CategoricalVariable::get_values(const std::vector<size_t>& index){
+    
+    // Generate empty output vector
+    auto result = std::vector<std::string>(index.size());
+    for (auto i = 0u; i < index.size(); ++i) {
+        // Determine which category the individual is within
+        for (auto cat: categories) {
+            if (indices.find(cat) == indices.end()) {
+                std::stringstream message;
+                message << "unknown category: " << cat;
+                Rcpp::stop(message.str());
+            }
+            if (indices.at(cat).find(index[i]) != indices.at(cat).end()) {
+                result[i] = cat;
+                break;
+            }
+        }
+    }
+    return result;
+}
 #endif /* INST_INCLUDE_CATEGORICAL_VARIABLE_H_ */
diff --git a/inst/include/IntegerVariable.h b/inst/include/IntegerVariable.h
index 346ee6d..294075b 100644
--- a/inst/include/IntegerVariable.h
+++ b/inst/include/IntegerVariable.h
@@ -30,6 +30,7 @@ struct IntegerVariable : public NumericVariable<int> {
     virtual size_t get_size_of_set(const std::vector<int>&) const;
     virtual size_t get_size_of_set(const int) const;
     virtual size_t get_size_of_range(const int, const int) const;
+    virtual individual_index_t get_modulo_differences(const int, const int) const;
 };
 
 inline IntegerVariable::IntegerVariable(const std::vector<int>& values)
@@ -66,6 +67,23 @@ inline individual_index_t IntegerVariable::get_index_of_set(
     return result;
 }
 
+//' @title return bitset giving index of individuals whose difference between
+// the current value and the queried value is a multiple of the queried difference
+inline individual_index_t IntegerVariable::get_modulo_differences(
+    const int value,
+    const int difference
+) const {
+    
+    auto result = individual_index_t(size());
+    for (auto i = 0u; i < values.size(); ++i) {
+        if ( (values[i] - value) % difference == 0 ) {
+            result.insert(i);
+        }
+    }
+    
+    return result;
+}
+
 //' @title return bitset giving index of individuals whose value is in some range [a,b]
 inline individual_index_t IntegerVariable::get_index_of_range(
         const int a, const int b
diff --git a/inst/include/individual_types.h b/inst/include/individual_types.h
index 8d4a925..8386ca9 100644
--- a/inst/include/individual_types.h
+++ b/inst/include/individual_types.h
@@ -10,6 +10,7 @@
 
 #include <Rcpp.h>
 #include "CategoricalVariable.h"
+// #include "FunctionalVariable.h"
 #include "IntegerVariable.h"
 #include "DoubleVariable.h"
 #include "RaggedInteger.h"
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 1c5e23d..7309f3e 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -1,1612 +1,1639 @@
-// Generated by using Rcpp::compileAttributes() -> do not edit by hand
-// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-#include "../inst/include/individual.h"
-#include "../inst/include/individual_types.h"
-#include <Rcpp.h>
-#include <string>
-#include <set>
-
-using namespace Rcpp;
-
-#ifdef RCPP_USE_GLOBAL_ROSTREAM
-Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
-Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
-#endif
-
-// create_bitset
-Rcpp::XPtr<individual_index_t> create_bitset(size_t size);
-RcppExport SEXP _individual_create_bitset(SEXP sizeSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_bitset(size));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_copy
-Rcpp::XPtr<individual_index_t> bitset_copy(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_copy(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_copy(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_insert
-void bitset_insert(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
-RcppExport SEXP _individual_bitset_insert(SEXP bSEXP, SEXP vSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
-    bitset_insert(b, v);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_remove
-void bitset_remove(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
-RcppExport SEXP _individual_bitset_remove(SEXP bSEXP, SEXP vSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
-    bitset_remove(b, v);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_clear
-void bitset_clear(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_clear(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_clear(b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_size
-size_t bitset_size(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_size(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_size(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_max_size
-size_t bitset_max_size(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_max_size(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_max_size(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_and
-void bitset_and(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_and(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_and(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_not
-Rcpp::XPtr<individual_index_t> bitset_not(const Rcpp::XPtr<individual_index_t> b, const bool inplace);
-RcppExport SEXP _individual_bitset_not(SEXP bSEXP, SEXP inplaceSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< const bool >::type inplace(inplaceSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_not(b, inplace));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_or
-void bitset_or(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_or(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_or(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_copy_from
-void bitset_copy_from(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_copy_from(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_copy_from(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_xor
-void bitset_xor(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_xor(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_xor(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_set_difference
-void bitset_set_difference(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_set_difference(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_set_difference(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_sample
-void bitset_sample(const Rcpp::XPtr<individual_index_t> b, double rate);
-RcppExport SEXP _individual_bitset_sample(SEXP bSEXP, SEXP rateSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< double >::type rate(rateSEXP);
-    bitset_sample(b, rate);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_sample_vector
-void bitset_sample_vector(const Rcpp::XPtr<individual_index_t> b, std::vector<double> rate);
-RcppExport SEXP _individual_bitset_sample_vector(SEXP bSEXP, SEXP rateSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type rate(rateSEXP);
-    bitset_sample_vector(b, rate);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_to_vector
-std::vector<size_t> bitset_to_vector(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_to_vector(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_to_vector(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// filter_bitset_integer
-Rcpp::XPtr<individual_index_t> filter_bitset_integer(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> other);
-RcppExport SEXP _individual_filter_bitset_integer(SEXP bSEXP, SEXP otherSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type other(otherSEXP);
-    rcpp_result_gen = Rcpp::wrap(filter_bitset_integer(b, other));
-    return rcpp_result_gen;
-END_RCPP
-}
-// filter_bitset_bitset
-Rcpp::XPtr<individual_index_t> filter_bitset_bitset(const Rcpp::XPtr<individual_index_t> b, const Rcpp::XPtr<individual_index_t> other);
-RcppExport SEXP _individual_filter_bitset_bitset(SEXP bSEXP, SEXP otherSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type other(otherSEXP);
-    rcpp_result_gen = Rcpp::wrap(filter_bitset_bitset(b, other));
-    return rcpp_result_gen;
-END_RCPP
-}
-// filter_bitset_logical
-Rcpp::XPtr<individual_index_t> filter_bitset_logical(const Rcpp::XPtr<individual_index_t> bitset, Rcpp::LogicalVector other);
-RcppExport SEXP _individual_filter_bitset_logical(SEXP bitsetSEXP, SEXP otherSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type bitset(bitsetSEXP);
-    Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type other(otherSEXP);
-    rcpp_result_gen = Rcpp::wrap(filter_bitset_logical(bitset, other));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_choose
-void bitset_choose(const Rcpp::XPtr<individual_index_t> b, const size_t k);
-RcppExport SEXP _individual_bitset_choose(SEXP bSEXP, SEXP kSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< const size_t >::type k(kSEXP);
-    bitset_choose(b, k);
-    return R_NilValue;
-END_RCPP
-}
-// create_categorical_variable
-Rcpp::XPtr<CategoricalVariable> create_categorical_variable(const std::vector<std::string>& categories, const std::vector<std::string>& values);
-RcppExport SEXP _individual_create_categorical_variable(SEXP categoriesSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type categories(categoriesSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_categorical_variable(categories, values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_get_size
-size_t categorical_variable_get_size(Rcpp::XPtr<CategoricalVariable> variable);
-RcppExport SEXP _individual_categorical_variable_get_size(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_queue_update
-void categorical_variable_queue_update(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_categorical_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    categorical_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_get_index_of
-Rcpp::XPtr<individual_index_t> categorical_variable_get_index_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
-RcppExport SEXP _individual_categorical_variable_get_index_of(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_index_of(variable, values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_get_size_of
-int categorical_variable_get_size_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
-RcppExport SEXP _individual_categorical_variable_get_size_of(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size_of(variable, values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_get_categories
-std::vector<std::string> categorical_variable_get_categories(Rcpp::XPtr<CategoricalVariable> variable);
-RcppExport SEXP _individual_categorical_variable_get_categories(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_categories(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_queue_update_vector
-void categorical_variable_queue_update_vector(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, std::vector<size_t>& index);
-RcppExport SEXP _individual_categorical_variable_queue_update_vector(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    categorical_variable_queue_update_vector(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_update
-void categorical_variable_update(Rcpp::XPtr<CategoricalVariable> variable);
-RcppExport SEXP _individual_categorical_variable_update(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    categorical_variable_update(variable);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_queue_extend
-void categorical_variable_queue_extend(Rcpp::XPtr<CategoricalVariable> variable, std::vector<std::string>& values);
-RcppExport SEXP _individual_categorical_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<std::string>& >::type values(valuesSEXP);
-    categorical_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_queue_shrink
-void categorical_variable_queue_shrink(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_categorical_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    categorical_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_queue_shrink_bitset
-void categorical_variable_queue_shrink_bitset(Rcpp::XPtr<CategoricalVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_categorical_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    categorical_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// dummy
-void dummy();
-static SEXP _individual_dummy_try() {
-BEGIN_RCPP
-    dummy();
-    return R_NilValue;
-END_RCPP_RETURN_ERROR
-}
-RcppExport SEXP _individual_dummy() {
-    SEXP rcpp_result_gen;
-    {
-        Rcpp::RNGScope rcpp_rngScope_gen;
-        rcpp_result_gen = PROTECT(_individual_dummy_try());
-    }
-    Rboolean rcpp_isInterrupt_gen = Rf_inherits(rcpp_result_gen, "interrupted-error");
-    if (rcpp_isInterrupt_gen) {
-        UNPROTECT(1);
-        Rf_onintr();
-    }
-    bool rcpp_isLongjump_gen = Rcpp::internal::isLongjumpSentinel(rcpp_result_gen);
-    if (rcpp_isLongjump_gen) {
-        Rcpp::internal::resumeJump(rcpp_result_gen);
-    }
-    Rboolean rcpp_isError_gen = Rf_inherits(rcpp_result_gen, "try-error");
-    if (rcpp_isError_gen) {
-        SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
-        UNPROTECT(1);
-        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
-    }
-    UNPROTECT(1);
-    return rcpp_result_gen;
-}
-// create_double_variable
-Rcpp::XPtr<DoubleVariable> create_double_variable(const std::vector<double>& values);
-RcppExport SEXP _individual_create_double_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<double>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_double_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_values
-const std::vector<double>& double_variable_get_values(Rcpp::XPtr<DoubleVariable> variable);
-RcppExport SEXP _individual_double_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_values_at_index
-std::vector<double> double_variable_get_values_at_index(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_values_at_index_vector
-std::vector<double> double_variable_get_values_at_index_vector(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_index_of_range
-Rcpp::XPtr<individual_index_t> double_variable_get_index_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
-RcppExport SEXP _individual_double_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_index_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_size_of_range
-size_t double_variable_get_size_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
-RcppExport SEXP _individual_double_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_size_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_queue_fill
-void double_variable_queue_fill(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value);
-RcppExport SEXP _individual_double_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
-    double_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_update
-void double_variable_queue_update(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, std::vector<size_t> index);
-RcppExport SEXP _individual_double_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    double_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_update_bitset
-void double_variable_queue_update_bitset(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_extend
-void double_variable_queue_extend(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> values);
-RcppExport SEXP _individual_double_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type values(valuesSEXP);
-    double_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_shrink
-void double_variable_queue_shrink(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    double_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_shrink_bitset
-void double_variable_queue_shrink_bitset(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// create_event
-Rcpp::XPtr<Event> create_event();
-RcppExport SEXP _individual_create_event() {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    rcpp_result_gen = Rcpp::wrap(create_event());
-    return rcpp_result_gen;
-END_RCPP
-}
-// create_targeted_event
-Rcpp::XPtr<TargetedEvent> create_targeted_event(size_t size);
-RcppExport SEXP _individual_create_targeted_event(SEXP sizeSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_targeted_event(size));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_base_tick
-void event_base_tick(const Rcpp::XPtr<EventBase> event);
-RcppExport SEXP _individual_event_base_tick(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    event_base_tick(event);
-    return R_NilValue;
-END_RCPP
-}
-// event_base_get_timestep
-size_t event_base_get_timestep(const Rcpp::XPtr<EventBase> event);
-RcppExport SEXP _individual_event_base_get_timestep(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(event_base_get_timestep(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_base_set_timestep
-void event_base_set_timestep(const Rcpp::XPtr<EventBase> event, size_t time);
-RcppExport SEXP _individual_event_base_set_timestep(SEXP eventSEXP, SEXP timeSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< size_t >::type time(timeSEXP);
-    event_base_set_timestep(event, time);
-    return R_NilValue;
-END_RCPP
-}
-// event_base_should_trigger
-bool event_base_should_trigger(const Rcpp::XPtr<EventBase> event);
-RcppExport SEXP _individual_event_base_should_trigger(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(event_base_should_trigger(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_schedule
-void event_schedule(const Rcpp::XPtr<Event> event, std::vector<double> delays);
-RcppExport SEXP _individual_event_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type delays(delaysSEXP);
-    event_schedule(event, delays);
-    return R_NilValue;
-END_RCPP
-}
-// event_clear_schedule
-void event_clear_schedule(const Rcpp::XPtr<Event> event);
-RcppExport SEXP _individual_event_clear_schedule(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    event_clear_schedule(event);
-    return R_NilValue;
-END_RCPP
-}
-// event_checkpoint
-std::vector<size_t> event_checkpoint(const Rcpp::XPtr<Event> event);
-RcppExport SEXP _individual_event_checkpoint(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(event_checkpoint(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_restore
-void event_restore(const Rcpp::XPtr<Event> event, std::vector<size_t> schedule);
-RcppExport SEXP _individual_event_restore(SEXP eventSEXP, SEXP scheduleSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type schedule(scheduleSEXP);
-    event_restore(event, schedule);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_clear_schedule_vector
-void targeted_event_clear_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target);
-RcppExport SEXP _individual_targeted_event_clear_schedule_vector(SEXP eventSEXP, SEXP targetSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
-    targeted_event_clear_schedule_vector(event, target);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_clear_schedule
-void targeted_event_clear_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target);
-RcppExport SEXP _individual_targeted_event_clear_schedule(SEXP eventSEXP, SEXP targetSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    targeted_event_clear_schedule(event, target);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_get_scheduled
-Rcpp::XPtr<individual_index_t> targeted_event_get_scheduled(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_get_scheduled(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(targeted_event_get_scheduled(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// targeted_event_schedule
-void targeted_event_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, double delay);
-RcppExport SEXP _individual_targeted_event_schedule(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
-    targeted_event_schedule(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_shrink_bitset
-void targeted_event_queue_shrink_bitset(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_targeted_event_queue_shrink_bitset(SEXP eventSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    targeted_event_queue_shrink_bitset(event, index);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_shrink
-void targeted_event_queue_shrink(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t>& index);
-RcppExport SEXP _individual_targeted_event_queue_shrink(SEXP eventSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    targeted_event_queue_shrink(event, index);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_extend
-void targeted_event_queue_extend(const Rcpp::XPtr<TargetedEvent> event, size_t n);
-RcppExport SEXP _individual_targeted_event_queue_extend(SEXP eventSEXP, SEXP nSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< size_t >::type n(nSEXP);
-    targeted_event_queue_extend(event, n);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_extend_with_schedule
-void targeted_event_queue_extend_with_schedule(const Rcpp::XPtr<TargetedEvent> event, const std::vector<double>& delays);
-RcppExport SEXP _individual_targeted_event_queue_extend_with_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double>& >::type delays(delaysSEXP);
-    targeted_event_queue_extend_with_schedule(event, delays);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_schedule_vector
-void targeted_event_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, double delay);
-RcppExport SEXP _individual_targeted_event_schedule_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
-    targeted_event_schedule_vector(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_schedule_multi_delay
-void targeted_event_schedule_multi_delay(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, const std::vector<double> delay);
-RcppExport SEXP _individual_targeted_event_schedule_multi_delay(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
-    targeted_event_schedule_multi_delay(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_schedule_multi_delay_vector
-void targeted_event_schedule_multi_delay_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, const std::vector<double> delay);
-RcppExport SEXP _individual_targeted_event_schedule_multi_delay_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
-    targeted_event_schedule_multi_delay_vector(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_get_target
-Rcpp::XPtr<individual_index_t> targeted_event_get_target(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_get_target(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(targeted_event_get_target(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// targeted_event_resize
-void targeted_event_resize(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_resize(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    targeted_event_resize(event);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_checkpoint
-Rcpp::List targeted_event_checkpoint(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_checkpoint(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(targeted_event_checkpoint(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// targeted_event_restore
-void targeted_event_restore(const Rcpp::XPtr<TargetedEvent> event, Rcpp::List state);
-RcppExport SEXP _individual_targeted_event_restore(SEXP eventSEXP, SEXP stateSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< Rcpp::List >::type state(stateSEXP);
-    targeted_event_restore(event, state);
-    return R_NilValue;
-END_RCPP
-}
-// process_listener
-void process_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<listener_t> listener);
-RcppExport SEXP _individual_process_listener(SEXP eventSEXP, SEXP listenerSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<listener_t> >::type listener(listenerSEXP);
-    process_listener(event, listener);
-    return R_NilValue;
-END_RCPP
-}
-// process_targeted_listener
-void process_targeted_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<targeted_listener_t> listener, const Rcpp::XPtr<individual_index_t> target);
-RcppExport SEXP _individual_process_targeted_listener(SEXP eventSEXP, SEXP listenerSEXP, SEXP targetSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<targeted_listener_t> >::type listener(listenerSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    process_targeted_listener(event, listener, target);
-    return R_NilValue;
-END_RCPP
-}
-// create_integer_variable
-Rcpp::XPtr<IntegerVariable> create_integer_variable(const std::vector<int>& values);
-RcppExport SEXP _individual_create_integer_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<int>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_integer_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_values
-const std::vector<int>& integer_variable_get_values(Rcpp::XPtr<IntegerVariable> variable);
-RcppExport SEXP _individual_integer_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_values_at_index
-std::vector<int> integer_variable_get_values_at_index(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_values_at_index_vector
-std::vector<int> integer_variable_get_values_at_index_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_index_of_set_vector
-Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values_set);
-RcppExport SEXP _individual_integer_variable_get_index_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type values_set(values_setSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_vector(variable, values_set));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_index_of_set_scalar
-Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int values_set);
-RcppExport SEXP _individual_integer_variable_get_index_of_set_scalar(SEXP variableSEXP, SEXP values_setSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type values_set(values_setSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_scalar(variable, values_set));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_index_of_range
-Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
-RcppExport SEXP _individual_integer_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_size_of_set_vector
-size_t integer_variable_get_size_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, const std::vector<int> values_set);
-RcppExport SEXP _individual_integer_variable_get_size_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<int> >::type values_set(values_setSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_vector(variable, values_set));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_size_of_set_scalar
-size_t integer_variable_get_size_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int value);
-RcppExport SEXP _individual_integer_variable_get_size_of_set_scalar(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_scalar(variable, value));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_size_of_range
-size_t integer_variable_get_size_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
-RcppExport SEXP _individual_integer_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_queue_fill
-void integer_variable_queue_fill(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value);
-RcppExport SEXP _individual_integer_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
-    integer_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_update
-void integer_variable_queue_update(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    integer_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_update_bitset
-void integer_variable_queue_update_bitset(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_extend
-void integer_variable_queue_extend(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values);
-RcppExport SEXP _individual_integer_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type values(valuesSEXP);
-    integer_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_shrink
-void integer_variable_queue_shrink(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    integer_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_shrink_bitset
-void integer_variable_queue_shrink_bitset(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// fixed_probability_multinomial_process_internal
-Rcpp::XPtr<process_t> fixed_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const double rate, const std::vector<double> destination_probabilities);
-RcppExport SEXP _individual_fixed_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rateSEXP, SEXP destination_probabilitiesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
-    Rcpp::traits::input_parameter< const double >::type rate(rateSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
-    rcpp_result_gen = Rcpp::wrap(fixed_probability_multinomial_process_internal(variable, source_state, destination_states, rate, destination_probabilities));
-    return rcpp_result_gen;
-END_RCPP
-}
-// multi_probability_multinomial_process_internal
-Rcpp::XPtr<process_t> multi_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const Rcpp::XPtr<DoubleVariable> rate_variable, const std::vector<double> destination_probabilities);
-RcppExport SEXP _individual_multi_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rate_variableSEXP, SEXP destination_probabilitiesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
-    rcpp_result_gen = Rcpp::wrap(multi_probability_multinomial_process_internal(variable, source_state, destination_states, rate_variable, destination_probabilities));
-    return rcpp_result_gen;
-END_RCPP
-}
-// multi_probability_bernoulli_process_internal
-Rcpp::XPtr<process_t> multi_probability_bernoulli_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string from, const std::string to, const Rcpp::XPtr<DoubleVariable> rate_variable);
-RcppExport SEXP _individual_multi_probability_bernoulli_process_internal(SEXP variableSEXP, SEXP fromSEXP, SEXP toSEXP, SEXP rate_variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type from(fromSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type to(toSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(multi_probability_bernoulli_process_internal(variable, from, to, rate_variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// infection_age_process_internal
-Rcpp::XPtr<process_t> infection_age_process_internal(Rcpp::XPtr<CategoricalVariable> state, const std::string susceptible, const std::string exposed, const std::string infectious, const Rcpp::XPtr<IntegerVariable> age, const int age_bins, const double p, const double dt, const Rcpp::NumericMatrix mixing);
-RcppExport SEXP _individual_infection_age_process_internal(SEXP stateSEXP, SEXP susceptibleSEXP, SEXP exposedSEXP, SEXP infectiousSEXP, SEXP ageSEXP, SEXP age_binsSEXP, SEXP pSEXP, SEXP dtSEXP, SEXP mixingSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type state(stateSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type susceptible(susceptibleSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type exposed(exposedSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type infectious(infectiousSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<IntegerVariable> >::type age(ageSEXP);
-    Rcpp::traits::input_parameter< const int >::type age_bins(age_binsSEXP);
-    Rcpp::traits::input_parameter< const double >::type p(pSEXP);
-    Rcpp::traits::input_parameter< const double >::type dt(dtSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::NumericMatrix >::type mixing(mixingSEXP);
-    rcpp_result_gen = Rcpp::wrap(infection_age_process_internal(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing));
-    return rcpp_result_gen;
-END_RCPP
-}
-// create_double_ragged_variable
-Rcpp::XPtr<RaggedDouble> create_double_ragged_variable(const std::vector<std::vector<double>>& values);
-RcppExport SEXP _individual_create_double_ragged_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_double_ragged_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_values
-std::vector<std::vector<double>> double_ragged_variable_get_values(Rcpp::XPtr<RaggedDouble> variable);
-RcppExport SEXP _individual_double_ragged_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_values_at_index_bitset
-std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_values_at_index_vector
-std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_length
-std::vector<size_t> double_ragged_variable_get_length(Rcpp::XPtr<RaggedDouble> variable);
-RcppExport SEXP _individual_double_ragged_variable_get_length(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_length_at_index_bitset
-std::vector<size_t> double_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_length_at_index_vector
-std::vector<size_t> double_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_queue_fill
-void double_ragged_variable_queue_fill(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value);
-RcppExport SEXP _individual_double_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
-    double_ragged_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_update
-void double_ragged_variable_queue_update(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value, std::vector<size_t> index);
-RcppExport SEXP _individual_double_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    double_ragged_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_update_bitset
-void double_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_ragged_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_extend
-void double_ragged_variable_queue_extend(Rcpp::XPtr<RaggedDouble> variable, std::vector<std::vector<double>>& values);
-RcppExport SEXP _individual_double_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<std::vector<double>>& >::type values(valuesSEXP);
-    double_ragged_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_shrink
-void double_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_double_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    double_ragged_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_shrink_bitset
-void double_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_ragged_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// create_integer_ragged_variable
-Rcpp::XPtr<RaggedInteger> create_integer_ragged_variable(const std::vector<std::vector<int>>& values);
-RcppExport SEXP _individual_create_integer_ragged_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_integer_ragged_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_values
-std::vector<std::vector<int>> integer_ragged_variable_get_values(Rcpp::XPtr<RaggedInteger> variable);
-RcppExport SEXP _individual_integer_ragged_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_values_at_index_bitset
-std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_values_at_index_vector
-std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_length
-std::vector<size_t> integer_ragged_variable_get_length(Rcpp::XPtr<RaggedInteger> variable);
-RcppExport SEXP _individual_integer_ragged_variable_get_length(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_length_at_index_bitset
-std::vector<size_t> integer_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_length_at_index_vector
-std::vector<size_t> integer_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_queue_fill
-void integer_ragged_variable_queue_fill(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value);
-RcppExport SEXP _individual_integer_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
-    integer_ragged_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_update
-void integer_ragged_variable_queue_update(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    integer_ragged_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_update_bitset
-void integer_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_ragged_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_extend
-void integer_ragged_variable_queue_extend(Rcpp::XPtr<RaggedInteger> variable, std::vector<std::vector<int>>& values);
-RcppExport SEXP _individual_integer_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<std::vector<int>>& >::type values(valuesSEXP);
-    integer_ragged_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_shrink
-void integer_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    integer_ragged_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_shrink_bitset
-void integer_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_ragged_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// create_render_vector
-Rcpp::XPtr<RenderVector> create_render_vector(std::vector<double> data);
-RcppExport SEXP _individual_create_render_vector(SEXP dataSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< std::vector<double> >::type data(dataSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_render_vector(data));
-    return rcpp_result_gen;
-END_RCPP
-}
-// render_vector_update
-void render_vector_update(Rcpp::XPtr<RenderVector> v, size_t index, double value);
-RcppExport SEXP _individual_render_vector_update(SEXP vSEXP, SEXP indexSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
-    Rcpp::traits::input_parameter< size_t >::type index(indexSEXP);
-    Rcpp::traits::input_parameter< double >::type value(valueSEXP);
-    render_vector_update(v, index, value);
-    return R_NilValue;
-END_RCPP
-}
-// render_vector_data
-std::vector<double> render_vector_data(Rcpp::XPtr<RenderVector> v);
-RcppExport SEXP _individual_render_vector_data(SEXP vSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
-    rcpp_result_gen = Rcpp::wrap(render_vector_data(v));
-    return rcpp_result_gen;
-END_RCPP
-}
-// execute_process
-void execute_process(Rcpp::XPtr<process_t> process, size_t timestep);
-RcppExport SEXP _individual_execute_process(SEXP processSEXP, SEXP timestepSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<process_t> >::type process(processSEXP);
-    Rcpp::traits::input_parameter< size_t >::type timestep(timestepSEXP);
-    execute_process(process, timestep);
-    return R_NilValue;
-END_RCPP
-}
-// variable_get_size
-size_t variable_get_size(Rcpp::XPtr<Variable> variable);
-RcppExport SEXP _individual_variable_get_size(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(variable_get_size(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// variable_update
-void variable_update(Rcpp::XPtr<Variable> variable);
-RcppExport SEXP _individual_variable_update(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
-    variable_update(variable);
-    return R_NilValue;
-END_RCPP
-}
-// variable_resize
-void variable_resize(Rcpp::XPtr<Variable> variable);
-RcppExport SEXP _individual_variable_resize(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
-    variable_resize(variable);
-    return R_NilValue;
-END_RCPP
-}
-
-// validate (ensure exported C++ functions exist before calling them)
-static int _individual_RcppExport_validate(const char* sig) { 
-    static std::set<std::string> signatures;
-    if (signatures.empty()) {
-        signatures.insert("void(*dummy)()");
-    }
-    return signatures.find(sig) != signatures.end();
-}
-
-// registerCCallable (register entry points for exported C++ functions)
-RcppExport SEXP _individual_RcppExport_registerCCallable() { 
-    R_RegisterCCallable("individual", "_individual_dummy", (DL_FUNC)_individual_dummy_try);
-    R_RegisterCCallable("individual", "_individual_RcppExport_validate", (DL_FUNC)_individual_RcppExport_validate);
-    return R_NilValue;
-}
-
-RcppExport SEXP run_testthat_tests(SEXP);
-
-static const R_CallMethodDef CallEntries[] = {
-    {"_individual_create_bitset", (DL_FUNC) &_individual_create_bitset, 1},
-    {"_individual_bitset_copy", (DL_FUNC) &_individual_bitset_copy, 1},
-    {"_individual_bitset_insert", (DL_FUNC) &_individual_bitset_insert, 2},
-    {"_individual_bitset_remove", (DL_FUNC) &_individual_bitset_remove, 2},
-    {"_individual_bitset_clear", (DL_FUNC) &_individual_bitset_clear, 1},
-    {"_individual_bitset_size", (DL_FUNC) &_individual_bitset_size, 1},
-    {"_individual_bitset_max_size", (DL_FUNC) &_individual_bitset_max_size, 1},
-    {"_individual_bitset_and", (DL_FUNC) &_individual_bitset_and, 2},
-    {"_individual_bitset_not", (DL_FUNC) &_individual_bitset_not, 2},
-    {"_individual_bitset_or", (DL_FUNC) &_individual_bitset_or, 2},
-    {"_individual_bitset_copy_from", (DL_FUNC) &_individual_bitset_copy_from, 2},
-    {"_individual_bitset_xor", (DL_FUNC) &_individual_bitset_xor, 2},
-    {"_individual_bitset_set_difference", (DL_FUNC) &_individual_bitset_set_difference, 2},
-    {"_individual_bitset_sample", (DL_FUNC) &_individual_bitset_sample, 2},
-    {"_individual_bitset_sample_vector", (DL_FUNC) &_individual_bitset_sample_vector, 2},
-    {"_individual_bitset_to_vector", (DL_FUNC) &_individual_bitset_to_vector, 1},
-    {"_individual_filter_bitset_integer", (DL_FUNC) &_individual_filter_bitset_integer, 2},
-    {"_individual_filter_bitset_bitset", (DL_FUNC) &_individual_filter_bitset_bitset, 2},
-    {"_individual_filter_bitset_logical", (DL_FUNC) &_individual_filter_bitset_logical, 2},
-    {"_individual_bitset_choose", (DL_FUNC) &_individual_bitset_choose, 2},
-    {"_individual_create_categorical_variable", (DL_FUNC) &_individual_create_categorical_variable, 2},
-    {"_individual_categorical_variable_get_size", (DL_FUNC) &_individual_categorical_variable_get_size, 1},
-    {"_individual_categorical_variable_queue_update", (DL_FUNC) &_individual_categorical_variable_queue_update, 3},
-    {"_individual_categorical_variable_get_index_of", (DL_FUNC) &_individual_categorical_variable_get_index_of, 2},
-    {"_individual_categorical_variable_get_size_of", (DL_FUNC) &_individual_categorical_variable_get_size_of, 2},
-    {"_individual_categorical_variable_get_categories", (DL_FUNC) &_individual_categorical_variable_get_categories, 1},
-    {"_individual_categorical_variable_queue_update_vector", (DL_FUNC) &_individual_categorical_variable_queue_update_vector, 3},
-    {"_individual_categorical_variable_update", (DL_FUNC) &_individual_categorical_variable_update, 1},
-    {"_individual_categorical_variable_queue_extend", (DL_FUNC) &_individual_categorical_variable_queue_extend, 2},
-    {"_individual_categorical_variable_queue_shrink", (DL_FUNC) &_individual_categorical_variable_queue_shrink, 2},
-    {"_individual_categorical_variable_queue_shrink_bitset", (DL_FUNC) &_individual_categorical_variable_queue_shrink_bitset, 2},
-    {"_individual_dummy", (DL_FUNC) &_individual_dummy, 0},
-    {"_individual_create_double_variable", (DL_FUNC) &_individual_create_double_variable, 1},
-    {"_individual_double_variable_get_values", (DL_FUNC) &_individual_double_variable_get_values, 1},
-    {"_individual_double_variable_get_values_at_index", (DL_FUNC) &_individual_double_variable_get_values_at_index, 2},
-    {"_individual_double_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_variable_get_values_at_index_vector, 2},
-    {"_individual_double_variable_get_index_of_range", (DL_FUNC) &_individual_double_variable_get_index_of_range, 3},
-    {"_individual_double_variable_get_size_of_range", (DL_FUNC) &_individual_double_variable_get_size_of_range, 3},
-    {"_individual_double_variable_queue_fill", (DL_FUNC) &_individual_double_variable_queue_fill, 2},
-    {"_individual_double_variable_queue_update", (DL_FUNC) &_individual_double_variable_queue_update, 3},
-    {"_individual_double_variable_queue_update_bitset", (DL_FUNC) &_individual_double_variable_queue_update_bitset, 3},
-    {"_individual_double_variable_queue_extend", (DL_FUNC) &_individual_double_variable_queue_extend, 2},
-    {"_individual_double_variable_queue_shrink", (DL_FUNC) &_individual_double_variable_queue_shrink, 2},
-    {"_individual_double_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_variable_queue_shrink_bitset, 2},
-    {"_individual_create_event", (DL_FUNC) &_individual_create_event, 0},
-    {"_individual_create_targeted_event", (DL_FUNC) &_individual_create_targeted_event, 1},
-    {"_individual_event_base_tick", (DL_FUNC) &_individual_event_base_tick, 1},
-    {"_individual_event_base_get_timestep", (DL_FUNC) &_individual_event_base_get_timestep, 1},
-    {"_individual_event_base_set_timestep", (DL_FUNC) &_individual_event_base_set_timestep, 2},
-    {"_individual_event_base_should_trigger", (DL_FUNC) &_individual_event_base_should_trigger, 1},
-    {"_individual_event_schedule", (DL_FUNC) &_individual_event_schedule, 2},
-    {"_individual_event_clear_schedule", (DL_FUNC) &_individual_event_clear_schedule, 1},
-    {"_individual_event_checkpoint", (DL_FUNC) &_individual_event_checkpoint, 1},
-    {"_individual_event_restore", (DL_FUNC) &_individual_event_restore, 2},
-    {"_individual_targeted_event_clear_schedule_vector", (DL_FUNC) &_individual_targeted_event_clear_schedule_vector, 2},
-    {"_individual_targeted_event_clear_schedule", (DL_FUNC) &_individual_targeted_event_clear_schedule, 2},
-    {"_individual_targeted_event_get_scheduled", (DL_FUNC) &_individual_targeted_event_get_scheduled, 1},
-    {"_individual_targeted_event_schedule", (DL_FUNC) &_individual_targeted_event_schedule, 3},
-    {"_individual_targeted_event_queue_shrink_bitset", (DL_FUNC) &_individual_targeted_event_queue_shrink_bitset, 2},
-    {"_individual_targeted_event_queue_shrink", (DL_FUNC) &_individual_targeted_event_queue_shrink, 2},
-    {"_individual_targeted_event_queue_extend", (DL_FUNC) &_individual_targeted_event_queue_extend, 2},
-    {"_individual_targeted_event_queue_extend_with_schedule", (DL_FUNC) &_individual_targeted_event_queue_extend_with_schedule, 2},
-    {"_individual_targeted_event_schedule_vector", (DL_FUNC) &_individual_targeted_event_schedule_vector, 3},
-    {"_individual_targeted_event_schedule_multi_delay", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay, 3},
-    {"_individual_targeted_event_schedule_multi_delay_vector", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay_vector, 3},
-    {"_individual_targeted_event_get_target", (DL_FUNC) &_individual_targeted_event_get_target, 1},
-    {"_individual_targeted_event_resize", (DL_FUNC) &_individual_targeted_event_resize, 1},
-    {"_individual_targeted_event_checkpoint", (DL_FUNC) &_individual_targeted_event_checkpoint, 1},
-    {"_individual_targeted_event_restore", (DL_FUNC) &_individual_targeted_event_restore, 2},
-    {"_individual_process_listener", (DL_FUNC) &_individual_process_listener, 2},
-    {"_individual_process_targeted_listener", (DL_FUNC) &_individual_process_targeted_listener, 3},
-    {"_individual_create_integer_variable", (DL_FUNC) &_individual_create_integer_variable, 1},
-    {"_individual_integer_variable_get_values", (DL_FUNC) &_individual_integer_variable_get_values, 1},
-    {"_individual_integer_variable_get_values_at_index", (DL_FUNC) &_individual_integer_variable_get_values_at_index, 2},
-    {"_individual_integer_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_variable_get_values_at_index_vector, 2},
-    {"_individual_integer_variable_get_index_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_index_of_set_vector, 2},
-    {"_individual_integer_variable_get_index_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_index_of_set_scalar, 2},
-    {"_individual_integer_variable_get_index_of_range", (DL_FUNC) &_individual_integer_variable_get_index_of_range, 3},
-    {"_individual_integer_variable_get_size_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_size_of_set_vector, 2},
-    {"_individual_integer_variable_get_size_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_size_of_set_scalar, 2},
-    {"_individual_integer_variable_get_size_of_range", (DL_FUNC) &_individual_integer_variable_get_size_of_range, 3},
-    {"_individual_integer_variable_queue_fill", (DL_FUNC) &_individual_integer_variable_queue_fill, 2},
-    {"_individual_integer_variable_queue_update", (DL_FUNC) &_individual_integer_variable_queue_update, 3},
-    {"_individual_integer_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_variable_queue_update_bitset, 3},
-    {"_individual_integer_variable_queue_extend", (DL_FUNC) &_individual_integer_variable_queue_extend, 2},
-    {"_individual_integer_variable_queue_shrink", (DL_FUNC) &_individual_integer_variable_queue_shrink, 2},
-    {"_individual_integer_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_variable_queue_shrink_bitset, 2},
-    {"_individual_fixed_probability_multinomial_process_internal", (DL_FUNC) &_individual_fixed_probability_multinomial_process_internal, 5},
-    {"_individual_multi_probability_multinomial_process_internal", (DL_FUNC) &_individual_multi_probability_multinomial_process_internal, 5},
-    {"_individual_multi_probability_bernoulli_process_internal", (DL_FUNC) &_individual_multi_probability_bernoulli_process_internal, 4},
-    {"_individual_infection_age_process_internal", (DL_FUNC) &_individual_infection_age_process_internal, 9},
-    {"_individual_create_double_ragged_variable", (DL_FUNC) &_individual_create_double_ragged_variable, 1},
-    {"_individual_double_ragged_variable_get_values", (DL_FUNC) &_individual_double_ragged_variable_get_values, 1},
-    {"_individual_double_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_bitset, 2},
-    {"_individual_double_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_vector, 2},
-    {"_individual_double_ragged_variable_get_length", (DL_FUNC) &_individual_double_ragged_variable_get_length, 1},
-    {"_individual_double_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_bitset, 2},
-    {"_individual_double_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_vector, 2},
-    {"_individual_double_ragged_variable_queue_fill", (DL_FUNC) &_individual_double_ragged_variable_queue_fill, 2},
-    {"_individual_double_ragged_variable_queue_update", (DL_FUNC) &_individual_double_ragged_variable_queue_update, 3},
-    {"_individual_double_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_update_bitset, 3},
-    {"_individual_double_ragged_variable_queue_extend", (DL_FUNC) &_individual_double_ragged_variable_queue_extend, 2},
-    {"_individual_double_ragged_variable_queue_shrink", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink, 2},
-    {"_individual_double_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink_bitset, 2},
-    {"_individual_create_integer_ragged_variable", (DL_FUNC) &_individual_create_integer_ragged_variable, 1},
-    {"_individual_integer_ragged_variable_get_values", (DL_FUNC) &_individual_integer_ragged_variable_get_values, 1},
-    {"_individual_integer_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_bitset, 2},
-    {"_individual_integer_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_vector, 2},
-    {"_individual_integer_ragged_variable_get_length", (DL_FUNC) &_individual_integer_ragged_variable_get_length, 1},
-    {"_individual_integer_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_bitset, 2},
-    {"_individual_integer_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_vector, 2},
-    {"_individual_integer_ragged_variable_queue_fill", (DL_FUNC) &_individual_integer_ragged_variable_queue_fill, 2},
-    {"_individual_integer_ragged_variable_queue_update", (DL_FUNC) &_individual_integer_ragged_variable_queue_update, 3},
-    {"_individual_integer_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_update_bitset, 3},
-    {"_individual_integer_ragged_variable_queue_extend", (DL_FUNC) &_individual_integer_ragged_variable_queue_extend, 2},
-    {"_individual_integer_ragged_variable_queue_shrink", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink, 2},
-    {"_individual_integer_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink_bitset, 2},
-    {"_individual_create_render_vector", (DL_FUNC) &_individual_create_render_vector, 1},
-    {"_individual_render_vector_update", (DL_FUNC) &_individual_render_vector_update, 3},
-    {"_individual_render_vector_data", (DL_FUNC) &_individual_render_vector_data, 1},
-    {"_individual_execute_process", (DL_FUNC) &_individual_execute_process, 2},
-    {"_individual_variable_get_size", (DL_FUNC) &_individual_variable_get_size, 1},
-    {"_individual_variable_update", (DL_FUNC) &_individual_variable_update, 1},
-    {"_individual_variable_resize", (DL_FUNC) &_individual_variable_resize, 1},
-    {"_individual_RcppExport_registerCCallable", (DL_FUNC) &_individual_RcppExport_registerCCallable, 0},
-    {"run_testthat_tests", (DL_FUNC) &run_testthat_tests, 1},
-    {NULL, NULL, 0}
-};
-
-RcppExport void R_init_individual(DllInfo *dll) {
-    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
-    R_useDynamicSymbols(dll, FALSE);
-}
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include "../inst/include/individual.h"
+#include "../inst/include/individual_types.h"
+#include <Rcpp.h>
+#include <string>
+#include <set>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+// create_bitset
+Rcpp::XPtr<individual_index_t> create_bitset(size_t size);
+RcppExport SEXP _individual_create_bitset(SEXP sizeSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_bitset(size));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_copy
+Rcpp::XPtr<individual_index_t> bitset_copy(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_copy(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_copy(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_insert
+void bitset_insert(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
+RcppExport SEXP _individual_bitset_insert(SEXP bSEXP, SEXP vSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
+    bitset_insert(b, v);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_remove
+void bitset_remove(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
+RcppExport SEXP _individual_bitset_remove(SEXP bSEXP, SEXP vSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
+    bitset_remove(b, v);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_clear
+void bitset_clear(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_clear(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_clear(b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_size
+size_t bitset_size(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_size(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_size(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_max_size
+size_t bitset_max_size(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_max_size(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_max_size(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_and
+void bitset_and(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_and(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_and(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_not
+Rcpp::XPtr<individual_index_t> bitset_not(const Rcpp::XPtr<individual_index_t> b, const bool inplace);
+RcppExport SEXP _individual_bitset_not(SEXP bSEXP, SEXP inplaceSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< const bool >::type inplace(inplaceSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_not(b, inplace));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_or
+void bitset_or(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_or(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_or(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_copy_from
+void bitset_copy_from(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_copy_from(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_copy_from(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_xor
+void bitset_xor(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_xor(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_xor(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_set_difference
+void bitset_set_difference(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_set_difference(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_set_difference(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_sample
+void bitset_sample(const Rcpp::XPtr<individual_index_t> b, double rate);
+RcppExport SEXP _individual_bitset_sample(SEXP bSEXP, SEXP rateSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< double >::type rate(rateSEXP);
+    bitset_sample(b, rate);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_sample_vector
+void bitset_sample_vector(const Rcpp::XPtr<individual_index_t> b, std::vector<double> rate);
+RcppExport SEXP _individual_bitset_sample_vector(SEXP bSEXP, SEXP rateSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type rate(rateSEXP);
+    bitset_sample_vector(b, rate);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_to_vector
+std::vector<size_t> bitset_to_vector(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_to_vector(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_to_vector(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// filter_bitset_integer
+Rcpp::XPtr<individual_index_t> filter_bitset_integer(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> other);
+RcppExport SEXP _individual_filter_bitset_integer(SEXP bSEXP, SEXP otherSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type other(otherSEXP);
+    rcpp_result_gen = Rcpp::wrap(filter_bitset_integer(b, other));
+    return rcpp_result_gen;
+END_RCPP
+}
+// filter_bitset_bitset
+Rcpp::XPtr<individual_index_t> filter_bitset_bitset(const Rcpp::XPtr<individual_index_t> b, const Rcpp::XPtr<individual_index_t> other);
+RcppExport SEXP _individual_filter_bitset_bitset(SEXP bSEXP, SEXP otherSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type other(otherSEXP);
+    rcpp_result_gen = Rcpp::wrap(filter_bitset_bitset(b, other));
+    return rcpp_result_gen;
+END_RCPP
+}
+// filter_bitset_logical
+Rcpp::XPtr<individual_index_t> filter_bitset_logical(const Rcpp::XPtr<individual_index_t> bitset, Rcpp::LogicalVector other);
+RcppExport SEXP _individual_filter_bitset_logical(SEXP bitsetSEXP, SEXP otherSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type bitset(bitsetSEXP);
+    Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type other(otherSEXP);
+    rcpp_result_gen = Rcpp::wrap(filter_bitset_logical(bitset, other));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_choose
+void bitset_choose(const Rcpp::XPtr<individual_index_t> b, const size_t k);
+RcppExport SEXP _individual_bitset_choose(SEXP bSEXP, SEXP kSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< const size_t >::type k(kSEXP);
+    bitset_choose(b, k);
+    return R_NilValue;
+END_RCPP
+}
+// create_categorical_variable
+Rcpp::XPtr<CategoricalVariable> create_categorical_variable(const std::vector<std::string>& categories, const std::vector<std::string>& values);
+RcppExport SEXP _individual_create_categorical_variable(SEXP categoriesSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type categories(categoriesSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_categorical_variable(categories, values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_size
+size_t categorical_variable_get_size(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_get_size(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_queue_update
+void categorical_variable_queue_update(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_categorical_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    categorical_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_get_index_of
+Rcpp::XPtr<individual_index_t> categorical_variable_get_index_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
+RcppExport SEXP _individual_categorical_variable_get_index_of(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_index_of(variable, values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_size_of
+int categorical_variable_get_size_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
+RcppExport SEXP _individual_categorical_variable_get_size_of(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size_of(variable, values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_categories
+std::vector<std::string> categorical_variable_get_categories(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_get_categories(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_categories(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_queue_update_vector
+void categorical_variable_queue_update_vector(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, std::vector<size_t>& index);
+RcppExport SEXP _individual_categorical_variable_queue_update_vector(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    categorical_variable_queue_update_vector(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_update
+void categorical_variable_update(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_update(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    categorical_variable_update(variable);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_queue_extend
+void categorical_variable_queue_extend(Rcpp::XPtr<CategoricalVariable> variable, std::vector<std::string>& values);
+RcppExport SEXP _individual_categorical_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<std::string>& >::type values(valuesSEXP);
+    categorical_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_queue_shrink
+void categorical_variable_queue_shrink(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_categorical_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    categorical_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_queue_shrink_bitset
+void categorical_variable_queue_shrink_bitset(Rcpp::XPtr<CategoricalVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_categorical_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    categorical_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_get_values
+std::vector<std::string> categorical_variable_get_values(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_categorical_variable_get_values(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// dummy
+void dummy();
+static SEXP _individual_dummy_try() {
+BEGIN_RCPP
+    dummy();
+    return R_NilValue;
+END_RCPP_RETURN_ERROR
+}
+RcppExport SEXP _individual_dummy() {
+    SEXP rcpp_result_gen;
+    {
+        Rcpp::RNGScope rcpp_rngScope_gen;
+        rcpp_result_gen = PROTECT(_individual_dummy_try());
+    }
+    Rboolean rcpp_isInterrupt_gen = Rf_inherits(rcpp_result_gen, "interrupted-error");
+    if (rcpp_isInterrupt_gen) {
+        UNPROTECT(1);
+        Rf_onintr();
+    }
+    bool rcpp_isLongjump_gen = Rcpp::internal::isLongjumpSentinel(rcpp_result_gen);
+    if (rcpp_isLongjump_gen) {
+        Rcpp::internal::resumeJump(rcpp_result_gen);
+    }
+    Rboolean rcpp_isError_gen = Rf_inherits(rcpp_result_gen, "try-error");
+    if (rcpp_isError_gen) {
+        SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
+        UNPROTECT(1);
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
+    }
+    UNPROTECT(1);
+    return rcpp_result_gen;
+}
+// create_double_variable
+Rcpp::XPtr<DoubleVariable> create_double_variable(const std::vector<double>& values);
+RcppExport SEXP _individual_create_double_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<double>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_double_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_values
+const std::vector<double>& double_variable_get_values(Rcpp::XPtr<DoubleVariable> variable);
+RcppExport SEXP _individual_double_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_values_at_index
+std::vector<double> double_variable_get_values_at_index(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_values_at_index_vector
+std::vector<double> double_variable_get_values_at_index_vector(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_index_of_range
+Rcpp::XPtr<individual_index_t> double_variable_get_index_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
+RcppExport SEXP _individual_double_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_index_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_size_of_range
+size_t double_variable_get_size_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
+RcppExport SEXP _individual_double_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_size_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_queue_fill
+void double_variable_queue_fill(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value);
+RcppExport SEXP _individual_double_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
+    double_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_update
+void double_variable_queue_update(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, std::vector<size_t> index);
+RcppExport SEXP _individual_double_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    double_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_update_bitset
+void double_variable_queue_update_bitset(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_extend
+void double_variable_queue_extend(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> values);
+RcppExport SEXP _individual_double_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type values(valuesSEXP);
+    double_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_shrink
+void double_variable_queue_shrink(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    double_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_shrink_bitset
+void double_variable_queue_shrink_bitset(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// create_event
+Rcpp::XPtr<Event> create_event();
+RcppExport SEXP _individual_create_event() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(create_event());
+    return rcpp_result_gen;
+END_RCPP
+}
+// create_targeted_event
+Rcpp::XPtr<TargetedEvent> create_targeted_event(size_t size);
+RcppExport SEXP _individual_create_targeted_event(SEXP sizeSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_targeted_event(size));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_base_tick
+void event_base_tick(const Rcpp::XPtr<EventBase> event);
+RcppExport SEXP _individual_event_base_tick(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    event_base_tick(event);
+    return R_NilValue;
+END_RCPP
+}
+// event_base_get_timestep
+size_t event_base_get_timestep(const Rcpp::XPtr<EventBase> event);
+RcppExport SEXP _individual_event_base_get_timestep(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(event_base_get_timestep(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_base_set_timestep
+void event_base_set_timestep(const Rcpp::XPtr<EventBase> event, size_t time);
+RcppExport SEXP _individual_event_base_set_timestep(SEXP eventSEXP, SEXP timeSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< size_t >::type time(timeSEXP);
+    event_base_set_timestep(event, time);
+    return R_NilValue;
+END_RCPP
+}
+// event_base_should_trigger
+bool event_base_should_trigger(const Rcpp::XPtr<EventBase> event);
+RcppExport SEXP _individual_event_base_should_trigger(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(event_base_should_trigger(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_schedule
+void event_schedule(const Rcpp::XPtr<Event> event, std::vector<double> delays);
+RcppExport SEXP _individual_event_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type delays(delaysSEXP);
+    event_schedule(event, delays);
+    return R_NilValue;
+END_RCPP
+}
+// event_clear_schedule
+void event_clear_schedule(const Rcpp::XPtr<Event> event);
+RcppExport SEXP _individual_event_clear_schedule(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    event_clear_schedule(event);
+    return R_NilValue;
+END_RCPP
+}
+// event_checkpoint
+std::vector<size_t> event_checkpoint(const Rcpp::XPtr<Event> event);
+RcppExport SEXP _individual_event_checkpoint(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(event_checkpoint(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_restore
+void event_restore(const Rcpp::XPtr<Event> event, std::vector<size_t> schedule);
+RcppExport SEXP _individual_event_restore(SEXP eventSEXP, SEXP scheduleSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type schedule(scheduleSEXP);
+    event_restore(event, schedule);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_clear_schedule_vector
+void targeted_event_clear_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target);
+RcppExport SEXP _individual_targeted_event_clear_schedule_vector(SEXP eventSEXP, SEXP targetSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
+    targeted_event_clear_schedule_vector(event, target);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_clear_schedule
+void targeted_event_clear_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target);
+RcppExport SEXP _individual_targeted_event_clear_schedule(SEXP eventSEXP, SEXP targetSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    targeted_event_clear_schedule(event, target);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_get_scheduled
+Rcpp::XPtr<individual_index_t> targeted_event_get_scheduled(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_get_scheduled(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(targeted_event_get_scheduled(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// targeted_event_schedule
+void targeted_event_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, double delay);
+RcppExport SEXP _individual_targeted_event_schedule(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
+    targeted_event_schedule(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_shrink_bitset
+void targeted_event_queue_shrink_bitset(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_targeted_event_queue_shrink_bitset(SEXP eventSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    targeted_event_queue_shrink_bitset(event, index);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_shrink
+void targeted_event_queue_shrink(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t>& index);
+RcppExport SEXP _individual_targeted_event_queue_shrink(SEXP eventSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    targeted_event_queue_shrink(event, index);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_extend
+void targeted_event_queue_extend(const Rcpp::XPtr<TargetedEvent> event, size_t n);
+RcppExport SEXP _individual_targeted_event_queue_extend(SEXP eventSEXP, SEXP nSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< size_t >::type n(nSEXP);
+    targeted_event_queue_extend(event, n);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_extend_with_schedule
+void targeted_event_queue_extend_with_schedule(const Rcpp::XPtr<TargetedEvent> event, const std::vector<double>& delays);
+RcppExport SEXP _individual_targeted_event_queue_extend_with_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double>& >::type delays(delaysSEXP);
+    targeted_event_queue_extend_with_schedule(event, delays);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_schedule_vector
+void targeted_event_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, double delay);
+RcppExport SEXP _individual_targeted_event_schedule_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
+    targeted_event_schedule_vector(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_schedule_multi_delay
+void targeted_event_schedule_multi_delay(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, const std::vector<double> delay);
+RcppExport SEXP _individual_targeted_event_schedule_multi_delay(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
+    targeted_event_schedule_multi_delay(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_schedule_multi_delay_vector
+void targeted_event_schedule_multi_delay_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, const std::vector<double> delay);
+RcppExport SEXP _individual_targeted_event_schedule_multi_delay_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
+    targeted_event_schedule_multi_delay_vector(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_get_target
+Rcpp::XPtr<individual_index_t> targeted_event_get_target(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_get_target(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(targeted_event_get_target(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// targeted_event_resize
+void targeted_event_resize(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_resize(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    targeted_event_resize(event);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_checkpoint
+Rcpp::List targeted_event_checkpoint(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_checkpoint(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(targeted_event_checkpoint(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// targeted_event_restore
+void targeted_event_restore(const Rcpp::XPtr<TargetedEvent> event, Rcpp::List state);
+RcppExport SEXP _individual_targeted_event_restore(SEXP eventSEXP, SEXP stateSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type state(stateSEXP);
+    targeted_event_restore(event, state);
+    return R_NilValue;
+END_RCPP
+}
+// process_listener
+void process_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<listener_t> listener);
+RcppExport SEXP _individual_process_listener(SEXP eventSEXP, SEXP listenerSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<listener_t> >::type listener(listenerSEXP);
+    process_listener(event, listener);
+    return R_NilValue;
+END_RCPP
+}
+// process_targeted_listener
+void process_targeted_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<targeted_listener_t> listener, const Rcpp::XPtr<individual_index_t> target);
+RcppExport SEXP _individual_process_targeted_listener(SEXP eventSEXP, SEXP listenerSEXP, SEXP targetSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<targeted_listener_t> >::type listener(listenerSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    process_targeted_listener(event, listener, target);
+    return R_NilValue;
+END_RCPP
+}
+// create_integer_variable
+Rcpp::XPtr<IntegerVariable> create_integer_variable(const std::vector<int>& values);
+RcppExport SEXP _individual_create_integer_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<int>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_integer_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_values
+const std::vector<int>& integer_variable_get_values(Rcpp::XPtr<IntegerVariable> variable);
+RcppExport SEXP _individual_integer_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_modulo_differences
+individual_index_t integer_variable_get_modulo_differences(Rcpp::XPtr<IntegerVariable> variable, const int value, const int difference);
+RcppExport SEXP _individual_integer_variable_get_modulo_differences(SEXP variableSEXP, SEXP valueSEXP, SEXP differenceSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< const int >::type difference(differenceSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_modulo_differences(variable, value, difference));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_values_at_index
+std::vector<int> integer_variable_get_values_at_index(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_values_at_index_vector
+std::vector<int> integer_variable_get_values_at_index_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_index_of_set_vector
+Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values_set);
+RcppExport SEXP _individual_integer_variable_get_index_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type values_set(values_setSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_vector(variable, values_set));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_index_of_set_scalar
+Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int values_set);
+RcppExport SEXP _individual_integer_variable_get_index_of_set_scalar(SEXP variableSEXP, SEXP values_setSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type values_set(values_setSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_scalar(variable, values_set));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_index_of_range
+Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
+RcppExport SEXP _individual_integer_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_size_of_set_vector
+size_t integer_variable_get_size_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, const std::vector<int> values_set);
+RcppExport SEXP _individual_integer_variable_get_size_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<int> >::type values_set(values_setSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_vector(variable, values_set));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_size_of_set_scalar
+size_t integer_variable_get_size_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int value);
+RcppExport SEXP _individual_integer_variable_get_size_of_set_scalar(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type value(valueSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_scalar(variable, value));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_size_of_range
+size_t integer_variable_get_size_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
+RcppExport SEXP _individual_integer_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_queue_fill
+void integer_variable_queue_fill(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value);
+RcppExport SEXP _individual_integer_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
+    integer_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_update
+void integer_variable_queue_update(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    integer_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_update_bitset
+void integer_variable_queue_update_bitset(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_extend
+void integer_variable_queue_extend(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values);
+RcppExport SEXP _individual_integer_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type values(valuesSEXP);
+    integer_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_shrink
+void integer_variable_queue_shrink(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    integer_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_shrink_bitset
+void integer_variable_queue_shrink_bitset(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// fixed_probability_multinomial_process_internal
+Rcpp::XPtr<process_t> fixed_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const double rate, const std::vector<double> destination_probabilities);
+RcppExport SEXP _individual_fixed_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rateSEXP, SEXP destination_probabilitiesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
+    Rcpp::traits::input_parameter< const double >::type rate(rateSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
+    rcpp_result_gen = Rcpp::wrap(fixed_probability_multinomial_process_internal(variable, source_state, destination_states, rate, destination_probabilities));
+    return rcpp_result_gen;
+END_RCPP
+}
+// multi_probability_multinomial_process_internal
+Rcpp::XPtr<process_t> multi_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const Rcpp::XPtr<DoubleVariable> rate_variable, const std::vector<double> destination_probabilities);
+RcppExport SEXP _individual_multi_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rate_variableSEXP, SEXP destination_probabilitiesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
+    rcpp_result_gen = Rcpp::wrap(multi_probability_multinomial_process_internal(variable, source_state, destination_states, rate_variable, destination_probabilities));
+    return rcpp_result_gen;
+END_RCPP
+}
+// multi_probability_bernoulli_process_internal
+Rcpp::XPtr<process_t> multi_probability_bernoulli_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string from, const std::string to, const Rcpp::XPtr<DoubleVariable> rate_variable);
+RcppExport SEXP _individual_multi_probability_bernoulli_process_internal(SEXP variableSEXP, SEXP fromSEXP, SEXP toSEXP, SEXP rate_variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type from(fromSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type to(toSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(multi_probability_bernoulli_process_internal(variable, from, to, rate_variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// infection_age_process_internal
+Rcpp::XPtr<process_t> infection_age_process_internal(Rcpp::XPtr<CategoricalVariable> state, const std::string susceptible, const std::string exposed, const std::string infectious, const Rcpp::XPtr<IntegerVariable> age, const int age_bins, const double p, const double dt, const Rcpp::NumericMatrix mixing);
+RcppExport SEXP _individual_infection_age_process_internal(SEXP stateSEXP, SEXP susceptibleSEXP, SEXP exposedSEXP, SEXP infectiousSEXP, SEXP ageSEXP, SEXP age_binsSEXP, SEXP pSEXP, SEXP dtSEXP, SEXP mixingSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type state(stateSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type susceptible(susceptibleSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type exposed(exposedSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type infectious(infectiousSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<IntegerVariable> >::type age(ageSEXP);
+    Rcpp::traits::input_parameter< const int >::type age_bins(age_binsSEXP);
+    Rcpp::traits::input_parameter< const double >::type p(pSEXP);
+    Rcpp::traits::input_parameter< const double >::type dt(dtSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::NumericMatrix >::type mixing(mixingSEXP);
+    rcpp_result_gen = Rcpp::wrap(infection_age_process_internal(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing));
+    return rcpp_result_gen;
+END_RCPP
+}
+// create_double_ragged_variable
+Rcpp::XPtr<RaggedDouble> create_double_ragged_variable(const std::vector<std::vector<double>>& values);
+RcppExport SEXP _individual_create_double_ragged_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_double_ragged_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_values
+std::vector<std::vector<double>> double_ragged_variable_get_values(Rcpp::XPtr<RaggedDouble> variable);
+RcppExport SEXP _individual_double_ragged_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_values_at_index_bitset
+std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_values_at_index_vector
+std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_length
+std::vector<size_t> double_ragged_variable_get_length(Rcpp::XPtr<RaggedDouble> variable);
+RcppExport SEXP _individual_double_ragged_variable_get_length(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_length_at_index_bitset
+std::vector<size_t> double_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_length_at_index_vector
+std::vector<size_t> double_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_queue_fill
+void double_ragged_variable_queue_fill(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value);
+RcppExport SEXP _individual_double_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
+    double_ragged_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_update
+void double_ragged_variable_queue_update(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value, std::vector<size_t> index);
+RcppExport SEXP _individual_double_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    double_ragged_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_update_bitset
+void double_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_ragged_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_extend
+void double_ragged_variable_queue_extend(Rcpp::XPtr<RaggedDouble> variable, std::vector<std::vector<double>>& values);
+RcppExport SEXP _individual_double_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<std::vector<double>>& >::type values(valuesSEXP);
+    double_ragged_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_shrink
+void double_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_double_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    double_ragged_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_shrink_bitset
+void double_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_ragged_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// create_integer_ragged_variable
+Rcpp::XPtr<RaggedInteger> create_integer_ragged_variable(const std::vector<std::vector<int>>& values);
+RcppExport SEXP _individual_create_integer_ragged_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_integer_ragged_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_values
+std::vector<std::vector<int>> integer_ragged_variable_get_values(Rcpp::XPtr<RaggedInteger> variable);
+RcppExport SEXP _individual_integer_ragged_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_values_at_index_bitset
+std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_values_at_index_vector
+std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_length
+std::vector<size_t> integer_ragged_variable_get_length(Rcpp::XPtr<RaggedInteger> variable);
+RcppExport SEXP _individual_integer_ragged_variable_get_length(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_length_at_index_bitset
+std::vector<size_t> integer_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_length_at_index_vector
+std::vector<size_t> integer_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_queue_fill
+void integer_ragged_variable_queue_fill(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value);
+RcppExport SEXP _individual_integer_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
+    integer_ragged_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_update
+void integer_ragged_variable_queue_update(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    integer_ragged_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_update_bitset
+void integer_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_ragged_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_extend
+void integer_ragged_variable_queue_extend(Rcpp::XPtr<RaggedInteger> variable, std::vector<std::vector<int>>& values);
+RcppExport SEXP _individual_integer_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<std::vector<int>>& >::type values(valuesSEXP);
+    integer_ragged_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_shrink
+void integer_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    integer_ragged_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_shrink_bitset
+void integer_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_ragged_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// create_render_vector
+Rcpp::XPtr<RenderVector> create_render_vector(std::vector<double> data);
+RcppExport SEXP _individual_create_render_vector(SEXP dataSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< std::vector<double> >::type data(dataSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_render_vector(data));
+    return rcpp_result_gen;
+END_RCPP
+}
+// render_vector_update
+void render_vector_update(Rcpp::XPtr<RenderVector> v, size_t index, double value);
+RcppExport SEXP _individual_render_vector_update(SEXP vSEXP, SEXP indexSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
+    Rcpp::traits::input_parameter< size_t >::type index(indexSEXP);
+    Rcpp::traits::input_parameter< double >::type value(valueSEXP);
+    render_vector_update(v, index, value);
+    return R_NilValue;
+END_RCPP
+}
+// render_vector_data
+std::vector<double> render_vector_data(Rcpp::XPtr<RenderVector> v);
+RcppExport SEXP _individual_render_vector_data(SEXP vSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
+    rcpp_result_gen = Rcpp::wrap(render_vector_data(v));
+    return rcpp_result_gen;
+END_RCPP
+}
+// execute_process
+void execute_process(Rcpp::XPtr<process_t> process, size_t timestep);
+RcppExport SEXP _individual_execute_process(SEXP processSEXP, SEXP timestepSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<process_t> >::type process(processSEXP);
+    Rcpp::traits::input_parameter< size_t >::type timestep(timestepSEXP);
+    execute_process(process, timestep);
+    return R_NilValue;
+END_RCPP
+}
+// variable_get_size
+size_t variable_get_size(Rcpp::XPtr<Variable> variable);
+RcppExport SEXP _individual_variable_get_size(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(variable_get_size(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// variable_update
+void variable_update(Rcpp::XPtr<Variable> variable);
+RcppExport SEXP _individual_variable_update(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
+    variable_update(variable);
+    return R_NilValue;
+END_RCPP
+}
+// variable_resize
+void variable_resize(Rcpp::XPtr<Variable> variable);
+RcppExport SEXP _individual_variable_resize(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
+    variable_resize(variable);
+    return R_NilValue;
+END_RCPP
+}
+
+// validate (ensure exported C++ functions exist before calling them)
+static int _individual_RcppExport_validate(const char* sig) { 
+    static std::set<std::string> signatures;
+    if (signatures.empty()) {
+        signatures.insert("void(*dummy)()");
+    }
+    return signatures.find(sig) != signatures.end();
+}
+
+// registerCCallable (register entry points for exported C++ functions)
+RcppExport SEXP _individual_RcppExport_registerCCallable() { 
+    R_RegisterCCallable("individual", "_individual_dummy", (DL_FUNC)_individual_dummy_try);
+    R_RegisterCCallable("individual", "_individual_RcppExport_validate", (DL_FUNC)_individual_RcppExport_validate);
+    return R_NilValue;
+}
+
+RcppExport SEXP run_testthat_tests(SEXP);
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_individual_create_bitset", (DL_FUNC) &_individual_create_bitset, 1},
+    {"_individual_bitset_copy", (DL_FUNC) &_individual_bitset_copy, 1},
+    {"_individual_bitset_insert", (DL_FUNC) &_individual_bitset_insert, 2},
+    {"_individual_bitset_remove", (DL_FUNC) &_individual_bitset_remove, 2},
+    {"_individual_bitset_clear", (DL_FUNC) &_individual_bitset_clear, 1},
+    {"_individual_bitset_size", (DL_FUNC) &_individual_bitset_size, 1},
+    {"_individual_bitset_max_size", (DL_FUNC) &_individual_bitset_max_size, 1},
+    {"_individual_bitset_and", (DL_FUNC) &_individual_bitset_and, 2},
+    {"_individual_bitset_not", (DL_FUNC) &_individual_bitset_not, 2},
+    {"_individual_bitset_or", (DL_FUNC) &_individual_bitset_or, 2},
+    {"_individual_bitset_copy_from", (DL_FUNC) &_individual_bitset_copy_from, 2},
+    {"_individual_bitset_xor", (DL_FUNC) &_individual_bitset_xor, 2},
+    {"_individual_bitset_set_difference", (DL_FUNC) &_individual_bitset_set_difference, 2},
+    {"_individual_bitset_sample", (DL_FUNC) &_individual_bitset_sample, 2},
+    {"_individual_bitset_sample_vector", (DL_FUNC) &_individual_bitset_sample_vector, 2},
+    {"_individual_bitset_to_vector", (DL_FUNC) &_individual_bitset_to_vector, 1},
+    {"_individual_filter_bitset_integer", (DL_FUNC) &_individual_filter_bitset_integer, 2},
+    {"_individual_filter_bitset_bitset", (DL_FUNC) &_individual_filter_bitset_bitset, 2},
+    {"_individual_filter_bitset_logical", (DL_FUNC) &_individual_filter_bitset_logical, 2},
+    {"_individual_bitset_choose", (DL_FUNC) &_individual_bitset_choose, 2},
+    {"_individual_create_categorical_variable", (DL_FUNC) &_individual_create_categorical_variable, 2},
+    {"_individual_categorical_variable_get_size", (DL_FUNC) &_individual_categorical_variable_get_size, 1},
+    {"_individual_categorical_variable_queue_update", (DL_FUNC) &_individual_categorical_variable_queue_update, 3},
+    {"_individual_categorical_variable_get_index_of", (DL_FUNC) &_individual_categorical_variable_get_index_of, 2},
+    {"_individual_categorical_variable_get_size_of", (DL_FUNC) &_individual_categorical_variable_get_size_of, 2},
+    {"_individual_categorical_variable_get_categories", (DL_FUNC) &_individual_categorical_variable_get_categories, 1},
+    {"_individual_categorical_variable_queue_update_vector", (DL_FUNC) &_individual_categorical_variable_queue_update_vector, 3},
+    {"_individual_categorical_variable_update", (DL_FUNC) &_individual_categorical_variable_update, 1},
+    {"_individual_categorical_variable_queue_extend", (DL_FUNC) &_individual_categorical_variable_queue_extend, 2},
+    {"_individual_categorical_variable_queue_shrink", (DL_FUNC) &_individual_categorical_variable_queue_shrink, 2},
+    {"_individual_categorical_variable_queue_shrink_bitset", (DL_FUNC) &_individual_categorical_variable_queue_shrink_bitset, 2},
+    {"_individual_categorical_variable_get_values", (DL_FUNC) &_individual_categorical_variable_get_values, 2},
+    {"_individual_dummy", (DL_FUNC) &_individual_dummy, 0},
+    {"_individual_create_double_variable", (DL_FUNC) &_individual_create_double_variable, 1},
+    {"_individual_double_variable_get_values", (DL_FUNC) &_individual_double_variable_get_values, 1},
+    {"_individual_double_variable_get_values_at_index", (DL_FUNC) &_individual_double_variable_get_values_at_index, 2},
+    {"_individual_double_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_variable_get_values_at_index_vector, 2},
+    {"_individual_double_variable_get_index_of_range", (DL_FUNC) &_individual_double_variable_get_index_of_range, 3},
+    {"_individual_double_variable_get_size_of_range", (DL_FUNC) &_individual_double_variable_get_size_of_range, 3},
+    {"_individual_double_variable_queue_fill", (DL_FUNC) &_individual_double_variable_queue_fill, 2},
+    {"_individual_double_variable_queue_update", (DL_FUNC) &_individual_double_variable_queue_update, 3},
+    {"_individual_double_variable_queue_update_bitset", (DL_FUNC) &_individual_double_variable_queue_update_bitset, 3},
+    {"_individual_double_variable_queue_extend", (DL_FUNC) &_individual_double_variable_queue_extend, 2},
+    {"_individual_double_variable_queue_shrink", (DL_FUNC) &_individual_double_variable_queue_shrink, 2},
+    {"_individual_double_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_variable_queue_shrink_bitset, 2},
+    {"_individual_create_event", (DL_FUNC) &_individual_create_event, 0},
+    {"_individual_create_targeted_event", (DL_FUNC) &_individual_create_targeted_event, 1},
+    {"_individual_event_base_tick", (DL_FUNC) &_individual_event_base_tick, 1},
+    {"_individual_event_base_get_timestep", (DL_FUNC) &_individual_event_base_get_timestep, 1},
+    {"_individual_event_base_set_timestep", (DL_FUNC) &_individual_event_base_set_timestep, 2},
+    {"_individual_event_base_should_trigger", (DL_FUNC) &_individual_event_base_should_trigger, 1},
+    {"_individual_event_schedule", (DL_FUNC) &_individual_event_schedule, 2},
+    {"_individual_event_clear_schedule", (DL_FUNC) &_individual_event_clear_schedule, 1},
+    {"_individual_event_checkpoint", (DL_FUNC) &_individual_event_checkpoint, 1},
+    {"_individual_event_restore", (DL_FUNC) &_individual_event_restore, 2},
+    {"_individual_targeted_event_clear_schedule_vector", (DL_FUNC) &_individual_targeted_event_clear_schedule_vector, 2},
+    {"_individual_targeted_event_clear_schedule", (DL_FUNC) &_individual_targeted_event_clear_schedule, 2},
+    {"_individual_targeted_event_get_scheduled", (DL_FUNC) &_individual_targeted_event_get_scheduled, 1},
+    {"_individual_targeted_event_schedule", (DL_FUNC) &_individual_targeted_event_schedule, 3},
+    {"_individual_targeted_event_queue_shrink_bitset", (DL_FUNC) &_individual_targeted_event_queue_shrink_bitset, 2},
+    {"_individual_targeted_event_queue_shrink", (DL_FUNC) &_individual_targeted_event_queue_shrink, 2},
+    {"_individual_targeted_event_queue_extend", (DL_FUNC) &_individual_targeted_event_queue_extend, 2},
+    {"_individual_targeted_event_queue_extend_with_schedule", (DL_FUNC) &_individual_targeted_event_queue_extend_with_schedule, 2},
+    {"_individual_targeted_event_schedule_vector", (DL_FUNC) &_individual_targeted_event_schedule_vector, 3},
+    {"_individual_targeted_event_schedule_multi_delay", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay, 3},
+    {"_individual_targeted_event_schedule_multi_delay_vector", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay_vector, 3},
+    {"_individual_targeted_event_get_target", (DL_FUNC) &_individual_targeted_event_get_target, 1},
+    {"_individual_targeted_event_resize", (DL_FUNC) &_individual_targeted_event_resize, 1},
+    {"_individual_targeted_event_checkpoint", (DL_FUNC) &_individual_targeted_event_checkpoint, 1},
+    {"_individual_targeted_event_restore", (DL_FUNC) &_individual_targeted_event_restore, 2},
+    {"_individual_process_listener", (DL_FUNC) &_individual_process_listener, 2},
+    {"_individual_process_targeted_listener", (DL_FUNC) &_individual_process_targeted_listener, 3},
+    {"_individual_create_integer_variable", (DL_FUNC) &_individual_create_integer_variable, 1},
+    {"_individual_integer_variable_get_values", (DL_FUNC) &_individual_integer_variable_get_values, 1},
+    {"_individual_integer_variable_get_modulo_differences", (DL_FUNC) &_individual_integer_variable_get_modulo_differences, 3},
+    {"_individual_integer_variable_get_values_at_index", (DL_FUNC) &_individual_integer_variable_get_values_at_index, 2},
+    {"_individual_integer_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_variable_get_values_at_index_vector, 2},
+    {"_individual_integer_variable_get_index_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_index_of_set_vector, 2},
+    {"_individual_integer_variable_get_index_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_index_of_set_scalar, 2},
+    {"_individual_integer_variable_get_index_of_range", (DL_FUNC) &_individual_integer_variable_get_index_of_range, 3},
+    {"_individual_integer_variable_get_size_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_size_of_set_vector, 2},
+    {"_individual_integer_variable_get_size_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_size_of_set_scalar, 2},
+    {"_individual_integer_variable_get_size_of_range", (DL_FUNC) &_individual_integer_variable_get_size_of_range, 3},
+    {"_individual_integer_variable_queue_fill", (DL_FUNC) &_individual_integer_variable_queue_fill, 2},
+    {"_individual_integer_variable_queue_update", (DL_FUNC) &_individual_integer_variable_queue_update, 3},
+    {"_individual_integer_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_variable_queue_update_bitset, 3},
+    {"_individual_integer_variable_queue_extend", (DL_FUNC) &_individual_integer_variable_queue_extend, 2},
+    {"_individual_integer_variable_queue_shrink", (DL_FUNC) &_individual_integer_variable_queue_shrink, 2},
+    {"_individual_integer_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_variable_queue_shrink_bitset, 2},
+    {"_individual_fixed_probability_multinomial_process_internal", (DL_FUNC) &_individual_fixed_probability_multinomial_process_internal, 5},
+    {"_individual_multi_probability_multinomial_process_internal", (DL_FUNC) &_individual_multi_probability_multinomial_process_internal, 5},
+    {"_individual_multi_probability_bernoulli_process_internal", (DL_FUNC) &_individual_multi_probability_bernoulli_process_internal, 4},
+    {"_individual_infection_age_process_internal", (DL_FUNC) &_individual_infection_age_process_internal, 9},
+    {"_individual_create_double_ragged_variable", (DL_FUNC) &_individual_create_double_ragged_variable, 1},
+    {"_individual_double_ragged_variable_get_values", (DL_FUNC) &_individual_double_ragged_variable_get_values, 1},
+    {"_individual_double_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_bitset, 2},
+    {"_individual_double_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_vector, 2},
+    {"_individual_double_ragged_variable_get_length", (DL_FUNC) &_individual_double_ragged_variable_get_length, 1},
+    {"_individual_double_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_bitset, 2},
+    {"_individual_double_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_vector, 2},
+    {"_individual_double_ragged_variable_queue_fill", (DL_FUNC) &_individual_double_ragged_variable_queue_fill, 2},
+    {"_individual_double_ragged_variable_queue_update", (DL_FUNC) &_individual_double_ragged_variable_queue_update, 3},
+    {"_individual_double_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_update_bitset, 3},
+    {"_individual_double_ragged_variable_queue_extend", (DL_FUNC) &_individual_double_ragged_variable_queue_extend, 2},
+    {"_individual_double_ragged_variable_queue_shrink", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink, 2},
+    {"_individual_double_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink_bitset, 2},
+    {"_individual_create_integer_ragged_variable", (DL_FUNC) &_individual_create_integer_ragged_variable, 1},
+    {"_individual_integer_ragged_variable_get_values", (DL_FUNC) &_individual_integer_ragged_variable_get_values, 1},
+    {"_individual_integer_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_bitset, 2},
+    {"_individual_integer_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_vector, 2},
+    {"_individual_integer_ragged_variable_get_length", (DL_FUNC) &_individual_integer_ragged_variable_get_length, 1},
+    {"_individual_integer_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_bitset, 2},
+    {"_individual_integer_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_vector, 2},
+    {"_individual_integer_ragged_variable_queue_fill", (DL_FUNC) &_individual_integer_ragged_variable_queue_fill, 2},
+    {"_individual_integer_ragged_variable_queue_update", (DL_FUNC) &_individual_integer_ragged_variable_queue_update, 3},
+    {"_individual_integer_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_update_bitset, 3},
+    {"_individual_integer_ragged_variable_queue_extend", (DL_FUNC) &_individual_integer_ragged_variable_queue_extend, 2},
+    {"_individual_integer_ragged_variable_queue_shrink", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink, 2},
+    {"_individual_integer_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink_bitset, 2},
+    {"_individual_create_render_vector", (DL_FUNC) &_individual_create_render_vector, 1},
+    {"_individual_render_vector_update", (DL_FUNC) &_individual_render_vector_update, 3},
+    {"_individual_render_vector_data", (DL_FUNC) &_individual_render_vector_data, 1},
+    {"_individual_execute_process", (DL_FUNC) &_individual_execute_process, 2},
+    {"_individual_variable_get_size", (DL_FUNC) &_individual_variable_get_size, 1},
+    {"_individual_variable_update", (DL_FUNC) &_individual_variable_update, 1},
+    {"_individual_variable_resize", (DL_FUNC) &_individual_variable_resize, 1},
+    {"_individual_RcppExport_registerCCallable", (DL_FUNC) &_individual_RcppExport_registerCCallable, 0},
+    {"run_testthat_tests", (DL_FUNC) &run_testthat_tests, 1},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_individual(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}
diff --git a/src/categorical_variable.cpp b/src/categorical_variable.cpp
index f8c99fa..3975b22 100644
--- a/src/categorical_variable.cpp
+++ b/src/categorical_variable.cpp
@@ -103,3 +103,14 @@ void categorical_variable_queue_shrink_bitset(
     ) {
     variable->queue_shrink(*index);
 }
+
+//[[Rcpp::export]]
+std::vector<std::string> categorical_variable_get_values(
+    Rcpp::XPtr<CategoricalVariable> variable,
+    std::vector<size_t>& index
+    ) {
+    decrement(index);
+    std::vector<std::string> results;
+    results = variable->get_values(index);
+    return results;
+}
\ No newline at end of file
diff --git a/src/integer_variable.cpp b/src/integer_variable.cpp
index b878520..90c362a 100644
--- a/src/integer_variable.cpp
+++ b/src/integer_variable.cpp
@@ -26,6 +26,15 @@ const std::vector<int>& integer_variable_get_values(
     return variable->get_values();
 }
 
+//[[Rcpp::export]]
+individual_index_t integer_variable_get_modulo_differences(
+    Rcpp::XPtr<IntegerVariable> variable,
+    const int value,
+    const int difference
+) {
+    return variable->get_modulo_differences(value, difference);
+}
+
 //[[Rcpp::export]]
 std::vector<int> integer_variable_get_values_at_index(
     Rcpp::XPtr<IntegerVariable> variable,

From ddfb1613f8695ec5dff9205f683d744e0ac75ff9 Mon Sep 17 00:00:00 2001
From: Jason Wood <91839602+JasonRWood@users.noreply.github.com>
Date: Wed, 6 Aug 2025 09:51:27 +0100
Subject: [PATCH 02/13] Update individual_types.h

Realised I'd left a commented out line that was part of an earlier idea
---
 inst/include/individual_types.h | 1 -
 1 file changed, 1 deletion(-)

diff --git a/inst/include/individual_types.h b/inst/include/individual_types.h
index 8386ca9..8d4a925 100644
--- a/inst/include/individual_types.h
+++ b/inst/include/individual_types.h
@@ -10,7 +10,6 @@
 
 #include <Rcpp.h>
 #include "CategoricalVariable.h"
-// #include "FunctionalVariable.h"
 #include "IntegerVariable.h"
 #include "DoubleVariable.h"
 #include "RaggedInteger.h"

From b6f1177d344bb5dd71ea87e089f7fa8f4fc34622 Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Wed, 6 Aug 2025 10:18:21 +0100
Subject: [PATCH 03/13] Update cache action

---
 .github/workflows/R-CMD-check.yaml  | 2 +-
 .github/workflows/pkgdown.yml       | 2 +-
 .github/workflows/test_coverage.yml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 8928644..6deca2c 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -43,7 +43,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Restore R package cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
index 3b8baf9..5422bdd 100644
--- a/.github/workflows/pkgdown.yml
+++ b/.github/workflows/pkgdown.yml
@@ -30,7 +30,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
index b8f2c4d..09b0098 100644
--- a/.github/workflows/test_coverage.yml
+++ b/.github/workflows/test_coverage.yml
@@ -27,7 +27,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

From 4c0df4286ff2cd414b5d9f270732b496bf49d177 Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Wed, 6 Aug 2025 10:27:44 +0100
Subject: [PATCH 04/13] Change ubuntu action

---
 .github/workflows/R-CMD-check.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 6deca2c..a35eaac 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -18,8 +18,7 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

From 42468bd12f8348ed8daf60e4ba4f99d7b5fc4a63 Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Wed, 6 Aug 2025 11:01:48 +0100
Subject: [PATCH 05/13] Update benchmarking documentation in contributing

---
 tests/performance/benchmark.sh | 2 --
 vignettes/Contributing.Rmd     | 6 +++++-
 2 files changed, 5 insertions(+), 3 deletions(-)
 delete mode 100644 tests/performance/benchmark.sh

diff --git a/tests/performance/benchmark.sh b/tests/performance/benchmark.sh
deleted file mode 100644
index 8793550..0000000
--- a/tests/performance/benchmark.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-R -e "library('remotes'); install_local()"
-/usr/bin/time -v Rscript tests/performance/big_deterministic.R
diff --git a/vignettes/Contributing.Rmd b/vignettes/Contributing.Rmd
index ed345ed..2a562cf 100644
--- a/vignettes/Contributing.Rmd
+++ b/vignettes/Contributing.Rmd
@@ -77,6 +77,10 @@ Our review process is based off of [RESIDE's PR review process](https://reside-i
 
 ## Microbenchmarks
 
+We have R based benchmarks in tests/performance. Please add new benchmarks for performance critical code.
+
+Please note the google benchmarks are deprecated. The below instructions will not work since building requires including R and Rcpp.
+
 We use [google benchmark](https://github.com/google/benchmark) for our
 microbenchmarks. You can compile and run the benchmarks like this:
 
@@ -92,4 +96,4 @@ g++ *_benchmark.cpp -std=c++14 -lbenchmark -lpthread -o benchmark.out
  * More Variables
  * Speed optimisations (tests TBC)
  * CRAN
- * Anything on the github issue board
\ No newline at end of file
+ * Anything on the github issue board

From 82baa863c172aa5fc572d78e4470bd537312a5db Mon Sep 17 00:00:00 2001
From: Jason Wood <jasonwood8123@gmail.com>
Date: Thu, 7 Aug 2025 12:06:35 +0100
Subject: [PATCH 06/13] adding no index case, adding tests to verify
 functionality

---
 R/RcppExports.R                               |   8 +-
 R/categorical_variable.R                      |  10 +-
 inst/include/CategoricalVariable.h            |  22 ++
 inst/include/individual_types.h               |   1 -
 src/RcppExports.cpp                           |  20 +-
 src/categorical_variable.cpp                  |   8 +
 .../test-categoricalvariable-resize.R         | 134 +++++-----
 tests/testthat/test-categoricalvariable.R     | 229 ++++++++++--------
 8 files changed, 258 insertions(+), 174 deletions(-)

diff --git a/R/RcppExports.R b/R/RcppExports.R
index 6967dfe..d941673 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -125,8 +125,12 @@ categorical_variable_queue_shrink_bitset <- function(variable, index) {
     invisible(.Call(`_individual_categorical_variable_queue_shrink_bitset`, variable, index))
 }
 
-categorical_variable_get_values <- function(variable, index) {
-    .Call(`_individual_categorical_variable_get_values`, variable, index)
+categorical_variable_get_values <- function(variable) {
+    .Call(`_individual_categorical_variable_get_values`, variable)
+}
+
+categorical_variable_get_values_with_index <- function(variable, index) {
+    .Call(`_individual_categorical_variable_get_values_with_index`, variable, index)
 }
 
 create_double_variable <- function(values) {
diff --git a/R/categorical_variable.R b/R/categorical_variable.R
index 93e5eb9..4a882af 100644
--- a/R/categorical_variable.R
+++ b/R/categorical_variable.R
@@ -45,10 +45,16 @@ CategoricalVariable <- R6Class(
 
     #' @description return the value of the variable for the given individuals
     #' @param index the indices of individuals whose categories will be returned
-    get_values = function(index) {
+    get_values = function(index = NULL) {
       stopifnot(is.finite(index))
       stopifnot(index > 0)
-      results <- categorical_variable_get_values(self$.variable, index)
+      if (length(index) == 0){
+        # temp_inds <- 
+        results <- categorical_variable_get_values(self$.variable)
+      }
+      else{
+        results <- categorical_variable_get_values_with_index(self$.variable, index)
+      }
       return(results)
     },
 
diff --git a/inst/include/CategoricalVariable.h b/inst/include/CategoricalVariable.h
index 66aefb0..91e1ce1 100644
--- a/inst/include/CategoricalVariable.h
+++ b/inst/include/CategoricalVariable.h
@@ -53,6 +53,7 @@ class CategoricalVariable : public Variable {
     virtual size_t size() const override;
     virtual void update() override;
     virtual std::vector<std::string> get_values(const std::vector<size_t>&);
+    virtual std::vector<std::string> get_values();
 };
 
 
@@ -250,4 +251,25 @@ inline std::vector<std::string> CategoricalVariable::get_values(const std::vecto
     }
     return result;
 }
+//' @title get values of full variable
+inline std::vector<std::string> CategoricalVariable::get_values(){
+    
+    // Generate empty output vector
+    auto result = std::vector<std::string>(size());
+    for(auto i = 0u; i < size(); ++i){
+        // Determine which category the individual is within
+        for (auto cat: categories) {
+            if (indices.find(cat) == indices.end()) {
+                std::stringstream message;
+                message << "unknown category: " << cat;
+                Rcpp::stop(message.str());
+            }
+            if (indices.at(cat).find(i) != indices.at(cat).end()) {
+                result[i] = cat;
+                break;
+            }
+        }
+    }
+    return result;
+}
 #endif /* INST_INCLUDE_CATEGORICAL_VARIABLE_H_ */
diff --git a/inst/include/individual_types.h b/inst/include/individual_types.h
index 8386ca9..8d4a925 100644
--- a/inst/include/individual_types.h
+++ b/inst/include/individual_types.h
@@ -10,7 +10,6 @@
 
 #include <Rcpp.h>
 #include "CategoricalVariable.h"
-// #include "FunctionalVariable.h"
 #include "IntegerVariable.h"
 #include "DoubleVariable.h"
 #include "RaggedInteger.h"
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 7309f3e..94c6a58 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -363,14 +363,25 @@ BEGIN_RCPP
 END_RCPP
 }
 // categorical_variable_get_values
-std::vector<std::string> categorical_variable_get_values(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_categorical_variable_get_values(SEXP variableSEXP, SEXP indexSEXP) {
+std::vector<std::string> categorical_variable_get_values(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_values_with_index
+std::vector<std::string> categorical_variable_get_values_with_index(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_categorical_variable_get_values_with_index(SEXP variableSEXP, SEXP indexSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
     Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values(variable, index));
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values_with_index(variable, index));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -1533,7 +1544,8 @@ static const R_CallMethodDef CallEntries[] = {
     {"_individual_categorical_variable_queue_extend", (DL_FUNC) &_individual_categorical_variable_queue_extend, 2},
     {"_individual_categorical_variable_queue_shrink", (DL_FUNC) &_individual_categorical_variable_queue_shrink, 2},
     {"_individual_categorical_variable_queue_shrink_bitset", (DL_FUNC) &_individual_categorical_variable_queue_shrink_bitset, 2},
-    {"_individual_categorical_variable_get_values", (DL_FUNC) &_individual_categorical_variable_get_values, 2},
+    {"_individual_categorical_variable_get_values", (DL_FUNC) &_individual_categorical_variable_get_values, 1},
+    {"_individual_categorical_variable_get_values_with_index", (DL_FUNC) &_individual_categorical_variable_get_values_with_index, 2},
     {"_individual_dummy", (DL_FUNC) &_individual_dummy, 0},
     {"_individual_create_double_variable", (DL_FUNC) &_individual_create_double_variable, 1},
     {"_individual_double_variable_get_values", (DL_FUNC) &_individual_double_variable_get_values, 1},
diff --git a/src/categorical_variable.cpp b/src/categorical_variable.cpp
index 3975b22..5ad2ba0 100644
--- a/src/categorical_variable.cpp
+++ b/src/categorical_variable.cpp
@@ -106,6 +106,14 @@ void categorical_variable_queue_shrink_bitset(
 
 //[[Rcpp::export]]
 std::vector<std::string> categorical_variable_get_values(
+    Rcpp::XPtr<CategoricalVariable> variable
+    ) {
+    std::vector<std::string> results;
+    results = variable->get_values();
+    return results;
+}
+//[[Rcpp::export]]
+std::vector<std::string> categorical_variable_get_values_with_index(
     Rcpp::XPtr<CategoricalVariable> variable,
     std::vector<size_t>& index
     ) {
diff --git a/tests/testthat/test-categoricalvariable-resize.R b/tests/testthat/test-categoricalvariable-resize.R
index 3b988bc..212b7d0 100644
--- a/tests/testthat/test-categoricalvariable-resize.R
+++ b/tests/testthat/test-categoricalvariable-resize.R
@@ -1,62 +1,72 @@
-SIR <- c('S', 'I', 'R')
-
-test_that("CategoricalVariable extending variables returns the new values", {
-  x <- CategoricalVariable$new(SIR, rep('S', 10))
-  expect_equal(x$get_index_of('S')$to_vector(), 1:10)
-  x$queue_extend(values = c('S', 'I', 'R'))
-  x$.resize()
-  expect_equal(x$get_index_of('S')$to_vector(), 1:11)
-  expect_equal(x$get_index_of('I')$to_vector(), 12)
-  expect_equal(x$get_index_of('R')$to_vector(), 13)
-})
-
-test_that("CategoricalVariable shrinking variables removes values (bitset)", {
-  x <- CategoricalVariable$new(SIR, rep('S', 10))
-  x$queue_shrink(index = Bitset$new(10)$insert(1:5))
-  x$.resize()
-  expect_equal(x$get_index_of('S')$to_vector(), 1:5)
-})
-
-test_that("CategoricalVariable shrinking variables removes values (vector)", {
-  x <- CategoricalVariable$new(SIR, rep('S', 10))
-  x$queue_shrink(index = 6:10)
-  x$.resize()
-  expect_equal(x$get_index_of('S')$to_vector(), 1:5)
-})
-
-test_that("CategoricalVariable resizing variables returns the correct size", {
-  x <- CategoricalVariable$new(SIR, rep('S', 10))
-  expect_equal(x$size(), 10)
-  x$queue_extend(values = rep('S', 10))
-  x$queue_shrink(index = 5:10)
-  x$.resize()
-  expect_equal(x$size(), 14)
-})
-
-
-test_that("CategoricalVariable shrinks are combined", {
-  x <- CategoricalVariable$new(SIR, rep('S', 10))
-  x$queue_shrink(index = 1:5)
-  x$queue_shrink(index = 3:8)
-  x$.resize()
-  expect_equal(x$get_index_of('S')$to_vector(), 1:2)
-})
-
-test_that("CategoricalVariable shrinks are applied before extentions", {
-  x <- CategoricalVariable$new(SIR, rep('S', 10))
-  x$queue_shrink(index = 5:10)
-  x$queue_extend(values = rep('I', 10))
-  x$queue_shrink(index = 1:5)
-  x$queue_extend(values = rep('R', 10))
-  x$.resize()
-  expect_equal(x$get_index_of('S')$to_vector(), double(0))
-  expect_equal(x$get_index_of('I')$to_vector(), 1:10)
-  expect_equal(x$get_index_of('R')$to_vector(), 11:20)
-})
-
-test_that("CategoricalVariable invalid shrinking operations error at queue time", {
-  x <- CategoricalVariable$new(SIR, rep('S', 10))
-  expect_error(x$queue_shrink(index = 1:20))
-  expect_error(x$queue_shrink(index = -1:5))
-  expect_error(x$queue_shrink(index = Bitset$new(size + 1)$insert(1:20)))
-})
+SIR <- c('S', 'I', 'R')
+
+test_that("CategoricalVariable extending variables returns the new values", {
+  x <- CategoricalVariable$new(SIR, rep('S', 10))
+  expect_equal(x$get_index_of('S')$to_vector(), 1:10)
+  x$queue_extend(values = c('S', 'I', 'R'))
+  x$.resize()
+  expect_equal(x$get_index_of('S')$to_vector(), 1:11)
+  expect_equal(x$get_index_of('I')$to_vector(), 12)
+  expect_equal(x$get_index_of('R')$to_vector(), 13)
+})
+
+test_that("CategoricalVariables returns correct values after resize", {
+  categories = c('S', 'S', 'R', 'I')
+  
+  # standard case
+  x <- CategoricalVariable$new(SIR, categories)
+  x$queue_extend(values = rep('I', 2))
+  x$.resize()
+  expect_equal(x$get_values(seq(1:length(c(categories, rep('I', 2))))), c(categories, rep('I', 2)))
+})
+
+test_that("CategoricalVariable shrinking variables removes values (bitset)", {
+  x <- CategoricalVariable$new(SIR, rep('S', 10))
+  x$queue_shrink(index = Bitset$new(10)$insert(1:5))
+  x$.resize()
+  expect_equal(x$get_index_of('S')$to_vector(), 1:5)
+})
+
+test_that("CategoricalVariable shrinking variables removes values (vector)", {
+  x <- CategoricalVariable$new(SIR, rep('S', 10))
+  x$queue_shrink(index = 6:10)
+  x$.resize()
+  expect_equal(x$get_index_of('S')$to_vector(), 1:5)
+})
+
+test_that("CategoricalVariable resizing variables returns the correct size", {
+  x <- CategoricalVariable$new(SIR, rep('S', 10))
+  expect_equal(x$size(), 10)
+  x$queue_extend(values = rep('S', 10))
+  x$queue_shrink(index = 5:10)
+  x$.resize()
+  expect_equal(x$size(), 14)
+})
+
+
+test_that("CategoricalVariable shrinks are combined", {
+  x <- CategoricalVariable$new(SIR, rep('S', 10))
+  x$queue_shrink(index = 1:5)
+  x$queue_shrink(index = 3:8)
+  x$.resize()
+  expect_equal(x$get_index_of('S')$to_vector(), 1:2)
+})
+
+test_that("CategoricalVariable shrinks are applied before extentions", {
+  x <- CategoricalVariable$new(SIR, rep('S', 10))
+  x$queue_shrink(index = 5:10)
+  x$queue_extend(values = rep('I', 10))
+  x$queue_shrink(index = 1:5)
+  x$queue_extend(values = rep('R', 10))
+  x$.resize()
+  expect_equal(x$get_index_of('S')$to_vector(), double(0))
+  expect_equal(x$get_index_of('I')$to_vector(), 1:10)
+  expect_equal(x$get_index_of('R')$to_vector(), 11:20)
+})
+
+test_that("CategoricalVariable invalid shrinking operations error at queue time", {
+  x <- CategoricalVariable$new(SIR, rep('S', 10))
+  expect_error(x$queue_shrink(index = 1:20))
+  expect_error(x$queue_shrink(index = -1:5))
+  expect_error(x$queue_shrink(index = Bitset$new(size + 1)$insert(1:20)))
+})
diff --git a/tests/testthat/test-categoricalvariable.R b/tests/testthat/test-categoricalvariable.R
index d748076..867bb4a 100644
--- a/tests/testthat/test-categoricalvariable.R
+++ b/tests/testthat/test-categoricalvariable.R
@@ -1,103 +1,126 @@
-SIR <- c('S', 'I', 'R')
-
-test_that("Creating CategoricalVariables errors with bad input", {
-  expect_error(CategoricalVariable$new(NULL, NULL))
-  expect_error(CategoricalVariable$new(NaN, NaN))
-  expect_error(CategoricalVariable$new(NA, NA))
-  expect_error(CategoricalVariable$new(categories = LETTERS[1:2], initial_values = letters[1:2]))
-  expect_error(CategoricalVariable$new(categories = character(0), initial_values = letters[1:2]))
-})
-
-test_that("CategoricalVariable get index works returns correct values", {
-  size <- 10
-  state <- CategoricalVariable$new(SIR, rep('S', size))
-  expect_setequal(state$get_index_of('S')$to_vector(), seq(10))
-  
-  state <- CategoricalVariable$new(
-    SIR,
-    c(rep('S', 10), rep('I', 100), rep('R', 20))
-  )
-  
-  expect_setequal(
-    state$get_index_of('S')$to_vector(),
-    seq(10)
-  )
-  
-  expect_setequal(
-    state$get_index_of(c('S', 'R'))$to_vector(),
-    c(seq(10), seq(20) + 110)
-  )
-  
-  expect_setequal(
-    state$get_index_of(c('S'))$to_vector(),
-    seq(10)
-  )
-  
-})
-
-test_that("CategoricalVariable get index errors with incorrect input", {
-  size <- 10
-  state <- CategoricalVariable$new(SIR, rep('S', size))
-  
-  expect_error(state$get_index_of(values = 'A'))
-  expect_error(state$get_index_of(values = c('S', 'A')))
-  expect_error(state$get_index_of(values = LETTERS[1:3]))
-  expect_error(state$get_index_of(values = integer(0)))
-  expect_error(state$get_index_of(values = NULL))
-  expect_error(state$get_index_of(values = NA))
-  expect_error(state$get_index_of(values = NaN))
-})
-
-test_that("CategoricalVariable get size of categories works returns correct values", {
-  size <- 10
-  state <- CategoricalVariable$new(SIR, rep('S', size))
-  expect_setequal(state$get_size_of('S'), size)
-  
-  state <- CategoricalVariable$new(
-    SIR,
-    c(rep('S', 10), rep('I', 100), rep('R', 20))
-  )
-  
-  expect_equal(state$get_size_of(c('S', 'R')), 30)
-  expect_equal(state$get_size_of(c('S', 'I')), 110)
-  expect_equal(state$get_size_of(c('S')), 10)
-  
-})
-
-test_that("CategoricalVariable get size of categories errors with incorrect input", {
-  size <- 10
-  state <- CategoricalVariable$new(SIR, rep('S', size))
-  
-  expect_error(state$get_size_of(values = 'A'))
-  expect_error(state$get_size_of(values = c('S', 'A')))
-  expect_error(state$get_size_of(values = LETTERS[1:3]))
-  expect_error(state$get_size_of(values = integer(0)))
-  expect_error(state$get_size_of(values = NULL))
-  expect_error(state$get_size_of(values = NA))
-  expect_error(state$get_size_of(values = NaN))
-})
-
-test_that("CategoricalVariables get categories works", {
-  size <- 10
-  state <- CategoricalVariable$new(SIR, rep('S', size))
-  expect_length(setdiff(state$get_categories(), SIR), 0)
-})
-
-test_that("CategoricalVariables supports checkpoint and restore", {
-  size <- 10
-
-  old_variable <- CategoricalVariable$new(SIR, rep('S', size))
-  old_variable$queue_update('I', c(1, 3))
-  old_variable$queue_update('R', c(2, 7))
-  old_variable$.update()
-
-  state <- old_variable$save_state()
-
-  new_variable <- CategoricalVariable$new(SIR, rep('S', size))
-  new_variable$restore_state(1, state)
-
-  expect_equal(new_variable$get_index_of('S')$to_vector(), c(4,5,6,8,9,10))
-  expect_equal(new_variable$get_index_of('I')$to_vector(), c(1,3))
-  expect_equal(new_variable$get_index_of('R')$to_vector(), c(2,7))
-  expect_equal(new_variable$save_state(), state)
-})
+SIR <- c('S', 'I', 'R')
+
+test_that("Creating CategoricalVariables errors with bad input", {
+  expect_error(CategoricalVariable$new(NULL, NULL))
+  expect_error(CategoricalVariable$new(NaN, NaN))
+  expect_error(CategoricalVariable$new(NA, NA))
+  expect_error(CategoricalVariable$new(categories = LETTERS[1:2], initial_values = letters[1:2]))
+  expect_error(CategoricalVariable$new(categories = character(0), initial_values = letters[1:2]))
+})
+
+test_that("CategoricalVariables returns correct values", {
+  categories = c('S', 'S', 'R', 'I')
+  
+  # standard case
+  variable <- CategoricalVariable$new(SIR, categories)
+  expect_equal(variable$get_values(seq(1,4)), categories)
+  expect_equal(variable$get_values(c(2,4)), c(categories[c(2,4)]))
+  
+  # empty case
+  variable <- CategoricalVariable$new(SIR, character(0))
+  expect_equal(variable$get_values() , character(0))
+})
+
+test_that("CategoricalVariables returns correct values after update", {
+  categories = c('S', 'S', 'R', 'I')
+  
+  # standard case
+  variable <- CategoricalVariable$new(SIR, categories)
+  variable$queue_update('I', 1)
+  variable$.update()
+  expect_equal(variable$get_values(seq(1,4)), c('I', 'S', 'R', 'I'))
+})
+
+test_that("CategoricalVariable get index works returns correct values", {
+  size <- 10
+  state <- CategoricalVariable$new(SIR, rep('S', size))
+  expect_setequal(state$get_index_of('S')$to_vector(), seq(10))
+  
+  state <- CategoricalVariable$new(
+    SIR,
+    c(rep('S', 10), rep('I', 100), rep('R', 20))
+  )
+  
+  expect_setequal(
+    state$get_index_of('S')$to_vector(),
+    seq(10)
+  )
+  
+  expect_setequal(
+    state$get_index_of(c('S', 'R'))$to_vector(),
+    c(seq(10), seq(20) + 110)
+  )
+  
+  expect_setequal(
+    state$get_index_of(c('S'))$to_vector(),
+    seq(10)
+  )
+  
+})
+
+test_that("CategoricalVariable get index errors with incorrect input", {
+  size <- 10
+  state <- CategoricalVariable$new(SIR, rep('S', size))
+  
+  expect_error(state$get_index_of(values = 'A'))
+  expect_error(state$get_index_of(values = c('S', 'A')))
+  expect_error(state$get_index_of(values = LETTERS[1:3]))
+  expect_error(state$get_index_of(values = integer(0)))
+  expect_error(state$get_index_of(values = NULL))
+  expect_error(state$get_index_of(values = NA))
+  expect_error(state$get_index_of(values = NaN))
+})
+
+test_that("CategoricalVariable get size of categories works returns correct values", {
+  size <- 10
+  state <- CategoricalVariable$new(SIR, rep('S', size))
+  expect_setequal(state$get_size_of('S'), size)
+  
+  state <- CategoricalVariable$new(
+    SIR,
+    c(rep('S', 10), rep('I', 100), rep('R', 20))
+  )
+  
+  expect_equal(state$get_size_of(c('S', 'R')), 30)
+  expect_equal(state$get_size_of(c('S', 'I')), 110)
+  expect_equal(state$get_size_of(c('S')), 10)
+  
+})
+
+test_that("CategoricalVariable get size of categories errors with incorrect input", {
+  size <- 10
+  state <- CategoricalVariable$new(SIR, rep('S', size))
+  
+  expect_error(state$get_size_of(values = 'A'))
+  expect_error(state$get_size_of(values = c('S', 'A')))
+  expect_error(state$get_size_of(values = LETTERS[1:3]))
+  expect_error(state$get_size_of(values = integer(0)))
+  expect_error(state$get_size_of(values = NULL))
+  expect_error(state$get_size_of(values = NA))
+  expect_error(state$get_size_of(values = NaN))
+})
+
+test_that("CategoricalVariables get categories works", {
+  size <- 10
+  state <- CategoricalVariable$new(SIR, rep('S', size))
+  expect_length(setdiff(state$get_categories(), SIR), 0)
+})
+
+test_that("CategoricalVariables supports checkpoint and restore", {
+  size <- 10
+
+  old_variable <- CategoricalVariable$new(SIR, rep('S', size))
+  old_variable$queue_update('I', c(1, 3))
+  old_variable$queue_update('R', c(2, 7))
+  old_variable$.update()
+
+  state <- old_variable$save_state()
+
+  new_variable <- CategoricalVariable$new(SIR, rep('S', size))
+  new_variable$restore_state(1, state)
+
+  expect_equal(new_variable$get_index_of('S')$to_vector(), c(4,5,6,8,9,10))
+  expect_equal(new_variable$get_index_of('I')$to_vector(), c(1,3))
+  expect_equal(new_variable$get_index_of('R')$to_vector(), c(2,7))
+  expect_equal(new_variable$save_state(), state)
+})

From dea944b9b526afa082137aaf1b801a5e1c853ca1 Mon Sep 17 00:00:00 2001
From: Jason Wood <jasonwood8123@gmail.com>
Date: Thu, 7 Aug 2025 14:00:25 +0100
Subject: [PATCH 07/13] tests for integer variable, error processing,
 documentation

---
 DESCRIPTION                           |   2 +-
 R/integer_variable.R                  |   4 +
 man/CategoricalVariable.Rd            |  18 ++
 man/IntegerVariable.Rd                |  22 ++
 tests/testthat/test-integervariable.R | 437 ++++++++++++++------------
 5 files changed, 275 insertions(+), 208 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9ead8fd..05ef975 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -65,7 +65,7 @@ Suggests:
     testthat (>= 2.1.0),
     xml2,
     bench
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 LinkingTo:
   Rcpp,
diff --git a/R/integer_variable.R b/R/integer_variable.R
index adc477d..0bd746a 100644
--- a/R/integer_variable.R
+++ b/R/integer_variable.R
@@ -45,6 +45,10 @@ IntegerVariable <- R6Class(
     #' @param difference the difference to check, e.g. difference = 2 checks whether the
     #' difference is even
     get_modulo_differences = function(value, difference){
+      stopifnot(!is.null(value))
+      stopifnot(is.finite(value))
+      stopifnot(!is.null(difference))
+      stopifnot(is.finite(difference))
       integer_variable_get_modulo_differences(self$.variable, value, difference)
     },
 
diff --git a/man/CategoricalVariable.Rd b/man/CategoricalVariable.Rd
index 09bbb5d..6778898 100644
--- a/man/CategoricalVariable.Rd
+++ b/man/CategoricalVariable.Rd
@@ -17,6 +17,7 @@ if possible because certain operations will be faster.
 \item \href{#method-CategoricalVariable-get_index_of}{\code{CategoricalVariable$get_index_of()}}
 \item \href{#method-CategoricalVariable-get_size_of}{\code{CategoricalVariable$get_size_of()}}
 \item \href{#method-CategoricalVariable-get_categories}{\code{CategoricalVariable$get_categories()}}
+\item \href{#method-CategoricalVariable-get_values}{\code{CategoricalVariable$get_values()}}
 \item \href{#method-CategoricalVariable-queue_update}{\code{CategoricalVariable$queue_update()}}
 \item \href{#method-CategoricalVariable-queue_extend}{\code{CategoricalVariable$queue_extend()}}
 \item \href{#method-CategoricalVariable-queue_shrink}{\code{CategoricalVariable$queue_shrink()}}
@@ -94,6 +95,23 @@ unordered storage type.
 \if{html}{\out{<div class="r">}}\preformatted{CategoricalVariable$get_categories()}\if{html}{\out{</div>}}
 }
 
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-CategoricalVariable-get_values"></a>}}
+\if{latex}{\out{\hypertarget{method-CategoricalVariable-get_values}{}}}
+\subsection{Method \code{get_values()}}{
+return the value of the variable for the given individuals
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{CategoricalVariable$get_values(index = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{index}}{the indices of individuals whose categories will be returned}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-CategoricalVariable-queue_update"></a>}}
diff --git a/man/IntegerVariable.Rd b/man/IntegerVariable.Rd
index 1215f6a..fcc2778 100644
--- a/man/IntegerVariable.Rd
+++ b/man/IntegerVariable.Rd
@@ -15,6 +15,7 @@ household or age bin.
 \itemize{
 \item \href{#method-IntegerVariable-new}{\code{IntegerVariable$new()}}
 \item \href{#method-IntegerVariable-get_values}{\code{IntegerVariable$get_values()}}
+\item \href{#method-IntegerVariable-get_modulo_differences}{\code{IntegerVariable$get_modulo_differences()}}
 \item \href{#method-IntegerVariable-get_index_of}{\code{IntegerVariable$get_index_of()}}
 \item \href{#method-IntegerVariable-get_size_of}{\code{IntegerVariable$get_size_of()}}
 \item \href{#method-IntegerVariable-queue_update}{\code{IntegerVariable$queue_update()}}
@@ -65,6 +66,27 @@ or integer vector, return values of those individuals.}
 }
 }
 \if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-IntegerVariable-get_modulo_differences"></a>}}
+\if{latex}{\out{\hypertarget{method-IntegerVariable-get_modulo_differences}{}}}
+\subsection{Method \code{get_modulo_differences()}}{
+Return a vector of individuals with 0 modulo difference from input value
+and the distance being compared
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{IntegerVariable$get_modulo_differences(value, difference)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{value}}{the value to check}
+
+\item{\code{difference}}{the difference to check, e.g. difference = 2 checks whether the
+difference is even}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-IntegerVariable-get_index_of"></a>}}
 \if{latex}{\out{\hypertarget{method-IntegerVariable-get_index_of}{}}}
 \subsection{Method \code{get_index_of()}}{
diff --git a/tests/testthat/test-integervariable.R b/tests/testthat/test-integervariable.R
index d79e994..5aea6c5 100644
--- a/tests/testthat/test-integervariable.R
+++ b/tests/testthat/test-integervariable.R
@@ -1,207 +1,230 @@
-test_that("Creating IntegerVariables errors with bad input", {
-  expect_error(IntegerVariable$new(NULL))
-  expect_error(IntegerVariable$new(NaN))
-  expect_error(IntegerVariable$new(c(1,NaN)))
-  expect_error(IntegerVariable$new(NA))
-  expect_error(IntegerVariable$new(c(1,NA)))
-  expect_error(IntegerVariable$new(Inf))
-  expect_error(IntegerVariable$new(c(1,Inf)))
-  expect_error(IntegerVariable$new(-Inf))
-  expect_error(IntegerVariable$new(c(1,-Inf)))
-  expect_error(IntegerVariable$new("1"))
-})
-
-test_that("IntegerVariable get values returns correct values without index", {
-  size <- 10
-  variable <- IntegerVariable$new(seq_len(size))
-  expect_equal(variable$get_values(), 1:10)
-  
-  variable <- IntegerVariable$new(seq_len(size) + 10)
-  expect_equal(variable$get_values(), (1:10) + 10)
-  
-  variable <- IntegerVariable$new(seq_len(size))
-  expect_equal(variable$get_values(c(1, 1, 2, 2)), c(1, 1, 2, 2))
-})
-
-test_that("IntegerVariable get values returns correct values with vector index", {
-  size <- 10
-  variable <- IntegerVariable$new(seq_len(size))
-  expect_equal(variable$get_values(NULL), 1:10)
-  
-  variable <- IntegerVariable$new(seq_len(size) + 10)
-  expect_equal(variable$get_values(5:10), 15:20)
-})
-
-test_that("IntegerVariable get values returns correct values with bitset index", {
-  size <- 10
-  variable <- IntegerVariable$new(seq_len(size) + 10)
-  expect_equal(variable$get_values(Bitset$new(size = size)$insert(5:10)), 15:20)
-})
-
-test_that("IntegerVariable get values fails with incorrect index", {
-  variable <- IntegerVariable$new(initial_values = 1:100)
-  b <- Bitset$new(1000)
-  expect_error(variable$get_values(b))
-  expect_error(variable$get_values(b$insert(90:110)))
-  expect_error(variable$get_values(90:110))
-  expect_error(variable$get_values(-5:2))
-  expect_error(variable$get_values(NaN))
-  expect_error(variable$get_values(NA))
-  expect_error(variable$get_values(Inf))
-  expect_error(variable$get_values("10"))
-})
-
-test_that("IntegerVariable get index of set works correctly", {
-  variable <- IntegerVariable$new(5:10)
-  
-  indices <- variable$get_index_of(set = 6:8)  
-  expect_equal(indices$to_vector(), 2:4)
-  
-  indices <- variable$get_index_of(set = 10)
-  expect_equal(indices$to_vector(), 6)
-  
-  indices <- variable$get_index_of(set = 1e3:1.001e3)  
-  expect_equal(indices$size(), 0)
-  
-  indices <- variable$get_index_of(set = -5)
-  expect_equal(indices$size(), 0)
-  
-  indices <- variable$get_index_of(set = integer(0))
-  expect_equal(indices$size(), 0)
-  
-  indices <- variable$get_index_of(set = numeric(0))
-  expect_equal(indices$size(), 0)
-  
-  variable <- IntegerVariable$new(-10:10)
-  indices <- variable$get_index_of(set = c(-2,-1,1,2))
-  expect_equal(indices$to_vector(), c(9, 10, 12, 13))
-})
-
-test_that("IntegerVariable get index of set fails with incorrect set", {
-  variable <- IntegerVariable$new(1:10)
-  expect_error(variable$get_index_of(set = Inf))
-  expect_error(variable$get_index_of(set = -Inf))
-  expect_error(variable$get_index_of(set = NULL))
-  expect_error(variable$get_index_of(set = NA))
-  expect_error(variable$get_index_of(set = NaN))
-  expect_error(variable$get_index_of(set = "5"))
-})
-
-
-test_that("IntegerVariable get index of bounds [a,b] works correctly", {
-  variable <- IntegerVariable$new(5:10)
-  
-  indices <- variable$get_index_of(a = 6, b = 8)  
-  expect_equal(indices$to_vector(), 2:4)
-  
-  indices <- variable$get_index_of(a = 7, b = 7)
-  expect_equal(indices$to_vector(), 3)
-  
-  indices <- variable$get_index_of(a = 1e3, b = 1.001e3)
-  expect_length(indices$to_vector(), 0)
-})
-
-test_that("IntegerVariable get index of bounds [a,b] fails with incorrect bounds", {
-  variable <- IntegerVariable$new(5:10)
-  
-  expect_error(variable$get_index_of(a = a, b = NULL))
-  expect_error(variable$get_index_of(a = a, b = a - 10))
-  expect_error(variable$get_index_of(a = a, b = NA))
-  expect_error(variable$get_index_of(a = a, b = NaN))
-  expect_error(variable$get_index_of(a = a, b = Inf))
-  expect_error(variable$get_index_of(a = a, b = -Inf))
-  
-  expect_error(variable$get_index_of(a = NULL, b = b))
-  expect_error(variable$get_index_of(a = b + 10, b = b))
-  expect_error(variable$get_index_of(a = NA, b = b))
-  expect_error(variable$get_index_of(a = NaN, b = b))
-  expect_error(variable$get_index_of(a = Inf, b = b))
-  expect_error(variable$get_index_of(a = -Inf, b = b))
-  
-  expect_error(variable$get_index_of(a = integer(0), b = b))
-  expect_error(variable$get_index_of(a = numeric(0), b = b))
-  
-  expect_error(variable$get_index_of(a = a, b = integer(0)))
-  expect_error(variable$get_index_of(a = a, b = integer(0)))
-  
-  expect_error(variable$get_index_of(a = integer(0), b = integer(0)))
-  expect_error(variable$get_index_of(a = numeric(0), b = numeric(0)))
-})
-
-test_that("IntegerVariable get size of set works correctly", {
-  variable <- IntegerVariable$new(-10:10)
-  set <- c(-2,-1,1,2) 
-  expect_equal(variable$get_size_of(set = set), length(set))
-  
-  expect_equal(variable$get_size_of(set = -20:-15), 0)
-  expect_equal(variable$get_size_of(set = 10), 1)
-  expect_equal(variable$get_size_of(set = numeric(0)), 0)
-  expect_equal(variable$get_size_of(set = integer(0)), 0)
-})
-
-test_that("IntegerVariable get size of set fails with incorrect input", {
-  variable <- IntegerVariable$new(-10:10)
-  expect_error(variable$get_size_of(set = NULL))
-  expect_error(variable$get_size_of(set = NA))
-  expect_error(variable$get_size_of(set = NaN))
-  expect_error(variable$get_size_of(set = Inf))
-  expect_error(variable$get_size_of(set = -Inf))
-  expect_error(variable$get_size_of(set = "5"))
-})
-
-test_that("IntegerVariable get size of set in bounds [a,b] works correctly", {
-  variable <- IntegerVariable$new(-10:10)
-  expect_equal(variable$get_size_of(a = 5, b = 7), 3)
-  expect_equal(variable$get_size_of(a = 5, b = 5), 1)
-  expect_equal(variable$get_size_of(a = -10, b = -5), 6)
-  expect_equal(variable$get_size_of(a = -50, b = -40), 0)
-})
-
-test_that("IntegerVariable get size of set in bounds [a,b] fails with incorrect input", {
-  variable <- IntegerVariable$new(-10:10)
-  
-  expect_error(variable$get_size_of(a = a, b = NULL))
-  expect_error(variable$get_size_of(a = a, b = a - 10))
-  expect_error(variable$get_size_of(a = a, b = NA))
-  expect_error(variable$get_size_of(a = a, b = NaN))
-  expect_error(variable$get_size_of(a = a, b = Inf))
-  expect_error(variable$get_size_of(a = a, b = -Inf))
-  
-  expect_error(variable$get_size_of(a = NULL, b = b))
-  expect_error(variable$get_size_of(a = b + 10, b = b))
-  expect_error(variable$get_size_of(a = NA, b = b))
-  expect_error(variable$get_size_of(a = NaN, b = b))
-  expect_error(variable$get_size_of(a = Inf, b = b))
-  expect_error(variable$get_size_of(a = -Inf, b = b))
-  
-  expect_error(variable$get_size_of(a = integer(0), b = b))
-  expect_error(variable$get_size_of(a = numeric(0), b = b))
-  
-  expect_error(variable$get_size_of(a = a, b = integer(0)))
-  expect_error(variable$get_size_of(a = a, b = integer(0)))
-  
-  expect_error(variable$get_size_of(a = integer(0), b = integer(0)))
-  expect_error(variable$get_size_of(a = numeric(0), b = numeric(0)))
-})
-
-test_that("IntegerVariable get size and index of set in bounds [a,b] and set gives same answer for equal intervals", {
-  variable <- IntegerVariable$new(-10:10)
-  expect_equal(variable$get_size_of(a = 5, b = 7), variable$get_size_of(set = 5:7))
-  expect_equal(variable$get_index_of(a = 5, b = 7)$to_vector(), variable$get_index_of(set = 5:7)$to_vector())
-})
-
-test_that("IntegerVariable supports checkpoint and restore", {
-  size <- 10
-
-  old_variable <- IntegerVariable$new(rep(0, size))
-  old_variable$queue_update(values = seq_len(size))
-  old_variable$.update()
-
-  state <- old_variable$save_state()
-
-  new_variable <- IntegerVariable$new(rep(0, size))
-  new_variable$restore_state(1, state)
-
-  expect_equal(new_variable$get_values(), seq_len(size))
-  expect_equal(new_variable$save_state(), state)
-})
+test_that("Creating IntegerVariables errors with bad input", {
+  expect_error(IntegerVariable$new(NULL))
+  expect_error(IntegerVariable$new(NaN))
+  expect_error(IntegerVariable$new(c(1,NaN)))
+  expect_error(IntegerVariable$new(NA))
+  expect_error(IntegerVariable$new(c(1,NA)))
+  expect_error(IntegerVariable$new(Inf))
+  expect_error(IntegerVariable$new(c(1,Inf)))
+  expect_error(IntegerVariable$new(-Inf))
+  expect_error(IntegerVariable$new(c(1,-Inf)))
+  expect_error(IntegerVariable$new("1"))
+})
+
+test_that("IntegerVariable get values returns correct values without index", {
+  size <- 10
+  variable <- IntegerVariable$new(seq_len(size))
+  expect_equal(variable$get_values(), 1:10)
+  
+  variable <- IntegerVariable$new(seq_len(size) + 10)
+  expect_equal(variable$get_values(), (1:10) + 10)
+  
+  variable <- IntegerVariable$new(seq_len(size))
+  expect_equal(variable$get_values(c(1, 1, 2, 2)), c(1, 1, 2, 2))
+})
+
+test_that("IntegerVariables returns correct modulo differences", {
+  size <- 10
+  variable <- IntegerVariable$new(seq_len(size))
+  vals <- variable$get_values()
+  x <- 3
+  d <- 3
+  expected_modulo_differences <- c()
+  ind <- 1
+  for(i in seq_len(size)){
+    val <- vals[i]
+    if ((val - x) %% d == 0){
+      expected_modulo_differences[ind] <- i - 1
+      ind <- ind + 1
+    }
+  }
+  expect_equal(variable$get_modulo_differences(x, d), expected_modulo_differences)
+})
+
+test_that("IntegerVariables errors for invalid modulo differences", {
+  expect_error(variable$get_modulo_differences())
+  expect_error(variable$get_modulo_differences("a", 1))
+  expect_error(variable$get_modulo_differences(1, "1"))
+})
+test_that("IntegerVariable get values returns correct values with vector index", {
+  size <- 10
+  variable <- IntegerVariable$new(seq_len(size))
+  expect_equal(variable$get_values(NULL), 1:10)
+  
+  variable <- IntegerVariable$new(seq_len(size) + 10)
+  expect_equal(variable$get_values(5:10), 15:20)
+})
+
+test_that("IntegerVariable get values returns correct values with bitset index", {
+  size <- 10
+  variable <- IntegerVariable$new(seq_len(size) + 10)
+  expect_equal(variable$get_values(Bitset$new(size = size)$insert(5:10)), 15:20)
+})
+
+test_that("IntegerVariable get values fails with incorrect index", {
+  variable <- IntegerVariable$new(initial_values = 1:100)
+  b <- Bitset$new(1000)
+  expect_error(variable$get_values(b))
+  expect_error(variable$get_values(b$insert(90:110)))
+  expect_error(variable$get_values(90:110))
+  expect_error(variable$get_values(-5:2))
+  expect_error(variable$get_values(NaN))
+  expect_error(variable$get_values(NA))
+  expect_error(variable$get_values(Inf))
+  expect_error(variable$get_values("10"))
+})
+
+test_that("IntegerVariable get index of set works correctly", {
+  variable <- IntegerVariable$new(5:10)
+  
+  indices <- variable$get_index_of(set = 6:8)  
+  expect_equal(indices$to_vector(), 2:4)
+  
+  indices <- variable$get_index_of(set = 10)
+  expect_equal(indices$to_vector(), 6)
+  
+  indices <- variable$get_index_of(set = 1e3:1.001e3)  
+  expect_equal(indices$size(), 0)
+  
+  indices <- variable$get_index_of(set = -5)
+  expect_equal(indices$size(), 0)
+  
+  indices <- variable$get_index_of(set = integer(0))
+  expect_equal(indices$size(), 0)
+  
+  indices <- variable$get_index_of(set = numeric(0))
+  expect_equal(indices$size(), 0)
+  
+  variable <- IntegerVariable$new(-10:10)
+  indices <- variable$get_index_of(set = c(-2,-1,1,2))
+  expect_equal(indices$to_vector(), c(9, 10, 12, 13))
+})
+
+test_that("IntegerVariable get index of set fails with incorrect set", {
+  variable <- IntegerVariable$new(1:10)
+  expect_error(variable$get_index_of(set = Inf))
+  expect_error(variable$get_index_of(set = -Inf))
+  expect_error(variable$get_index_of(set = NULL))
+  expect_error(variable$get_index_of(set = NA))
+  expect_error(variable$get_index_of(set = NaN))
+  expect_error(variable$get_index_of(set = "5"))
+})
+
+
+test_that("IntegerVariable get index of bounds [a,b] works correctly", {
+  variable <- IntegerVariable$new(5:10)
+  
+  indices <- variable$get_index_of(a = 6, b = 8)  
+  expect_equal(indices$to_vector(), 2:4)
+  
+  indices <- variable$get_index_of(a = 7, b = 7)
+  expect_equal(indices$to_vector(), 3)
+  
+  indices <- variable$get_index_of(a = 1e3, b = 1.001e3)
+  expect_length(indices$to_vector(), 0)
+})
+
+test_that("IntegerVariable get index of bounds [a,b] fails with incorrect bounds", {
+  variable <- IntegerVariable$new(5:10)
+  
+  expect_error(variable$get_index_of(a = a, b = NULL))
+  expect_error(variable$get_index_of(a = a, b = a - 10))
+  expect_error(variable$get_index_of(a = a, b = NA))
+  expect_error(variable$get_index_of(a = a, b = NaN))
+  expect_error(variable$get_index_of(a = a, b = Inf))
+  expect_error(variable$get_index_of(a = a, b = -Inf))
+  
+  expect_error(variable$get_index_of(a = NULL, b = b))
+  expect_error(variable$get_index_of(a = b + 10, b = b))
+  expect_error(variable$get_index_of(a = NA, b = b))
+  expect_error(variable$get_index_of(a = NaN, b = b))
+  expect_error(variable$get_index_of(a = Inf, b = b))
+  expect_error(variable$get_index_of(a = -Inf, b = b))
+  
+  expect_error(variable$get_index_of(a = integer(0), b = b))
+  expect_error(variable$get_index_of(a = numeric(0), b = b))
+  
+  expect_error(variable$get_index_of(a = a, b = integer(0)))
+  expect_error(variable$get_index_of(a = a, b = integer(0)))
+  
+  expect_error(variable$get_index_of(a = integer(0), b = integer(0)))
+  expect_error(variable$get_index_of(a = numeric(0), b = numeric(0)))
+})
+
+test_that("IntegerVariable get size of set works correctly", {
+  variable <- IntegerVariable$new(-10:10)
+  set <- c(-2,-1,1,2) 
+  expect_equal(variable$get_size_of(set = set), length(set))
+  
+  expect_equal(variable$get_size_of(set = -20:-15), 0)
+  expect_equal(variable$get_size_of(set = 10), 1)
+  expect_equal(variable$get_size_of(set = numeric(0)), 0)
+  expect_equal(variable$get_size_of(set = integer(0)), 0)
+})
+
+test_that("IntegerVariable get size of set fails with incorrect input", {
+  variable <- IntegerVariable$new(-10:10)
+  expect_error(variable$get_size_of(set = NULL))
+  expect_error(variable$get_size_of(set = NA))
+  expect_error(variable$get_size_of(set = NaN))
+  expect_error(variable$get_size_of(set = Inf))
+  expect_error(variable$get_size_of(set = -Inf))
+  expect_error(variable$get_size_of(set = "5"))
+})
+
+test_that("IntegerVariable get size of set in bounds [a,b] works correctly", {
+  variable <- IntegerVariable$new(-10:10)
+  expect_equal(variable$get_size_of(a = 5, b = 7), 3)
+  expect_equal(variable$get_size_of(a = 5, b = 5), 1)
+  expect_equal(variable$get_size_of(a = -10, b = -5), 6)
+  expect_equal(variable$get_size_of(a = -50, b = -40), 0)
+})
+
+test_that("IntegerVariable get size of set in bounds [a,b] fails with incorrect input", {
+  variable <- IntegerVariable$new(-10:10)
+  
+  expect_error(variable$get_size_of(a = a, b = NULL))
+  expect_error(variable$get_size_of(a = a, b = a - 10))
+  expect_error(variable$get_size_of(a = a, b = NA))
+  expect_error(variable$get_size_of(a = a, b = NaN))
+  expect_error(variable$get_size_of(a = a, b = Inf))
+  expect_error(variable$get_size_of(a = a, b = -Inf))
+  
+  expect_error(variable$get_size_of(a = NULL, b = b))
+  expect_error(variable$get_size_of(a = b + 10, b = b))
+  expect_error(variable$get_size_of(a = NA, b = b))
+  expect_error(variable$get_size_of(a = NaN, b = b))
+  expect_error(variable$get_size_of(a = Inf, b = b))
+  expect_error(variable$get_size_of(a = -Inf, b = b))
+  
+  expect_error(variable$get_size_of(a = integer(0), b = b))
+  expect_error(variable$get_size_of(a = numeric(0), b = b))
+  
+  expect_error(variable$get_size_of(a = a, b = integer(0)))
+  expect_error(variable$get_size_of(a = a, b = integer(0)))
+  
+  expect_error(variable$get_size_of(a = integer(0), b = integer(0)))
+  expect_error(variable$get_size_of(a = numeric(0), b = numeric(0)))
+})
+
+test_that("IntegerVariable get size and index of set in bounds [a,b] and set gives same answer for equal intervals", {
+  variable <- IntegerVariable$new(-10:10)
+  expect_equal(variable$get_size_of(a = 5, b = 7), variable$get_size_of(set = 5:7))
+  expect_equal(variable$get_index_of(a = 5, b = 7)$to_vector(), variable$get_index_of(set = 5:7)$to_vector())
+})
+
+test_that("IntegerVariable supports checkpoint and restore", {
+  size <- 10
+
+  old_variable <- IntegerVariable$new(rep(0, size))
+  old_variable$queue_update(values = seq_len(size))
+  old_variable$.update()
+
+  state <- old_variable$save_state()
+
+  new_variable <- IntegerVariable$new(rep(0, size))
+  new_variable$restore_state(1, state)
+
+  expect_equal(new_variable$get_values(), seq_len(size))
+  expect_equal(new_variable$save_state(), state)
+})

From b9d1529c37f56355adb916bc15437fa30d346e9a Mon Sep 17 00:00:00 2001
From: Jason Wood <91839602+JasonRWood@users.noreply.github.com>
Date: Thu, 7 Aug 2025 14:20:02 +0100
Subject: [PATCH 08/13] Apply suggestions from code review

Co-authored-by: Giovanni <giovanni.charles@gmail.com>
---
 R/categorical_variable.R | 1 -
 R/integer_variable.R     | 2 --
 2 files changed, 3 deletions(-)

diff --git a/R/categorical_variable.R b/R/categorical_variable.R
index 4a882af..bce3a8e 100644
--- a/R/categorical_variable.R
+++ b/R/categorical_variable.R
@@ -49,7 +49,6 @@ CategoricalVariable <- R6Class(
       stopifnot(is.finite(index))
       stopifnot(index > 0)
       if (length(index) == 0){
-        # temp_inds <- 
         results <- categorical_variable_get_values(self$.variable)
       }
       else{
diff --git a/R/integer_variable.R b/R/integer_variable.R
index 0bd746a..f39b0e1 100644
--- a/R/integer_variable.R
+++ b/R/integer_variable.R
@@ -45,9 +45,7 @@ IntegerVariable <- R6Class(
     #' @param difference the difference to check, e.g. difference = 2 checks whether the
     #' difference is even
     get_modulo_differences = function(value, difference){
-      stopifnot(!is.null(value))
       stopifnot(is.finite(value))
-      stopifnot(!is.null(difference))
       stopifnot(is.finite(difference))
       integer_variable_get_modulo_differences(self$.variable, value, difference)
     },

From fb5bfd01d1908c85193f852e520d9a173af17a14 Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Wed, 7 Aug 2024 11:55:40 +0100
Subject: [PATCH 09/13] Add bitset_count_and

---
 R/RcppExports.R               | 1026 +++++-----
 R/bitset.R                    |   12 +
 inst/include/IterableBitset.h |   13 +
 src/RcppExports.cpp           | 3315 +++++++++++++++++----------------
 src/bitset.cpp                |    8 +
 tests/testthat/test-bitset.R  |   38 +
 6 files changed, 2250 insertions(+), 2162 deletions(-)

diff --git a/R/RcppExports.R b/R/RcppExports.R
index d941673..354ab8f 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -1,511 +1,515 @@
-# Generated by using Rcpp::compileAttributes() -> do not edit by hand
-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-create_bitset <- function(size) {
-    .Call(`_individual_create_bitset`, size)
-}
-
-bitset_copy <- function(b) {
-    .Call(`_individual_bitset_copy`, b)
-}
-
-bitset_insert <- function(b, v) {
-    invisible(.Call(`_individual_bitset_insert`, b, v))
-}
-
-bitset_remove <- function(b, v) {
-    invisible(.Call(`_individual_bitset_remove`, b, v))
-}
-
-bitset_clear <- function(b) {
-    invisible(.Call(`_individual_bitset_clear`, b))
-}
-
-bitset_size <- function(b) {
-    .Call(`_individual_bitset_size`, b)
-}
-
-bitset_max_size <- function(b) {
-    .Call(`_individual_bitset_max_size`, b)
-}
-
-bitset_and <- function(a, b) {
-    invisible(.Call(`_individual_bitset_and`, a, b))
-}
-
-bitset_not <- function(b, inplace) {
-    .Call(`_individual_bitset_not`, b, inplace)
-}
-
-bitset_or <- function(a, b) {
-    invisible(.Call(`_individual_bitset_or`, a, b))
-}
-
-bitset_copy_from <- function(a, b) {
-    invisible(.Call(`_individual_bitset_copy_from`, a, b))
-}
-
-bitset_xor <- function(a, b) {
-    invisible(.Call(`_individual_bitset_xor`, a, b))
-}
-
-bitset_set_difference <- function(a, b) {
-    invisible(.Call(`_individual_bitset_set_difference`, a, b))
-}
-
-bitset_sample <- function(b, rate) {
-    invisible(.Call(`_individual_bitset_sample`, b, rate))
-}
-
-bitset_sample_vector <- function(b, rate) {
-    invisible(.Call(`_individual_bitset_sample_vector`, b, rate))
-}
-
-bitset_to_vector <- function(b) {
-    .Call(`_individual_bitset_to_vector`, b)
-}
-
-filter_bitset_integer <- function(b, other) {
-    .Call(`_individual_filter_bitset_integer`, b, other)
-}
-
-filter_bitset_bitset <- function(b, other) {
-    .Call(`_individual_filter_bitset_bitset`, b, other)
-}
-
-filter_bitset_logical <- function(bitset, other) {
-    .Call(`_individual_filter_bitset_logical`, bitset, other)
-}
-
-bitset_choose <- function(b, k) {
-    invisible(.Call(`_individual_bitset_choose`, b, k))
-}
-
-create_categorical_variable <- function(categories, values) {
-    .Call(`_individual_create_categorical_variable`, categories, values)
-}
-
-categorical_variable_get_size <- function(variable) {
-    .Call(`_individual_categorical_variable_get_size`, variable)
-}
-
-categorical_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_update`, variable, value, index))
-}
-
-categorical_variable_get_index_of <- function(variable, values) {
-    .Call(`_individual_categorical_variable_get_index_of`, variable, values)
-}
-
-categorical_variable_get_size_of <- function(variable, values) {
-    .Call(`_individual_categorical_variable_get_size_of`, variable, values)
-}
-
-categorical_variable_get_categories <- function(variable) {
-    .Call(`_individual_categorical_variable_get_categories`, variable)
-}
-
-categorical_variable_queue_update_vector <- function(variable, value, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_update_vector`, variable, value, index))
-}
-
-categorical_variable_update <- function(variable) {
-    invisible(.Call(`_individual_categorical_variable_update`, variable))
-}
-
-categorical_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_categorical_variable_queue_extend`, variable, values))
-}
-
-categorical_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_shrink`, variable, index))
-}
-
-categorical_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_categorical_variable_queue_shrink_bitset`, variable, index))
-}
-
-categorical_variable_get_values <- function(variable) {
-    .Call(`_individual_categorical_variable_get_values`, variable)
-}
-
-categorical_variable_get_values_with_index <- function(variable, index) {
-    .Call(`_individual_categorical_variable_get_values_with_index`, variable, index)
-}
-
-create_double_variable <- function(values) {
-    .Call(`_individual_create_double_variable`, values)
-}
-
-double_variable_get_values <- function(variable) {
-    .Call(`_individual_double_variable_get_values`, variable)
-}
-
-double_variable_get_values_at_index <- function(variable, index) {
-    .Call(`_individual_double_variable_get_values_at_index`, variable, index)
-}
-
-double_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_double_variable_get_values_at_index_vector`, variable, index)
-}
-
-double_variable_get_index_of_range <- function(variable, a, b) {
-    .Call(`_individual_double_variable_get_index_of_range`, variable, a, b)
-}
-
-double_variable_get_size_of_range <- function(variable, a, b) {
-    .Call(`_individual_double_variable_get_size_of_range`, variable, a, b)
-}
-
-double_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_double_variable_queue_fill`, variable, value))
-}
-
-double_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_variable_queue_update`, variable, value, index))
-}
-
-double_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_variable_queue_update_bitset`, variable, value, index))
-}
-
-double_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_double_variable_queue_extend`, variable, values))
-}
-
-double_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_double_variable_queue_shrink`, variable, index))
-}
-
-double_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_double_variable_queue_shrink_bitset`, variable, index))
-}
-
-create_event <- function() {
-    .Call(`_individual_create_event`)
-}
-
-create_targeted_event <- function(size) {
-    .Call(`_individual_create_targeted_event`, size)
-}
-
-event_base_tick <- function(event) {
-    invisible(.Call(`_individual_event_base_tick`, event))
-}
-
-event_base_get_timestep <- function(event) {
-    .Call(`_individual_event_base_get_timestep`, event)
-}
-
-event_base_set_timestep <- function(event, time) {
-    invisible(.Call(`_individual_event_base_set_timestep`, event, time))
-}
-
-event_base_should_trigger <- function(event) {
-    .Call(`_individual_event_base_should_trigger`, event)
-}
-
-event_schedule <- function(event, delays) {
-    invisible(.Call(`_individual_event_schedule`, event, delays))
-}
-
-event_clear_schedule <- function(event) {
-    invisible(.Call(`_individual_event_clear_schedule`, event))
-}
-
-event_checkpoint <- function(event) {
-    .Call(`_individual_event_checkpoint`, event)
-}
-
-event_restore <- function(event, schedule) {
-    invisible(.Call(`_individual_event_restore`, event, schedule))
-}
-
-targeted_event_clear_schedule_vector <- function(event, target) {
-    invisible(.Call(`_individual_targeted_event_clear_schedule_vector`, event, target))
-}
-
-targeted_event_clear_schedule <- function(event, target) {
-    invisible(.Call(`_individual_targeted_event_clear_schedule`, event, target))
-}
-
-targeted_event_get_scheduled <- function(event) {
-    .Call(`_individual_targeted_event_get_scheduled`, event)
-}
-
-targeted_event_schedule <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule`, event, target, delay))
-}
-
-targeted_event_queue_shrink_bitset <- function(event, index) {
-    invisible(.Call(`_individual_targeted_event_queue_shrink_bitset`, event, index))
-}
-
-targeted_event_queue_shrink <- function(event, index) {
-    invisible(.Call(`_individual_targeted_event_queue_shrink`, event, index))
-}
-
-targeted_event_queue_extend <- function(event, n) {
-    invisible(.Call(`_individual_targeted_event_queue_extend`, event, n))
-}
-
-targeted_event_queue_extend_with_schedule <- function(event, delays) {
-    invisible(.Call(`_individual_targeted_event_queue_extend_with_schedule`, event, delays))
-}
-
-targeted_event_schedule_vector <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule_vector`, event, target, delay))
-}
-
-targeted_event_schedule_multi_delay <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule_multi_delay`, event, target, delay))
-}
-
-targeted_event_schedule_multi_delay_vector <- function(event, target, delay) {
-    invisible(.Call(`_individual_targeted_event_schedule_multi_delay_vector`, event, target, delay))
-}
-
-targeted_event_get_target <- function(event) {
-    .Call(`_individual_targeted_event_get_target`, event)
-}
-
-targeted_event_resize <- function(event) {
-    invisible(.Call(`_individual_targeted_event_resize`, event))
-}
-
-targeted_event_checkpoint <- function(event) {
-    .Call(`_individual_targeted_event_checkpoint`, event)
-}
-
-targeted_event_restore <- function(event, state) {
-    invisible(.Call(`_individual_targeted_event_restore`, event, state))
-}
-
-process_listener <- function(event, listener) {
-    invisible(.Call(`_individual_process_listener`, event, listener))
-}
-
-process_targeted_listener <- function(event, listener, target) {
-    invisible(.Call(`_individual_process_targeted_listener`, event, listener, target))
-}
-
-create_integer_variable <- function(values) {
-    .Call(`_individual_create_integer_variable`, values)
-}
-
-integer_variable_get_values <- function(variable) {
-    .Call(`_individual_integer_variable_get_values`, variable)
-}
-
-integer_variable_get_modulo_differences <- function(variable, value, difference) {
-    .Call(`_individual_integer_variable_get_modulo_differences`, variable, value, difference)
-}
-
-integer_variable_get_values_at_index <- function(variable, index) {
-    .Call(`_individual_integer_variable_get_values_at_index`, variable, index)
-}
-
-integer_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_integer_variable_get_values_at_index_vector`, variable, index)
-}
-
-integer_variable_get_index_of_set_vector <- function(variable, values_set) {
-    .Call(`_individual_integer_variable_get_index_of_set_vector`, variable, values_set)
-}
-
-integer_variable_get_index_of_set_scalar <- function(variable, values_set) {
-    .Call(`_individual_integer_variable_get_index_of_set_scalar`, variable, values_set)
-}
-
-integer_variable_get_index_of_range <- function(variable, a, b) {
-    .Call(`_individual_integer_variable_get_index_of_range`, variable, a, b)
-}
-
-integer_variable_get_size_of_set_vector <- function(variable, values_set) {
-    .Call(`_individual_integer_variable_get_size_of_set_vector`, variable, values_set)
-}
-
-integer_variable_get_size_of_set_scalar <- function(variable, value) {
-    .Call(`_individual_integer_variable_get_size_of_set_scalar`, variable, value)
-}
-
-integer_variable_get_size_of_range <- function(variable, a, b) {
-    .Call(`_individual_integer_variable_get_size_of_range`, variable, a, b)
-}
-
-integer_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_integer_variable_queue_fill`, variable, value))
-}
-
-integer_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_variable_queue_update`, variable, value, index))
-}
-
-integer_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_variable_queue_update_bitset`, variable, value, index))
-}
-
-integer_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_integer_variable_queue_extend`, variable, values))
-}
-
-integer_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_integer_variable_queue_shrink`, variable, index))
-}
-
-integer_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_integer_variable_queue_shrink_bitset`, variable, index))
-}
-
-fixed_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate, destination_probabilities) {
-    .Call(`_individual_fixed_probability_multinomial_process_internal`, variable, source_state, destination_states, rate, destination_probabilities)
-}
-
-multi_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate_variable, destination_probabilities) {
-    .Call(`_individual_multi_probability_multinomial_process_internal`, variable, source_state, destination_states, rate_variable, destination_probabilities)
-}
-
-multi_probability_bernoulli_process_internal <- function(variable, from, to, rate_variable) {
-    .Call(`_individual_multi_probability_bernoulli_process_internal`, variable, from, to, rate_variable)
-}
-
-infection_age_process_internal <- function(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing) {
-    .Call(`_individual_infection_age_process_internal`, state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing)
-}
-
-create_double_ragged_variable <- function(values) {
-    .Call(`_individual_create_double_ragged_variable`, values)
-}
-
-double_ragged_variable_get_values <- function(variable) {
-    .Call(`_individual_double_ragged_variable_get_values`, variable)
-}
-
-double_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_values_at_index_bitset`, variable, index)
-}
-
-double_ragged_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_values_at_index_vector`, variable, index)
-}
-
-double_ragged_variable_get_length <- function(variable) {
-    .Call(`_individual_double_ragged_variable_get_length`, variable)
-}
-
-double_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_length_at_index_bitset`, variable, index)
-}
-
-double_ragged_variable_get_length_at_index_vector <- function(variable, index) {
-    .Call(`_individual_double_ragged_variable_get_length_at_index_vector`, variable, index)
-}
-
-double_ragged_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_fill`, variable, value))
-}
-
-double_ragged_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_update`, variable, value, index))
-}
-
-double_ragged_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_update_bitset`, variable, value, index))
-}
-
-double_ragged_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_extend`, variable, values))
-}
-
-double_ragged_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_shrink`, variable, index))
-}
-
-double_ragged_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_double_ragged_variable_queue_shrink_bitset`, variable, index))
-}
-
-create_integer_ragged_variable <- function(values) {
-    .Call(`_individual_create_integer_ragged_variable`, values)
-}
-
-integer_ragged_variable_get_values <- function(variable) {
-    .Call(`_individual_integer_ragged_variable_get_values`, variable)
-}
-
-integer_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_values_at_index_bitset`, variable, index)
-}
-
-integer_ragged_variable_get_values_at_index_vector <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_values_at_index_vector`, variable, index)
-}
-
-integer_ragged_variable_get_length <- function(variable) {
-    .Call(`_individual_integer_ragged_variable_get_length`, variable)
-}
-
-integer_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_length_at_index_bitset`, variable, index)
-}
-
-integer_ragged_variable_get_length_at_index_vector <- function(variable, index) {
-    .Call(`_individual_integer_ragged_variable_get_length_at_index_vector`, variable, index)
-}
-
-integer_ragged_variable_queue_fill <- function(variable, value) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_fill`, variable, value))
-}
-
-integer_ragged_variable_queue_update <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_update`, variable, value, index))
-}
-
-integer_ragged_variable_queue_update_bitset <- function(variable, value, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_update_bitset`, variable, value, index))
-}
-
-integer_ragged_variable_queue_extend <- function(variable, values) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_extend`, variable, values))
-}
-
-integer_ragged_variable_queue_shrink <- function(variable, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink`, variable, index))
-}
-
-integer_ragged_variable_queue_shrink_bitset <- function(variable, index) {
-    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink_bitset`, variable, index))
-}
-
-create_render_vector <- function(data) {
-    .Call(`_individual_create_render_vector`, data)
-}
-
-render_vector_update <- function(v, index, value) {
-    invisible(.Call(`_individual_render_vector_update`, v, index, value))
-}
-
-render_vector_data <- function(v) {
-    .Call(`_individual_render_vector_data`, v)
-}
-
-execute_process <- function(process, timestep) {
-    invisible(.Call(`_individual_execute_process`, process, timestep))
-}
-
-variable_get_size <- function(variable) {
-    .Call(`_individual_variable_get_size`, variable)
-}
-
-variable_update <- function(variable) {
-    invisible(.Call(`_individual_variable_update`, variable))
-}
-
-variable_resize <- function(variable) {
-    invisible(.Call(`_individual_variable_resize`, variable))
-}
-
-# Register entry points for exported C++ functions
-methods::setLoadAction(function(ns) {
-    .Call(`_individual_RcppExport_registerCCallable`)
-})
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+create_bitset <- function(size) {
+    .Call(`_individual_create_bitset`, size)
+}
+
+bitset_copy <- function(b) {
+    .Call(`_individual_bitset_copy`, b)
+}
+
+bitset_insert <- function(b, v) {
+    invisible(.Call(`_individual_bitset_insert`, b, v))
+}
+
+bitset_remove <- function(b, v) {
+    invisible(.Call(`_individual_bitset_remove`, b, v))
+}
+
+bitset_clear <- function(b) {
+    invisible(.Call(`_individual_bitset_clear`, b))
+}
+
+bitset_size <- function(b) {
+    .Call(`_individual_bitset_size`, b)
+}
+
+bitset_max_size <- function(b) {
+    .Call(`_individual_bitset_max_size`, b)
+}
+
+bitset_and <- function(a, b) {
+    invisible(.Call(`_individual_bitset_and`, a, b))
+}
+
+bitset_not <- function(b, inplace) {
+    .Call(`_individual_bitset_not`, b, inplace)
+}
+
+bitset_or <- function(a, b) {
+    invisible(.Call(`_individual_bitset_or`, a, b))
+}
+
+bitset_copy_from <- function(a, b) {
+    invisible(.Call(`_individual_bitset_copy_from`, a, b))
+}
+
+bitset_xor <- function(a, b) {
+    invisible(.Call(`_individual_bitset_xor`, a, b))
+}
+
+bitset_set_difference <- function(a, b) {
+    invisible(.Call(`_individual_bitset_set_difference`, a, b))
+}
+
+bitset_sample <- function(b, rate) {
+    invisible(.Call(`_individual_bitset_sample`, b, rate))
+}
+
+bitset_sample_vector <- function(b, rate) {
+    invisible(.Call(`_individual_bitset_sample_vector`, b, rate))
+}
+
+bitset_to_vector <- function(b) {
+    .Call(`_individual_bitset_to_vector`, b)
+}
+
+filter_bitset_integer <- function(b, other) {
+    .Call(`_individual_filter_bitset_integer`, b, other)
+}
+
+filter_bitset_bitset <- function(b, other) {
+    .Call(`_individual_filter_bitset_bitset`, b, other)
+}
+
+filter_bitset_logical <- function(bitset, other) {
+    .Call(`_individual_filter_bitset_logical`, bitset, other)
+}
+
+bitset_choose <- function(b, k) {
+    invisible(.Call(`_individual_bitset_choose`, b, k))
+}
+
+bitset_count_and_cpp <- function(a, b) {
+    .Call(`_individual_bitset_count_and_cpp`, a, b)
+}
+
+create_categorical_variable <- function(categories, values) {
+    .Call(`_individual_create_categorical_variable`, categories, values)
+}
+
+categorical_variable_get_size <- function(variable) {
+    .Call(`_individual_categorical_variable_get_size`, variable)
+}
+
+categorical_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_update`, variable, value, index))
+}
+
+categorical_variable_get_index_of <- function(variable, values) {
+    .Call(`_individual_categorical_variable_get_index_of`, variable, values)
+}
+
+categorical_variable_get_size_of <- function(variable, values) {
+    .Call(`_individual_categorical_variable_get_size_of`, variable, values)
+}
+
+categorical_variable_get_categories <- function(variable) {
+    .Call(`_individual_categorical_variable_get_categories`, variable)
+}
+
+categorical_variable_queue_update_vector <- function(variable, value, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_update_vector`, variable, value, index))
+}
+
+categorical_variable_update <- function(variable) {
+    invisible(.Call(`_individual_categorical_variable_update`, variable))
+}
+
+categorical_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_categorical_variable_queue_extend`, variable, values))
+}
+
+categorical_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_shrink`, variable, index))
+}
+
+categorical_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_categorical_variable_queue_shrink_bitset`, variable, index))
+}
+
+categorical_variable_get_values <- function(variable) {
+    .Call(`_individual_categorical_variable_get_values`, variable)
+}
+
+categorical_variable_get_values_with_index <- function(variable, index) {
+    .Call(`_individual_categorical_variable_get_values_with_index`, variable, index)
+}
+
+create_double_variable <- function(values) {
+    .Call(`_individual_create_double_variable`, values)
+}
+
+double_variable_get_values <- function(variable) {
+    .Call(`_individual_double_variable_get_values`, variable)
+}
+
+double_variable_get_values_at_index <- function(variable, index) {
+    .Call(`_individual_double_variable_get_values_at_index`, variable, index)
+}
+
+double_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_double_variable_get_values_at_index_vector`, variable, index)
+}
+
+double_variable_get_index_of_range <- function(variable, a, b) {
+    .Call(`_individual_double_variable_get_index_of_range`, variable, a, b)
+}
+
+double_variable_get_size_of_range <- function(variable, a, b) {
+    .Call(`_individual_double_variable_get_size_of_range`, variable, a, b)
+}
+
+double_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_double_variable_queue_fill`, variable, value))
+}
+
+double_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_variable_queue_update`, variable, value, index))
+}
+
+double_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_variable_queue_update_bitset`, variable, value, index))
+}
+
+double_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_double_variable_queue_extend`, variable, values))
+}
+
+double_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_double_variable_queue_shrink`, variable, index))
+}
+
+double_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_double_variable_queue_shrink_bitset`, variable, index))
+}
+
+create_event <- function() {
+    .Call(`_individual_create_event`)
+}
+
+create_targeted_event <- function(size) {
+    .Call(`_individual_create_targeted_event`, size)
+}
+
+event_base_tick <- function(event) {
+    invisible(.Call(`_individual_event_base_tick`, event))
+}
+
+event_base_get_timestep <- function(event) {
+    .Call(`_individual_event_base_get_timestep`, event)
+}
+
+event_base_set_timestep <- function(event, time) {
+    invisible(.Call(`_individual_event_base_set_timestep`, event, time))
+}
+
+event_base_should_trigger <- function(event) {
+    .Call(`_individual_event_base_should_trigger`, event)
+}
+
+event_schedule <- function(event, delays) {
+    invisible(.Call(`_individual_event_schedule`, event, delays))
+}
+
+event_clear_schedule <- function(event) {
+    invisible(.Call(`_individual_event_clear_schedule`, event))
+}
+
+event_checkpoint <- function(event) {
+    .Call(`_individual_event_checkpoint`, event)
+}
+
+event_restore <- function(event, schedule) {
+    invisible(.Call(`_individual_event_restore`, event, schedule))
+}
+
+targeted_event_clear_schedule_vector <- function(event, target) {
+    invisible(.Call(`_individual_targeted_event_clear_schedule_vector`, event, target))
+}
+
+targeted_event_clear_schedule <- function(event, target) {
+    invisible(.Call(`_individual_targeted_event_clear_schedule`, event, target))
+}
+
+targeted_event_get_scheduled <- function(event) {
+    .Call(`_individual_targeted_event_get_scheduled`, event)
+}
+
+targeted_event_schedule <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule`, event, target, delay))
+}
+
+targeted_event_queue_shrink_bitset <- function(event, index) {
+    invisible(.Call(`_individual_targeted_event_queue_shrink_bitset`, event, index))
+}
+
+targeted_event_queue_shrink <- function(event, index) {
+    invisible(.Call(`_individual_targeted_event_queue_shrink`, event, index))
+}
+
+targeted_event_queue_extend <- function(event, n) {
+    invisible(.Call(`_individual_targeted_event_queue_extend`, event, n))
+}
+
+targeted_event_queue_extend_with_schedule <- function(event, delays) {
+    invisible(.Call(`_individual_targeted_event_queue_extend_with_schedule`, event, delays))
+}
+
+targeted_event_schedule_vector <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule_vector`, event, target, delay))
+}
+
+targeted_event_schedule_multi_delay <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule_multi_delay`, event, target, delay))
+}
+
+targeted_event_schedule_multi_delay_vector <- function(event, target, delay) {
+    invisible(.Call(`_individual_targeted_event_schedule_multi_delay_vector`, event, target, delay))
+}
+
+targeted_event_get_target <- function(event) {
+    .Call(`_individual_targeted_event_get_target`, event)
+}
+
+targeted_event_resize <- function(event) {
+    invisible(.Call(`_individual_targeted_event_resize`, event))
+}
+
+targeted_event_checkpoint <- function(event) {
+    .Call(`_individual_targeted_event_checkpoint`, event)
+}
+
+targeted_event_restore <- function(event, state) {
+    invisible(.Call(`_individual_targeted_event_restore`, event, state))
+}
+
+process_listener <- function(event, listener) {
+    invisible(.Call(`_individual_process_listener`, event, listener))
+}
+
+process_targeted_listener <- function(event, listener, target) {
+    invisible(.Call(`_individual_process_targeted_listener`, event, listener, target))
+}
+
+create_integer_variable <- function(values) {
+    .Call(`_individual_create_integer_variable`, values)
+}
+
+integer_variable_get_values <- function(variable) {
+    .Call(`_individual_integer_variable_get_values`, variable)
+}
+
+integer_variable_get_modulo_differences <- function(variable, value, difference) {
+    .Call(`_individual_integer_variable_get_modulo_differences`, variable, value, difference)
+}
+
+integer_variable_get_values_at_index <- function(variable, index) {
+    .Call(`_individual_integer_variable_get_values_at_index`, variable, index)
+}
+
+integer_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_integer_variable_get_values_at_index_vector`, variable, index)
+}
+
+integer_variable_get_index_of_set_vector <- function(variable, values_set) {
+    .Call(`_individual_integer_variable_get_index_of_set_vector`, variable, values_set)
+}
+
+integer_variable_get_index_of_set_scalar <- function(variable, values_set) {
+    .Call(`_individual_integer_variable_get_index_of_set_scalar`, variable, values_set)
+}
+
+integer_variable_get_index_of_range <- function(variable, a, b) {
+    .Call(`_individual_integer_variable_get_index_of_range`, variable, a, b)
+}
+
+integer_variable_get_size_of_set_vector <- function(variable, values_set) {
+    .Call(`_individual_integer_variable_get_size_of_set_vector`, variable, values_set)
+}
+
+integer_variable_get_size_of_set_scalar <- function(variable, value) {
+    .Call(`_individual_integer_variable_get_size_of_set_scalar`, variable, value)
+}
+
+integer_variable_get_size_of_range <- function(variable, a, b) {
+    .Call(`_individual_integer_variable_get_size_of_range`, variable, a, b)
+}
+
+integer_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_integer_variable_queue_fill`, variable, value))
+}
+
+integer_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_variable_queue_update`, variable, value, index))
+}
+
+integer_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_variable_queue_update_bitset`, variable, value, index))
+}
+
+integer_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_integer_variable_queue_extend`, variable, values))
+}
+
+integer_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_integer_variable_queue_shrink`, variable, index))
+}
+
+integer_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_integer_variable_queue_shrink_bitset`, variable, index))
+}
+
+fixed_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate, destination_probabilities) {
+    .Call(`_individual_fixed_probability_multinomial_process_internal`, variable, source_state, destination_states, rate, destination_probabilities)
+}
+
+multi_probability_multinomial_process_internal <- function(variable, source_state, destination_states, rate_variable, destination_probabilities) {
+    .Call(`_individual_multi_probability_multinomial_process_internal`, variable, source_state, destination_states, rate_variable, destination_probabilities)
+}
+
+multi_probability_bernoulli_process_internal <- function(variable, from, to, rate_variable) {
+    .Call(`_individual_multi_probability_bernoulli_process_internal`, variable, from, to, rate_variable)
+}
+
+infection_age_process_internal <- function(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing) {
+    .Call(`_individual_infection_age_process_internal`, state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing)
+}
+
+create_double_ragged_variable <- function(values) {
+    .Call(`_individual_create_double_ragged_variable`, values)
+}
+
+double_ragged_variable_get_values <- function(variable) {
+    .Call(`_individual_double_ragged_variable_get_values`, variable)
+}
+
+double_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_values_at_index_bitset`, variable, index)
+}
+
+double_ragged_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_values_at_index_vector`, variable, index)
+}
+
+double_ragged_variable_get_length <- function(variable) {
+    .Call(`_individual_double_ragged_variable_get_length`, variable)
+}
+
+double_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_length_at_index_bitset`, variable, index)
+}
+
+double_ragged_variable_get_length_at_index_vector <- function(variable, index) {
+    .Call(`_individual_double_ragged_variable_get_length_at_index_vector`, variable, index)
+}
+
+double_ragged_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_fill`, variable, value))
+}
+
+double_ragged_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_update`, variable, value, index))
+}
+
+double_ragged_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_update_bitset`, variable, value, index))
+}
+
+double_ragged_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_extend`, variable, values))
+}
+
+double_ragged_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_shrink`, variable, index))
+}
+
+double_ragged_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_double_ragged_variable_queue_shrink_bitset`, variable, index))
+}
+
+create_integer_ragged_variable <- function(values) {
+    .Call(`_individual_create_integer_ragged_variable`, values)
+}
+
+integer_ragged_variable_get_values <- function(variable) {
+    .Call(`_individual_integer_ragged_variable_get_values`, variable)
+}
+
+integer_ragged_variable_get_values_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_values_at_index_bitset`, variable, index)
+}
+
+integer_ragged_variable_get_values_at_index_vector <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_values_at_index_vector`, variable, index)
+}
+
+integer_ragged_variable_get_length <- function(variable) {
+    .Call(`_individual_integer_ragged_variable_get_length`, variable)
+}
+
+integer_ragged_variable_get_length_at_index_bitset <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_length_at_index_bitset`, variable, index)
+}
+
+integer_ragged_variable_get_length_at_index_vector <- function(variable, index) {
+    .Call(`_individual_integer_ragged_variable_get_length_at_index_vector`, variable, index)
+}
+
+integer_ragged_variable_queue_fill <- function(variable, value) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_fill`, variable, value))
+}
+
+integer_ragged_variable_queue_update <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_update`, variable, value, index))
+}
+
+integer_ragged_variable_queue_update_bitset <- function(variable, value, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_update_bitset`, variable, value, index))
+}
+
+integer_ragged_variable_queue_extend <- function(variable, values) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_extend`, variable, values))
+}
+
+integer_ragged_variable_queue_shrink <- function(variable, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink`, variable, index))
+}
+
+integer_ragged_variable_queue_shrink_bitset <- function(variable, index) {
+    invisible(.Call(`_individual_integer_ragged_variable_queue_shrink_bitset`, variable, index))
+}
+
+create_render_vector <- function(data) {
+    .Call(`_individual_create_render_vector`, data)
+}
+
+render_vector_update <- function(v, index, value) {
+    invisible(.Call(`_individual_render_vector_update`, v, index, value))
+}
+
+render_vector_data <- function(v) {
+    .Call(`_individual_render_vector_data`, v)
+}
+
+execute_process <- function(process, timestep) {
+    invisible(.Call(`_individual_execute_process`, process, timestep))
+}
+
+variable_get_size <- function(variable) {
+    .Call(`_individual_variable_get_size`, variable)
+}
+
+variable_update <- function(variable) {
+    invisible(.Call(`_individual_variable_update`, variable))
+}
+
+variable_resize <- function(variable) {
+    invisible(.Call(`_individual_variable_resize`, variable))
+}
+
+# Register entry points for exported C++ functions
+methods::setLoadAction(function(ns) {
+    .Call('_individual_RcppExport_registerCCallable', PACKAGE = 'individual')
+})
diff --git a/R/bitset.R b/R/bitset.R
index 7c551a8..b0da440 100644
--- a/R/bitset.R
+++ b/R/bitset.R
@@ -291,3 +291,15 @@ filter_bitset = function(bitset, other) {
     }
   }
 }
+
+#' @title Count bitset and
+#' @description This non-modifying function returns the number of intersecting 
+#' elements between two bitsets \code{a} and \code{b}. This should be faster than
+#' writing \code{a$copy()$and(b)$size()} as it avoids the memory allocations of $copy().
+#'
+#' @param a a \code{\link{Bitset}}
+#' @param b another \code{\link{Bitset}}
+#' @export
+bitset_count_and = function(a, b) {
+  bitset_count_and_cpp(a$.bitset, b$.bitset)
+}
diff --git a/inst/include/IterableBitset.h b/inst/include/IterableBitset.h
index 6643aaf..a942f62 100644
--- a/inst/include/IterableBitset.h
+++ b/inst/include/IterableBitset.h
@@ -79,6 +79,7 @@ class IterableBitset {
     IterableBitset& operator&=(const IterableBitset&);
     IterableBitset& operator|=(const IterableBitset&);
     IterableBitset& operator^=(const IterableBitset&);
+    size_t count_and(const IterableBitset&) const;
     IterableBitset& clear();
     IterableBitset& inverse();
     iterator begin();
@@ -293,6 +294,18 @@ inline IterableBitset<A>& IterableBitset<A>::operator &=(const IterableBitset<A>
     return *this;
 }
 
+template<class A>
+inline size_t IterableBitset<A>::count_and(const IterableBitset<A>& other) const {
+    if (max_size() != other.max_size()) {
+        Rcpp::stop("Incompatible bitmap sizes");
+    }
+    auto n = 0u;
+    for (auto i = 0u; i < bitmap.size(); ++i) {
+        n += popcount(bitmap[i] & other.bitmap[i]);
+    }
+    return n;
+}
+
 template<class A>
 inline IterableBitset<A>& IterableBitset<A>::operator |=(const IterableBitset<A>& other) {
     if (max_size() != other.max_size()) {
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 94c6a58..4c34b84 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -1,1651 +1,1664 @@
-// Generated by using Rcpp::compileAttributes() -> do not edit by hand
-// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-#include "../inst/include/individual.h"
-#include "../inst/include/individual_types.h"
-#include <Rcpp.h>
-#include <string>
-#include <set>
-
-using namespace Rcpp;
-
-#ifdef RCPP_USE_GLOBAL_ROSTREAM
-Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
-Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
-#endif
-
-// create_bitset
-Rcpp::XPtr<individual_index_t> create_bitset(size_t size);
-RcppExport SEXP _individual_create_bitset(SEXP sizeSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_bitset(size));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_copy
-Rcpp::XPtr<individual_index_t> bitset_copy(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_copy(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_copy(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_insert
-void bitset_insert(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
-RcppExport SEXP _individual_bitset_insert(SEXP bSEXP, SEXP vSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
-    bitset_insert(b, v);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_remove
-void bitset_remove(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
-RcppExport SEXP _individual_bitset_remove(SEXP bSEXP, SEXP vSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
-    bitset_remove(b, v);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_clear
-void bitset_clear(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_clear(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_clear(b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_size
-size_t bitset_size(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_size(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_size(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_max_size
-size_t bitset_max_size(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_max_size(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_max_size(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_and
-void bitset_and(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_and(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_and(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_not
-Rcpp::XPtr<individual_index_t> bitset_not(const Rcpp::XPtr<individual_index_t> b, const bool inplace);
-RcppExport SEXP _individual_bitset_not(SEXP bSEXP, SEXP inplaceSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< const bool >::type inplace(inplaceSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_not(b, inplace));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_or
-void bitset_or(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_or(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_or(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_copy_from
-void bitset_copy_from(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_copy_from(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_copy_from(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_xor
-void bitset_xor(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_xor(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_xor(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_set_difference
-void bitset_set_difference(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_set_difference(SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    bitset_set_difference(a, b);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_sample
-void bitset_sample(const Rcpp::XPtr<individual_index_t> b, double rate);
-RcppExport SEXP _individual_bitset_sample(SEXP bSEXP, SEXP rateSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< double >::type rate(rateSEXP);
-    bitset_sample(b, rate);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_sample_vector
-void bitset_sample_vector(const Rcpp::XPtr<individual_index_t> b, std::vector<double> rate);
-RcppExport SEXP _individual_bitset_sample_vector(SEXP bSEXP, SEXP rateSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type rate(rateSEXP);
-    bitset_sample_vector(b, rate);
-    return R_NilValue;
-END_RCPP
-}
-// bitset_to_vector
-std::vector<size_t> bitset_to_vector(const Rcpp::XPtr<individual_index_t> b);
-RcppExport SEXP _individual_bitset_to_vector(SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(bitset_to_vector(b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// filter_bitset_integer
-Rcpp::XPtr<individual_index_t> filter_bitset_integer(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> other);
-RcppExport SEXP _individual_filter_bitset_integer(SEXP bSEXP, SEXP otherSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type other(otherSEXP);
-    rcpp_result_gen = Rcpp::wrap(filter_bitset_integer(b, other));
-    return rcpp_result_gen;
-END_RCPP
-}
-// filter_bitset_bitset
-Rcpp::XPtr<individual_index_t> filter_bitset_bitset(const Rcpp::XPtr<individual_index_t> b, const Rcpp::XPtr<individual_index_t> other);
-RcppExport SEXP _individual_filter_bitset_bitset(SEXP bSEXP, SEXP otherSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type other(otherSEXP);
-    rcpp_result_gen = Rcpp::wrap(filter_bitset_bitset(b, other));
-    return rcpp_result_gen;
-END_RCPP
-}
-// filter_bitset_logical
-Rcpp::XPtr<individual_index_t> filter_bitset_logical(const Rcpp::XPtr<individual_index_t> bitset, Rcpp::LogicalVector other);
-RcppExport SEXP _individual_filter_bitset_logical(SEXP bitsetSEXP, SEXP otherSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type bitset(bitsetSEXP);
-    Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type other(otherSEXP);
-    rcpp_result_gen = Rcpp::wrap(filter_bitset_logical(bitset, other));
-    return rcpp_result_gen;
-END_RCPP
-}
-// bitset_choose
-void bitset_choose(const Rcpp::XPtr<individual_index_t> b, const size_t k);
-RcppExport SEXP _individual_bitset_choose(SEXP bSEXP, SEXP kSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
-    Rcpp::traits::input_parameter< const size_t >::type k(kSEXP);
-    bitset_choose(b, k);
-    return R_NilValue;
-END_RCPP
-}
-// create_categorical_variable
-Rcpp::XPtr<CategoricalVariable> create_categorical_variable(const std::vector<std::string>& categories, const std::vector<std::string>& values);
-RcppExport SEXP _individual_create_categorical_variable(SEXP categoriesSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type categories(categoriesSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_categorical_variable(categories, values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_get_size
-size_t categorical_variable_get_size(Rcpp::XPtr<CategoricalVariable> variable);
-RcppExport SEXP _individual_categorical_variable_get_size(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_queue_update
-void categorical_variable_queue_update(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_categorical_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    categorical_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_get_index_of
-Rcpp::XPtr<individual_index_t> categorical_variable_get_index_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
-RcppExport SEXP _individual_categorical_variable_get_index_of(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_index_of(variable, values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_get_size_of
-int categorical_variable_get_size_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
-RcppExport SEXP _individual_categorical_variable_get_size_of(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size_of(variable, values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_get_categories
-std::vector<std::string> categorical_variable_get_categories(Rcpp::XPtr<CategoricalVariable> variable);
-RcppExport SEXP _individual_categorical_variable_get_categories(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_categories(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_queue_update_vector
-void categorical_variable_queue_update_vector(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, std::vector<size_t>& index);
-RcppExport SEXP _individual_categorical_variable_queue_update_vector(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    categorical_variable_queue_update_vector(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_update
-void categorical_variable_update(Rcpp::XPtr<CategoricalVariable> variable);
-RcppExport SEXP _individual_categorical_variable_update(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    categorical_variable_update(variable);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_queue_extend
-void categorical_variable_queue_extend(Rcpp::XPtr<CategoricalVariable> variable, std::vector<std::string>& values);
-RcppExport SEXP _individual_categorical_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<std::string>& >::type values(valuesSEXP);
-    categorical_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_queue_shrink
-void categorical_variable_queue_shrink(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_categorical_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    categorical_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_queue_shrink_bitset
-void categorical_variable_queue_shrink_bitset(Rcpp::XPtr<CategoricalVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_categorical_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    categorical_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// categorical_variable_get_values
-std::vector<std::string> categorical_variable_get_values(Rcpp::XPtr<CategoricalVariable> variable);
-RcppExport SEXP _individual_categorical_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// categorical_variable_get_values_with_index
-std::vector<std::string> categorical_variable_get_values_with_index(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_categorical_variable_get_values_with_index(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values_with_index(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// dummy
-void dummy();
-static SEXP _individual_dummy_try() {
-BEGIN_RCPP
-    dummy();
-    return R_NilValue;
-END_RCPP_RETURN_ERROR
-}
-RcppExport SEXP _individual_dummy() {
-    SEXP rcpp_result_gen;
-    {
-        Rcpp::RNGScope rcpp_rngScope_gen;
-        rcpp_result_gen = PROTECT(_individual_dummy_try());
-    }
-    Rboolean rcpp_isInterrupt_gen = Rf_inherits(rcpp_result_gen, "interrupted-error");
-    if (rcpp_isInterrupt_gen) {
-        UNPROTECT(1);
-        Rf_onintr();
-    }
-    bool rcpp_isLongjump_gen = Rcpp::internal::isLongjumpSentinel(rcpp_result_gen);
-    if (rcpp_isLongjump_gen) {
-        Rcpp::internal::resumeJump(rcpp_result_gen);
-    }
-    Rboolean rcpp_isError_gen = Rf_inherits(rcpp_result_gen, "try-error");
-    if (rcpp_isError_gen) {
-        SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
-        UNPROTECT(1);
-        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
-    }
-    UNPROTECT(1);
-    return rcpp_result_gen;
-}
-// create_double_variable
-Rcpp::XPtr<DoubleVariable> create_double_variable(const std::vector<double>& values);
-RcppExport SEXP _individual_create_double_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<double>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_double_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_values
-const std::vector<double>& double_variable_get_values(Rcpp::XPtr<DoubleVariable> variable);
-RcppExport SEXP _individual_double_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_values_at_index
-std::vector<double> double_variable_get_values_at_index(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_values_at_index_vector
-std::vector<double> double_variable_get_values_at_index_vector(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_index_of_range
-Rcpp::XPtr<individual_index_t> double_variable_get_index_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
-RcppExport SEXP _individual_double_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_index_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_get_size_of_range
-size_t double_variable_get_size_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
-RcppExport SEXP _individual_double_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_variable_get_size_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_variable_queue_fill
-void double_variable_queue_fill(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value);
-RcppExport SEXP _individual_double_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
-    double_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_update
-void double_variable_queue_update(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, std::vector<size_t> index);
-RcppExport SEXP _individual_double_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    double_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_update_bitset
-void double_variable_queue_update_bitset(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_extend
-void double_variable_queue_extend(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> values);
-RcppExport SEXP _individual_double_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type values(valuesSEXP);
-    double_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_shrink
-void double_variable_queue_shrink(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    double_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_variable_queue_shrink_bitset
-void double_variable_queue_shrink_bitset(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// create_event
-Rcpp::XPtr<Event> create_event();
-RcppExport SEXP _individual_create_event() {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    rcpp_result_gen = Rcpp::wrap(create_event());
-    return rcpp_result_gen;
-END_RCPP
-}
-// create_targeted_event
-Rcpp::XPtr<TargetedEvent> create_targeted_event(size_t size);
-RcppExport SEXP _individual_create_targeted_event(SEXP sizeSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_targeted_event(size));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_base_tick
-void event_base_tick(const Rcpp::XPtr<EventBase> event);
-RcppExport SEXP _individual_event_base_tick(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    event_base_tick(event);
-    return R_NilValue;
-END_RCPP
-}
-// event_base_get_timestep
-size_t event_base_get_timestep(const Rcpp::XPtr<EventBase> event);
-RcppExport SEXP _individual_event_base_get_timestep(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(event_base_get_timestep(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_base_set_timestep
-void event_base_set_timestep(const Rcpp::XPtr<EventBase> event, size_t time);
-RcppExport SEXP _individual_event_base_set_timestep(SEXP eventSEXP, SEXP timeSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< size_t >::type time(timeSEXP);
-    event_base_set_timestep(event, time);
-    return R_NilValue;
-END_RCPP
-}
-// event_base_should_trigger
-bool event_base_should_trigger(const Rcpp::XPtr<EventBase> event);
-RcppExport SEXP _individual_event_base_should_trigger(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(event_base_should_trigger(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_schedule
-void event_schedule(const Rcpp::XPtr<Event> event, std::vector<double> delays);
-RcppExport SEXP _individual_event_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<double> >::type delays(delaysSEXP);
-    event_schedule(event, delays);
-    return R_NilValue;
-END_RCPP
-}
-// event_clear_schedule
-void event_clear_schedule(const Rcpp::XPtr<Event> event);
-RcppExport SEXP _individual_event_clear_schedule(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    event_clear_schedule(event);
-    return R_NilValue;
-END_RCPP
-}
-// event_checkpoint
-std::vector<size_t> event_checkpoint(const Rcpp::XPtr<Event> event);
-RcppExport SEXP _individual_event_checkpoint(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(event_checkpoint(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// event_restore
-void event_restore(const Rcpp::XPtr<Event> event, std::vector<size_t> schedule);
-RcppExport SEXP _individual_event_restore(SEXP eventSEXP, SEXP scheduleSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type schedule(scheduleSEXP);
-    event_restore(event, schedule);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_clear_schedule_vector
-void targeted_event_clear_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target);
-RcppExport SEXP _individual_targeted_event_clear_schedule_vector(SEXP eventSEXP, SEXP targetSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
-    targeted_event_clear_schedule_vector(event, target);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_clear_schedule
-void targeted_event_clear_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target);
-RcppExport SEXP _individual_targeted_event_clear_schedule(SEXP eventSEXP, SEXP targetSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    targeted_event_clear_schedule(event, target);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_get_scheduled
-Rcpp::XPtr<individual_index_t> targeted_event_get_scheduled(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_get_scheduled(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(targeted_event_get_scheduled(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// targeted_event_schedule
-void targeted_event_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, double delay);
-RcppExport SEXP _individual_targeted_event_schedule(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
-    targeted_event_schedule(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_shrink_bitset
-void targeted_event_queue_shrink_bitset(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_targeted_event_queue_shrink_bitset(SEXP eventSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    targeted_event_queue_shrink_bitset(event, index);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_shrink
-void targeted_event_queue_shrink(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t>& index);
-RcppExport SEXP _individual_targeted_event_queue_shrink(SEXP eventSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    targeted_event_queue_shrink(event, index);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_extend
-void targeted_event_queue_extend(const Rcpp::XPtr<TargetedEvent> event, size_t n);
-RcppExport SEXP _individual_targeted_event_queue_extend(SEXP eventSEXP, SEXP nSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< size_t >::type n(nSEXP);
-    targeted_event_queue_extend(event, n);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_queue_extend_with_schedule
-void targeted_event_queue_extend_with_schedule(const Rcpp::XPtr<TargetedEvent> event, const std::vector<double>& delays);
-RcppExport SEXP _individual_targeted_event_queue_extend_with_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double>& >::type delays(delaysSEXP);
-    targeted_event_queue_extend_with_schedule(event, delays);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_schedule_vector
-void targeted_event_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, double delay);
-RcppExport SEXP _individual_targeted_event_schedule_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
-    targeted_event_schedule_vector(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_schedule_multi_delay
-void targeted_event_schedule_multi_delay(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, const std::vector<double> delay);
-RcppExport SEXP _individual_targeted_event_schedule_multi_delay(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
-    targeted_event_schedule_multi_delay(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_schedule_multi_delay_vector
-void targeted_event_schedule_multi_delay_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, const std::vector<double> delay);
-RcppExport SEXP _individual_targeted_event_schedule_multi_delay_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
-    targeted_event_schedule_multi_delay_vector(event, target, delay);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_get_target
-Rcpp::XPtr<individual_index_t> targeted_event_get_target(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_get_target(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(targeted_event_get_target(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// targeted_event_resize
-void targeted_event_resize(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_resize(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    targeted_event_resize(event);
-    return R_NilValue;
-END_RCPP
-}
-// targeted_event_checkpoint
-Rcpp::List targeted_event_checkpoint(const Rcpp::XPtr<TargetedEvent> event);
-RcppExport SEXP _individual_targeted_event_checkpoint(SEXP eventSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    rcpp_result_gen = Rcpp::wrap(targeted_event_checkpoint(event));
-    return rcpp_result_gen;
-END_RCPP
-}
-// targeted_event_restore
-void targeted_event_restore(const Rcpp::XPtr<TargetedEvent> event, Rcpp::List state);
-RcppExport SEXP _individual_targeted_event_restore(SEXP eventSEXP, SEXP stateSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< Rcpp::List >::type state(stateSEXP);
-    targeted_event_restore(event, state);
-    return R_NilValue;
-END_RCPP
-}
-// process_listener
-void process_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<listener_t> listener);
-RcppExport SEXP _individual_process_listener(SEXP eventSEXP, SEXP listenerSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<listener_t> >::type listener(listenerSEXP);
-    process_listener(event, listener);
-    return R_NilValue;
-END_RCPP
-}
-// process_targeted_listener
-void process_targeted_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<targeted_listener_t> listener, const Rcpp::XPtr<individual_index_t> target);
-RcppExport SEXP _individual_process_targeted_listener(SEXP eventSEXP, SEXP listenerSEXP, SEXP targetSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<targeted_listener_t> >::type listener(listenerSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
-    process_targeted_listener(event, listener, target);
-    return R_NilValue;
-END_RCPP
-}
-// create_integer_variable
-Rcpp::XPtr<IntegerVariable> create_integer_variable(const std::vector<int>& values);
-RcppExport SEXP _individual_create_integer_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<int>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_integer_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_values
-const std::vector<int>& integer_variable_get_values(Rcpp::XPtr<IntegerVariable> variable);
-RcppExport SEXP _individual_integer_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_modulo_differences
-individual_index_t integer_variable_get_modulo_differences(Rcpp::XPtr<IntegerVariable> variable, const int value, const int difference);
-RcppExport SEXP _individual_integer_variable_get_modulo_differences(SEXP variableSEXP, SEXP valueSEXP, SEXP differenceSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< const int >::type difference(differenceSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_modulo_differences(variable, value, difference));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_values_at_index
-std::vector<int> integer_variable_get_values_at_index(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_values_at_index_vector
-std::vector<int> integer_variable_get_values_at_index_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_index_of_set_vector
-Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values_set);
-RcppExport SEXP _individual_integer_variable_get_index_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type values_set(values_setSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_vector(variable, values_set));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_index_of_set_scalar
-Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int values_set);
-RcppExport SEXP _individual_integer_variable_get_index_of_set_scalar(SEXP variableSEXP, SEXP values_setSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type values_set(values_setSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_scalar(variable, values_set));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_index_of_range
-Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
-RcppExport SEXP _individual_integer_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_size_of_set_vector
-size_t integer_variable_get_size_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, const std::vector<int> values_set);
-RcppExport SEXP _individual_integer_variable_get_size_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<int> >::type values_set(values_setSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_vector(variable, values_set));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_size_of_set_scalar
-size_t integer_variable_get_size_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int value);
-RcppExport SEXP _individual_integer_variable_get_size_of_set_scalar(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_scalar(variable, value));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_get_size_of_range
-size_t integer_variable_get_size_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
-RcppExport SEXP _individual_integer_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
-    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_range(variable, a, b));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_variable_queue_fill
-void integer_variable_queue_fill(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value);
-RcppExport SEXP _individual_integer_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
-    integer_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_update
-void integer_variable_queue_update(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    integer_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_update_bitset
-void integer_variable_queue_update_bitset(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_extend
-void integer_variable_queue_extend(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values);
-RcppExport SEXP _individual_integer_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<int> >::type values(valuesSEXP);
-    integer_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_shrink
-void integer_variable_queue_shrink(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    integer_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_variable_queue_shrink_bitset
-void integer_variable_queue_shrink_bitset(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// fixed_probability_multinomial_process_internal
-Rcpp::XPtr<process_t> fixed_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const double rate, const std::vector<double> destination_probabilities);
-RcppExport SEXP _individual_fixed_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rateSEXP, SEXP destination_probabilitiesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
-    Rcpp::traits::input_parameter< const double >::type rate(rateSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
-    rcpp_result_gen = Rcpp::wrap(fixed_probability_multinomial_process_internal(variable, source_state, destination_states, rate, destination_probabilities));
-    return rcpp_result_gen;
-END_RCPP
-}
-// multi_probability_multinomial_process_internal
-Rcpp::XPtr<process_t> multi_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const Rcpp::XPtr<DoubleVariable> rate_variable, const std::vector<double> destination_probabilities);
-RcppExport SEXP _individual_multi_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rate_variableSEXP, SEXP destination_probabilitiesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
-    rcpp_result_gen = Rcpp::wrap(multi_probability_multinomial_process_internal(variable, source_state, destination_states, rate_variable, destination_probabilities));
-    return rcpp_result_gen;
-END_RCPP
-}
-// multi_probability_bernoulli_process_internal
-Rcpp::XPtr<process_t> multi_probability_bernoulli_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string from, const std::string to, const Rcpp::XPtr<DoubleVariable> rate_variable);
-RcppExport SEXP _individual_multi_probability_bernoulli_process_internal(SEXP variableSEXP, SEXP fromSEXP, SEXP toSEXP, SEXP rate_variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type from(fromSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type to(toSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(multi_probability_bernoulli_process_internal(variable, from, to, rate_variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// infection_age_process_internal
-Rcpp::XPtr<process_t> infection_age_process_internal(Rcpp::XPtr<CategoricalVariable> state, const std::string susceptible, const std::string exposed, const std::string infectious, const Rcpp::XPtr<IntegerVariable> age, const int age_bins, const double p, const double dt, const Rcpp::NumericMatrix mixing);
-RcppExport SEXP _individual_infection_age_process_internal(SEXP stateSEXP, SEXP susceptibleSEXP, SEXP exposedSEXP, SEXP infectiousSEXP, SEXP ageSEXP, SEXP age_binsSEXP, SEXP pSEXP, SEXP dtSEXP, SEXP mixingSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type state(stateSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type susceptible(susceptibleSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type exposed(exposedSEXP);
-    Rcpp::traits::input_parameter< const std::string >::type infectious(infectiousSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::XPtr<IntegerVariable> >::type age(ageSEXP);
-    Rcpp::traits::input_parameter< const int >::type age_bins(age_binsSEXP);
-    Rcpp::traits::input_parameter< const double >::type p(pSEXP);
-    Rcpp::traits::input_parameter< const double >::type dt(dtSEXP);
-    Rcpp::traits::input_parameter< const Rcpp::NumericMatrix >::type mixing(mixingSEXP);
-    rcpp_result_gen = Rcpp::wrap(infection_age_process_internal(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing));
-    return rcpp_result_gen;
-END_RCPP
-}
-// create_double_ragged_variable
-Rcpp::XPtr<RaggedDouble> create_double_ragged_variable(const std::vector<std::vector<double>>& values);
-RcppExport SEXP _individual_create_double_ragged_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_double_ragged_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_values
-std::vector<std::vector<double>> double_ragged_variable_get_values(Rcpp::XPtr<RaggedDouble> variable);
-RcppExport SEXP _individual_double_ragged_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_values_at_index_bitset
-std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_values_at_index_vector
-std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_length
-std::vector<size_t> double_ragged_variable_get_length(Rcpp::XPtr<RaggedDouble> variable);
-RcppExport SEXP _individual_double_ragged_variable_get_length(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_length_at_index_bitset
-std::vector<size_t> double_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_get_length_at_index_vector
-std::vector<size_t> double_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// double_ragged_variable_queue_fill
-void double_ragged_variable_queue_fill(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value);
-RcppExport SEXP _individual_double_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
-    double_ragged_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_update
-void double_ragged_variable_queue_update(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value, std::vector<size_t> index);
-RcppExport SEXP _individual_double_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    double_ragged_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_update_bitset
-void double_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<double>> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_ragged_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_extend
-void double_ragged_variable_queue_extend(Rcpp::XPtr<RaggedDouble> variable, std::vector<std::vector<double>>& values);
-RcppExport SEXP _individual_double_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<std::vector<double>>& >::type values(valuesSEXP);
-    double_ragged_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_shrink
-void double_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_double_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    double_ragged_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// double_ragged_variable_queue_shrink_bitset
-void double_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_double_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    double_ragged_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// create_integer_ragged_variable
-Rcpp::XPtr<RaggedInteger> create_integer_ragged_variable(const std::vector<std::vector<int>>& values);
-RcppExport SEXP _individual_create_integer_ragged_variable(SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type values(valuesSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_integer_ragged_variable(values));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_values
-std::vector<std::vector<int>> integer_ragged_variable_get_values(Rcpp::XPtr<RaggedInteger> variable);
-RcppExport SEXP _individual_integer_ragged_variable_get_values(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_values_at_index_bitset
-std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_values_at_index_vector
-std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_length
-std::vector<size_t> integer_ragged_variable_get_length(Rcpp::XPtr<RaggedInteger> variable);
-RcppExport SEXP _individual_integer_ragged_variable_get_length(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_length_at_index_bitset
-std::vector<size_t> integer_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_bitset(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_get_length_at_index_vector
-std::vector<size_t> integer_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_vector(variable, index));
-    return rcpp_result_gen;
-END_RCPP
-}
-// integer_ragged_variable_queue_fill
-void integer_ragged_variable_queue_fill(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value);
-RcppExport SEXP _individual_integer_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
-    integer_ragged_variable_queue_fill(variable, value);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_update
-void integer_ragged_variable_queue_update(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value, std::vector<size_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
-    integer_ragged_variable_queue_update(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_update_bitset
-void integer_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>> value, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< const std::vector<std::vector<int>> >::type value(valueSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_ragged_variable_queue_update_bitset(variable, value, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_extend
-void integer_ragged_variable_queue_extend(Rcpp::XPtr<RaggedInteger> variable, std::vector<std::vector<int>>& values);
-RcppExport SEXP _individual_integer_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<std::vector<int>>& >::type values(valuesSEXP);
-    integer_ragged_variable_queue_extend(variable, values);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_shrink
-void integer_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t>& index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
-    integer_ragged_variable_queue_shrink(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// integer_ragged_variable_queue_shrink_bitset
-void integer_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
-RcppExport SEXP _individual_integer_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
-    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
-    integer_ragged_variable_queue_shrink_bitset(variable, index);
-    return R_NilValue;
-END_RCPP
-}
-// create_render_vector
-Rcpp::XPtr<RenderVector> create_render_vector(std::vector<double> data);
-RcppExport SEXP _individual_create_render_vector(SEXP dataSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< std::vector<double> >::type data(dataSEXP);
-    rcpp_result_gen = Rcpp::wrap(create_render_vector(data));
-    return rcpp_result_gen;
-END_RCPP
-}
-// render_vector_update
-void render_vector_update(Rcpp::XPtr<RenderVector> v, size_t index, double value);
-RcppExport SEXP _individual_render_vector_update(SEXP vSEXP, SEXP indexSEXP, SEXP valueSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
-    Rcpp::traits::input_parameter< size_t >::type index(indexSEXP);
-    Rcpp::traits::input_parameter< double >::type value(valueSEXP);
-    render_vector_update(v, index, value);
-    return R_NilValue;
-END_RCPP
-}
-// render_vector_data
-std::vector<double> render_vector_data(Rcpp::XPtr<RenderVector> v);
-RcppExport SEXP _individual_render_vector_data(SEXP vSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
-    rcpp_result_gen = Rcpp::wrap(render_vector_data(v));
-    return rcpp_result_gen;
-END_RCPP
-}
-// execute_process
-void execute_process(Rcpp::XPtr<process_t> process, size_t timestep);
-RcppExport SEXP _individual_execute_process(SEXP processSEXP, SEXP timestepSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<process_t> >::type process(processSEXP);
-    Rcpp::traits::input_parameter< size_t >::type timestep(timestepSEXP);
-    execute_process(process, timestep);
-    return R_NilValue;
-END_RCPP
-}
-// variable_get_size
-size_t variable_get_size(Rcpp::XPtr<Variable> variable);
-RcppExport SEXP _individual_variable_get_size(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
-    rcpp_result_gen = Rcpp::wrap(variable_get_size(variable));
-    return rcpp_result_gen;
-END_RCPP
-}
-// variable_update
-void variable_update(Rcpp::XPtr<Variable> variable);
-RcppExport SEXP _individual_variable_update(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
-    variable_update(variable);
-    return R_NilValue;
-END_RCPP
-}
-// variable_resize
-void variable_resize(Rcpp::XPtr<Variable> variable);
-RcppExport SEXP _individual_variable_resize(SEXP variableSEXP) {
-BEGIN_RCPP
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
-    variable_resize(variable);
-    return R_NilValue;
-END_RCPP
-}
-
-// validate (ensure exported C++ functions exist before calling them)
-static int _individual_RcppExport_validate(const char* sig) { 
-    static std::set<std::string> signatures;
-    if (signatures.empty()) {
-        signatures.insert("void(*dummy)()");
-    }
-    return signatures.find(sig) != signatures.end();
-}
-
-// registerCCallable (register entry points for exported C++ functions)
-RcppExport SEXP _individual_RcppExport_registerCCallable() { 
-    R_RegisterCCallable("individual", "_individual_dummy", (DL_FUNC)_individual_dummy_try);
-    R_RegisterCCallable("individual", "_individual_RcppExport_validate", (DL_FUNC)_individual_RcppExport_validate);
-    return R_NilValue;
-}
-
-RcppExport SEXP run_testthat_tests(SEXP);
-
-static const R_CallMethodDef CallEntries[] = {
-    {"_individual_create_bitset", (DL_FUNC) &_individual_create_bitset, 1},
-    {"_individual_bitset_copy", (DL_FUNC) &_individual_bitset_copy, 1},
-    {"_individual_bitset_insert", (DL_FUNC) &_individual_bitset_insert, 2},
-    {"_individual_bitset_remove", (DL_FUNC) &_individual_bitset_remove, 2},
-    {"_individual_bitset_clear", (DL_FUNC) &_individual_bitset_clear, 1},
-    {"_individual_bitset_size", (DL_FUNC) &_individual_bitset_size, 1},
-    {"_individual_bitset_max_size", (DL_FUNC) &_individual_bitset_max_size, 1},
-    {"_individual_bitset_and", (DL_FUNC) &_individual_bitset_and, 2},
-    {"_individual_bitset_not", (DL_FUNC) &_individual_bitset_not, 2},
-    {"_individual_bitset_or", (DL_FUNC) &_individual_bitset_or, 2},
-    {"_individual_bitset_copy_from", (DL_FUNC) &_individual_bitset_copy_from, 2},
-    {"_individual_bitset_xor", (DL_FUNC) &_individual_bitset_xor, 2},
-    {"_individual_bitset_set_difference", (DL_FUNC) &_individual_bitset_set_difference, 2},
-    {"_individual_bitset_sample", (DL_FUNC) &_individual_bitset_sample, 2},
-    {"_individual_bitset_sample_vector", (DL_FUNC) &_individual_bitset_sample_vector, 2},
-    {"_individual_bitset_to_vector", (DL_FUNC) &_individual_bitset_to_vector, 1},
-    {"_individual_filter_bitset_integer", (DL_FUNC) &_individual_filter_bitset_integer, 2},
-    {"_individual_filter_bitset_bitset", (DL_FUNC) &_individual_filter_bitset_bitset, 2},
-    {"_individual_filter_bitset_logical", (DL_FUNC) &_individual_filter_bitset_logical, 2},
-    {"_individual_bitset_choose", (DL_FUNC) &_individual_bitset_choose, 2},
-    {"_individual_create_categorical_variable", (DL_FUNC) &_individual_create_categorical_variable, 2},
-    {"_individual_categorical_variable_get_size", (DL_FUNC) &_individual_categorical_variable_get_size, 1},
-    {"_individual_categorical_variable_queue_update", (DL_FUNC) &_individual_categorical_variable_queue_update, 3},
-    {"_individual_categorical_variable_get_index_of", (DL_FUNC) &_individual_categorical_variable_get_index_of, 2},
-    {"_individual_categorical_variable_get_size_of", (DL_FUNC) &_individual_categorical_variable_get_size_of, 2},
-    {"_individual_categorical_variable_get_categories", (DL_FUNC) &_individual_categorical_variable_get_categories, 1},
-    {"_individual_categorical_variable_queue_update_vector", (DL_FUNC) &_individual_categorical_variable_queue_update_vector, 3},
-    {"_individual_categorical_variable_update", (DL_FUNC) &_individual_categorical_variable_update, 1},
-    {"_individual_categorical_variable_queue_extend", (DL_FUNC) &_individual_categorical_variable_queue_extend, 2},
-    {"_individual_categorical_variable_queue_shrink", (DL_FUNC) &_individual_categorical_variable_queue_shrink, 2},
-    {"_individual_categorical_variable_queue_shrink_bitset", (DL_FUNC) &_individual_categorical_variable_queue_shrink_bitset, 2},
-    {"_individual_categorical_variable_get_values", (DL_FUNC) &_individual_categorical_variable_get_values, 1},
-    {"_individual_categorical_variable_get_values_with_index", (DL_FUNC) &_individual_categorical_variable_get_values_with_index, 2},
-    {"_individual_dummy", (DL_FUNC) &_individual_dummy, 0},
-    {"_individual_create_double_variable", (DL_FUNC) &_individual_create_double_variable, 1},
-    {"_individual_double_variable_get_values", (DL_FUNC) &_individual_double_variable_get_values, 1},
-    {"_individual_double_variable_get_values_at_index", (DL_FUNC) &_individual_double_variable_get_values_at_index, 2},
-    {"_individual_double_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_variable_get_values_at_index_vector, 2},
-    {"_individual_double_variable_get_index_of_range", (DL_FUNC) &_individual_double_variable_get_index_of_range, 3},
-    {"_individual_double_variable_get_size_of_range", (DL_FUNC) &_individual_double_variable_get_size_of_range, 3},
-    {"_individual_double_variable_queue_fill", (DL_FUNC) &_individual_double_variable_queue_fill, 2},
-    {"_individual_double_variable_queue_update", (DL_FUNC) &_individual_double_variable_queue_update, 3},
-    {"_individual_double_variable_queue_update_bitset", (DL_FUNC) &_individual_double_variable_queue_update_bitset, 3},
-    {"_individual_double_variable_queue_extend", (DL_FUNC) &_individual_double_variable_queue_extend, 2},
-    {"_individual_double_variable_queue_shrink", (DL_FUNC) &_individual_double_variable_queue_shrink, 2},
-    {"_individual_double_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_variable_queue_shrink_bitset, 2},
-    {"_individual_create_event", (DL_FUNC) &_individual_create_event, 0},
-    {"_individual_create_targeted_event", (DL_FUNC) &_individual_create_targeted_event, 1},
-    {"_individual_event_base_tick", (DL_FUNC) &_individual_event_base_tick, 1},
-    {"_individual_event_base_get_timestep", (DL_FUNC) &_individual_event_base_get_timestep, 1},
-    {"_individual_event_base_set_timestep", (DL_FUNC) &_individual_event_base_set_timestep, 2},
-    {"_individual_event_base_should_trigger", (DL_FUNC) &_individual_event_base_should_trigger, 1},
-    {"_individual_event_schedule", (DL_FUNC) &_individual_event_schedule, 2},
-    {"_individual_event_clear_schedule", (DL_FUNC) &_individual_event_clear_schedule, 1},
-    {"_individual_event_checkpoint", (DL_FUNC) &_individual_event_checkpoint, 1},
-    {"_individual_event_restore", (DL_FUNC) &_individual_event_restore, 2},
-    {"_individual_targeted_event_clear_schedule_vector", (DL_FUNC) &_individual_targeted_event_clear_schedule_vector, 2},
-    {"_individual_targeted_event_clear_schedule", (DL_FUNC) &_individual_targeted_event_clear_schedule, 2},
-    {"_individual_targeted_event_get_scheduled", (DL_FUNC) &_individual_targeted_event_get_scheduled, 1},
-    {"_individual_targeted_event_schedule", (DL_FUNC) &_individual_targeted_event_schedule, 3},
-    {"_individual_targeted_event_queue_shrink_bitset", (DL_FUNC) &_individual_targeted_event_queue_shrink_bitset, 2},
-    {"_individual_targeted_event_queue_shrink", (DL_FUNC) &_individual_targeted_event_queue_shrink, 2},
-    {"_individual_targeted_event_queue_extend", (DL_FUNC) &_individual_targeted_event_queue_extend, 2},
-    {"_individual_targeted_event_queue_extend_with_schedule", (DL_FUNC) &_individual_targeted_event_queue_extend_with_schedule, 2},
-    {"_individual_targeted_event_schedule_vector", (DL_FUNC) &_individual_targeted_event_schedule_vector, 3},
-    {"_individual_targeted_event_schedule_multi_delay", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay, 3},
-    {"_individual_targeted_event_schedule_multi_delay_vector", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay_vector, 3},
-    {"_individual_targeted_event_get_target", (DL_FUNC) &_individual_targeted_event_get_target, 1},
-    {"_individual_targeted_event_resize", (DL_FUNC) &_individual_targeted_event_resize, 1},
-    {"_individual_targeted_event_checkpoint", (DL_FUNC) &_individual_targeted_event_checkpoint, 1},
-    {"_individual_targeted_event_restore", (DL_FUNC) &_individual_targeted_event_restore, 2},
-    {"_individual_process_listener", (DL_FUNC) &_individual_process_listener, 2},
-    {"_individual_process_targeted_listener", (DL_FUNC) &_individual_process_targeted_listener, 3},
-    {"_individual_create_integer_variable", (DL_FUNC) &_individual_create_integer_variable, 1},
-    {"_individual_integer_variable_get_values", (DL_FUNC) &_individual_integer_variable_get_values, 1},
-    {"_individual_integer_variable_get_modulo_differences", (DL_FUNC) &_individual_integer_variable_get_modulo_differences, 3},
-    {"_individual_integer_variable_get_values_at_index", (DL_FUNC) &_individual_integer_variable_get_values_at_index, 2},
-    {"_individual_integer_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_variable_get_values_at_index_vector, 2},
-    {"_individual_integer_variable_get_index_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_index_of_set_vector, 2},
-    {"_individual_integer_variable_get_index_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_index_of_set_scalar, 2},
-    {"_individual_integer_variable_get_index_of_range", (DL_FUNC) &_individual_integer_variable_get_index_of_range, 3},
-    {"_individual_integer_variable_get_size_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_size_of_set_vector, 2},
-    {"_individual_integer_variable_get_size_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_size_of_set_scalar, 2},
-    {"_individual_integer_variable_get_size_of_range", (DL_FUNC) &_individual_integer_variable_get_size_of_range, 3},
-    {"_individual_integer_variable_queue_fill", (DL_FUNC) &_individual_integer_variable_queue_fill, 2},
-    {"_individual_integer_variable_queue_update", (DL_FUNC) &_individual_integer_variable_queue_update, 3},
-    {"_individual_integer_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_variable_queue_update_bitset, 3},
-    {"_individual_integer_variable_queue_extend", (DL_FUNC) &_individual_integer_variable_queue_extend, 2},
-    {"_individual_integer_variable_queue_shrink", (DL_FUNC) &_individual_integer_variable_queue_shrink, 2},
-    {"_individual_integer_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_variable_queue_shrink_bitset, 2},
-    {"_individual_fixed_probability_multinomial_process_internal", (DL_FUNC) &_individual_fixed_probability_multinomial_process_internal, 5},
-    {"_individual_multi_probability_multinomial_process_internal", (DL_FUNC) &_individual_multi_probability_multinomial_process_internal, 5},
-    {"_individual_multi_probability_bernoulli_process_internal", (DL_FUNC) &_individual_multi_probability_bernoulli_process_internal, 4},
-    {"_individual_infection_age_process_internal", (DL_FUNC) &_individual_infection_age_process_internal, 9},
-    {"_individual_create_double_ragged_variable", (DL_FUNC) &_individual_create_double_ragged_variable, 1},
-    {"_individual_double_ragged_variable_get_values", (DL_FUNC) &_individual_double_ragged_variable_get_values, 1},
-    {"_individual_double_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_bitset, 2},
-    {"_individual_double_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_vector, 2},
-    {"_individual_double_ragged_variable_get_length", (DL_FUNC) &_individual_double_ragged_variable_get_length, 1},
-    {"_individual_double_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_bitset, 2},
-    {"_individual_double_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_vector, 2},
-    {"_individual_double_ragged_variable_queue_fill", (DL_FUNC) &_individual_double_ragged_variable_queue_fill, 2},
-    {"_individual_double_ragged_variable_queue_update", (DL_FUNC) &_individual_double_ragged_variable_queue_update, 3},
-    {"_individual_double_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_update_bitset, 3},
-    {"_individual_double_ragged_variable_queue_extend", (DL_FUNC) &_individual_double_ragged_variable_queue_extend, 2},
-    {"_individual_double_ragged_variable_queue_shrink", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink, 2},
-    {"_individual_double_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink_bitset, 2},
-    {"_individual_create_integer_ragged_variable", (DL_FUNC) &_individual_create_integer_ragged_variable, 1},
-    {"_individual_integer_ragged_variable_get_values", (DL_FUNC) &_individual_integer_ragged_variable_get_values, 1},
-    {"_individual_integer_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_bitset, 2},
-    {"_individual_integer_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_vector, 2},
-    {"_individual_integer_ragged_variable_get_length", (DL_FUNC) &_individual_integer_ragged_variable_get_length, 1},
-    {"_individual_integer_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_bitset, 2},
-    {"_individual_integer_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_vector, 2},
-    {"_individual_integer_ragged_variable_queue_fill", (DL_FUNC) &_individual_integer_ragged_variable_queue_fill, 2},
-    {"_individual_integer_ragged_variable_queue_update", (DL_FUNC) &_individual_integer_ragged_variable_queue_update, 3},
-    {"_individual_integer_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_update_bitset, 3},
-    {"_individual_integer_ragged_variable_queue_extend", (DL_FUNC) &_individual_integer_ragged_variable_queue_extend, 2},
-    {"_individual_integer_ragged_variable_queue_shrink", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink, 2},
-    {"_individual_integer_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink_bitset, 2},
-    {"_individual_create_render_vector", (DL_FUNC) &_individual_create_render_vector, 1},
-    {"_individual_render_vector_update", (DL_FUNC) &_individual_render_vector_update, 3},
-    {"_individual_render_vector_data", (DL_FUNC) &_individual_render_vector_data, 1},
-    {"_individual_execute_process", (DL_FUNC) &_individual_execute_process, 2},
-    {"_individual_variable_get_size", (DL_FUNC) &_individual_variable_get_size, 1},
-    {"_individual_variable_update", (DL_FUNC) &_individual_variable_update, 1},
-    {"_individual_variable_resize", (DL_FUNC) &_individual_variable_resize, 1},
-    {"_individual_RcppExport_registerCCallable", (DL_FUNC) &_individual_RcppExport_registerCCallable, 0},
-    {"run_testthat_tests", (DL_FUNC) &run_testthat_tests, 1},
-    {NULL, NULL, 0}
-};
-
-RcppExport void R_init_individual(DllInfo *dll) {
-    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
-    R_useDynamicSymbols(dll, FALSE);
-}
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include "../inst/include/individual.h"
+#include "../inst/include/individual_types.h"
+#include <Rcpp.h>
+#include <string>
+#include <set>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+// create_bitset
+Rcpp::XPtr<individual_index_t> create_bitset(size_t size);
+RcppExport SEXP _individual_create_bitset(SEXP sizeSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_bitset(size));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_copy
+Rcpp::XPtr<individual_index_t> bitset_copy(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_copy(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_copy(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_insert
+void bitset_insert(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
+RcppExport SEXP _individual_bitset_insert(SEXP bSEXP, SEXP vSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
+    bitset_insert(b, v);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_remove
+void bitset_remove(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> v);
+RcppExport SEXP _individual_bitset_remove(SEXP bSEXP, SEXP vSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type v(vSEXP);
+    bitset_remove(b, v);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_clear
+void bitset_clear(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_clear(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_clear(b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_size
+size_t bitset_size(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_size(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_size(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_max_size
+size_t bitset_max_size(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_max_size(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_max_size(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_and
+void bitset_and(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_and(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_and(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_not
+Rcpp::XPtr<individual_index_t> bitset_not(const Rcpp::XPtr<individual_index_t> b, const bool inplace);
+RcppExport SEXP _individual_bitset_not(SEXP bSEXP, SEXP inplaceSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< const bool >::type inplace(inplaceSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_not(b, inplace));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_or
+void bitset_or(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_or(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_or(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_copy_from
+void bitset_copy_from(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_copy_from(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_copy_from(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_xor
+void bitset_xor(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_xor(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_xor(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_set_difference
+void bitset_set_difference(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_set_difference(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    bitset_set_difference(a, b);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_sample
+void bitset_sample(const Rcpp::XPtr<individual_index_t> b, double rate);
+RcppExport SEXP _individual_bitset_sample(SEXP bSEXP, SEXP rateSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< double >::type rate(rateSEXP);
+    bitset_sample(b, rate);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_sample_vector
+void bitset_sample_vector(const Rcpp::XPtr<individual_index_t> b, std::vector<double> rate);
+RcppExport SEXP _individual_bitset_sample_vector(SEXP bSEXP, SEXP rateSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type rate(rateSEXP);
+    bitset_sample_vector(b, rate);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_to_vector
+std::vector<size_t> bitset_to_vector(const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_to_vector(SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_to_vector(b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// filter_bitset_integer
+Rcpp::XPtr<individual_index_t> filter_bitset_integer(const Rcpp::XPtr<individual_index_t> b, std::vector<size_t> other);
+RcppExport SEXP _individual_filter_bitset_integer(SEXP bSEXP, SEXP otherSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type other(otherSEXP);
+    rcpp_result_gen = Rcpp::wrap(filter_bitset_integer(b, other));
+    return rcpp_result_gen;
+END_RCPP
+}
+// filter_bitset_bitset
+Rcpp::XPtr<individual_index_t> filter_bitset_bitset(const Rcpp::XPtr<individual_index_t> b, const Rcpp::XPtr<individual_index_t> other);
+RcppExport SEXP _individual_filter_bitset_bitset(SEXP bSEXP, SEXP otherSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type other(otherSEXP);
+    rcpp_result_gen = Rcpp::wrap(filter_bitset_bitset(b, other));
+    return rcpp_result_gen;
+END_RCPP
+}
+// filter_bitset_logical
+Rcpp::XPtr<individual_index_t> filter_bitset_logical(const Rcpp::XPtr<individual_index_t> bitset, Rcpp::LogicalVector other);
+RcppExport SEXP _individual_filter_bitset_logical(SEXP bitsetSEXP, SEXP otherSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type bitset(bitsetSEXP);
+    Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type other(otherSEXP);
+    rcpp_result_gen = Rcpp::wrap(filter_bitset_logical(bitset, other));
+    return rcpp_result_gen;
+END_RCPP
+}
+// bitset_choose
+void bitset_choose(const Rcpp::XPtr<individual_index_t> b, const size_t k);
+RcppExport SEXP _individual_bitset_choose(SEXP bSEXP, SEXP kSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    Rcpp::traits::input_parameter< const size_t >::type k(kSEXP);
+    bitset_choose(b, k);
+    return R_NilValue;
+END_RCPP
+}
+// bitset_count_and_cpp
+size_t bitset_count_and_cpp(const Rcpp::XPtr<individual_index_t> a, const Rcpp::XPtr<individual_index_t> b);
+RcppExport SEXP _individual_bitset_count_and_cpp(SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(bitset_count_and_cpp(a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// create_categorical_variable
+Rcpp::XPtr<CategoricalVariable> create_categorical_variable(const std::vector<std::string>& categories, const std::vector<std::string>& values);
+RcppExport SEXP _individual_create_categorical_variable(SEXP categoriesSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type categories(categoriesSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_categorical_variable(categories, values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_size
+size_t categorical_variable_get_size(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_get_size(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_queue_update
+void categorical_variable_queue_update(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_categorical_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    categorical_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_get_index_of
+Rcpp::XPtr<individual_index_t> categorical_variable_get_index_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
+RcppExport SEXP _individual_categorical_variable_get_index_of(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_index_of(variable, values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_size_of
+int categorical_variable_get_size_of(Rcpp::XPtr<CategoricalVariable> variable, const std::vector<std::string>& values);
+RcppExport SEXP _individual_categorical_variable_get_size_of(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_size_of(variable, values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_categories
+std::vector<std::string> categorical_variable_get_categories(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_get_categories(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_categories(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_queue_update_vector
+void categorical_variable_queue_update_vector(Rcpp::XPtr<CategoricalVariable> variable, const std::string& value, std::vector<size_t>& index);
+RcppExport SEXP _individual_categorical_variable_queue_update_vector(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    categorical_variable_queue_update_vector(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_update
+void categorical_variable_update(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_update(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    categorical_variable_update(variable);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_queue_extend
+void categorical_variable_queue_extend(Rcpp::XPtr<CategoricalVariable> variable, std::vector<std::string>& values);
+RcppExport SEXP _individual_categorical_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<std::string>& >::type values(valuesSEXP);
+    categorical_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_queue_shrink
+void categorical_variable_queue_shrink(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_categorical_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    categorical_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_queue_shrink_bitset
+void categorical_variable_queue_shrink_bitset(Rcpp::XPtr<CategoricalVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_categorical_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    categorical_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// categorical_variable_get_values
+std::vector<std::string> categorical_variable_get_values(Rcpp::XPtr<CategoricalVariable> variable);
+RcppExport SEXP _individual_categorical_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// categorical_variable_get_values_with_index
+std::vector<std::string> categorical_variable_get_values_with_index(Rcpp::XPtr<CategoricalVariable> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_categorical_variable_get_values_with_index(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(categorical_variable_get_values_with_index(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// dummy
+void dummy();
+static SEXP _individual_dummy_try() {
+BEGIN_RCPP
+    dummy();
+    return R_NilValue;
+END_RCPP_RETURN_ERROR
+}
+RcppExport SEXP _individual_dummy() {
+    SEXP rcpp_result_gen;
+    {
+        Rcpp::RNGScope rcpp_rngScope_gen;
+        rcpp_result_gen = PROTECT(_individual_dummy_try());
+    }
+    Rboolean rcpp_isInterrupt_gen = Rf_inherits(rcpp_result_gen, "interrupted-error");
+    if (rcpp_isInterrupt_gen) {
+        UNPROTECT(1);
+        Rf_onintr();
+    }
+    bool rcpp_isLongjump_gen = Rcpp::internal::isLongjumpSentinel(rcpp_result_gen);
+    if (rcpp_isLongjump_gen) {
+        Rcpp::internal::resumeJump(rcpp_result_gen);
+    }
+    Rboolean rcpp_isError_gen = Rf_inherits(rcpp_result_gen, "try-error");
+    if (rcpp_isError_gen) {
+        SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
+        UNPROTECT(1);
+        Rf_error(CHAR(rcpp_msgSEXP_gen));
+    }
+    UNPROTECT(1);
+    return rcpp_result_gen;
+}
+// create_double_variable
+Rcpp::XPtr<DoubleVariable> create_double_variable(const std::vector<double>& values);
+RcppExport SEXP _individual_create_double_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<double>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_double_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_values
+const std::vector<double>& double_variable_get_values(Rcpp::XPtr<DoubleVariable> variable);
+RcppExport SEXP _individual_double_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_values_at_index
+std::vector<double> double_variable_get_values_at_index(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_values_at_index_vector
+std::vector<double> double_variable_get_values_at_index_vector(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_index_of_range
+Rcpp::XPtr<individual_index_t> double_variable_get_index_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
+RcppExport SEXP _individual_double_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_index_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_get_size_of_range
+size_t double_variable_get_size_of_range(Rcpp::XPtr<DoubleVariable> variable, const double a, const double b);
+RcppExport SEXP _individual_double_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const double >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const double >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_variable_get_size_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_variable_queue_fill
+void double_variable_queue_fill(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value);
+RcppExport SEXP _individual_double_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
+    double_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_update
+void double_variable_queue_update(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, std::vector<size_t> index);
+RcppExport SEXP _individual_double_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    double_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_update_bitset
+void double_variable_queue_update_bitset(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_extend
+void double_variable_queue_extend(Rcpp::XPtr<DoubleVariable> variable, std::vector<double> values);
+RcppExport SEXP _individual_double_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type values(valuesSEXP);
+    double_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_shrink
+void double_variable_queue_shrink(Rcpp::XPtr<DoubleVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    double_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_variable_queue_shrink_bitset
+void double_variable_queue_shrink_bitset(Rcpp::XPtr<DoubleVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<DoubleVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// create_event
+Rcpp::XPtr<Event> create_event();
+RcppExport SEXP _individual_create_event() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(create_event());
+    return rcpp_result_gen;
+END_RCPP
+}
+// create_targeted_event
+Rcpp::XPtr<TargetedEvent> create_targeted_event(size_t size);
+RcppExport SEXP _individual_create_targeted_event(SEXP sizeSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< size_t >::type size(sizeSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_targeted_event(size));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_base_tick
+void event_base_tick(const Rcpp::XPtr<EventBase> event);
+RcppExport SEXP _individual_event_base_tick(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    event_base_tick(event);
+    return R_NilValue;
+END_RCPP
+}
+// event_base_get_timestep
+size_t event_base_get_timestep(const Rcpp::XPtr<EventBase> event);
+RcppExport SEXP _individual_event_base_get_timestep(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(event_base_get_timestep(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_base_set_timestep
+void event_base_set_timestep(const Rcpp::XPtr<EventBase> event, size_t time);
+RcppExport SEXP _individual_event_base_set_timestep(SEXP eventSEXP, SEXP timeSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< size_t >::type time(timeSEXP);
+    event_base_set_timestep(event, time);
+    return R_NilValue;
+END_RCPP
+}
+// event_base_should_trigger
+bool event_base_should_trigger(const Rcpp::XPtr<EventBase> event);
+RcppExport SEXP _individual_event_base_should_trigger(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<EventBase> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(event_base_should_trigger(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_schedule
+void event_schedule(const Rcpp::XPtr<Event> event, std::vector<double> delays);
+RcppExport SEXP _individual_event_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<double> >::type delays(delaysSEXP);
+    event_schedule(event, delays);
+    return R_NilValue;
+END_RCPP
+}
+// event_clear_schedule
+void event_clear_schedule(const Rcpp::XPtr<Event> event);
+RcppExport SEXP _individual_event_clear_schedule(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    event_clear_schedule(event);
+    return R_NilValue;
+END_RCPP
+}
+// event_checkpoint
+std::vector<size_t> event_checkpoint(const Rcpp::XPtr<Event> event);
+RcppExport SEXP _individual_event_checkpoint(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(event_checkpoint(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// event_restore
+void event_restore(const Rcpp::XPtr<Event> event, std::vector<size_t> schedule);
+RcppExport SEXP _individual_event_restore(SEXP eventSEXP, SEXP scheduleSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type schedule(scheduleSEXP);
+    event_restore(event, schedule);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_clear_schedule_vector
+void targeted_event_clear_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target);
+RcppExport SEXP _individual_targeted_event_clear_schedule_vector(SEXP eventSEXP, SEXP targetSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
+    targeted_event_clear_schedule_vector(event, target);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_clear_schedule
+void targeted_event_clear_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target);
+RcppExport SEXP _individual_targeted_event_clear_schedule(SEXP eventSEXP, SEXP targetSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    targeted_event_clear_schedule(event, target);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_get_scheduled
+Rcpp::XPtr<individual_index_t> targeted_event_get_scheduled(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_get_scheduled(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(targeted_event_get_scheduled(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// targeted_event_schedule
+void targeted_event_schedule(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, double delay);
+RcppExport SEXP _individual_targeted_event_schedule(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
+    targeted_event_schedule(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_shrink_bitset
+void targeted_event_queue_shrink_bitset(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_targeted_event_queue_shrink_bitset(SEXP eventSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    targeted_event_queue_shrink_bitset(event, index);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_shrink
+void targeted_event_queue_shrink(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t>& index);
+RcppExport SEXP _individual_targeted_event_queue_shrink(SEXP eventSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    targeted_event_queue_shrink(event, index);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_extend
+void targeted_event_queue_extend(const Rcpp::XPtr<TargetedEvent> event, size_t n);
+RcppExport SEXP _individual_targeted_event_queue_extend(SEXP eventSEXP, SEXP nSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< size_t >::type n(nSEXP);
+    targeted_event_queue_extend(event, n);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_queue_extend_with_schedule
+void targeted_event_queue_extend_with_schedule(const Rcpp::XPtr<TargetedEvent> event, const std::vector<double>& delays);
+RcppExport SEXP _individual_targeted_event_queue_extend_with_schedule(SEXP eventSEXP, SEXP delaysSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double>& >::type delays(delaysSEXP);
+    targeted_event_queue_extend_with_schedule(event, delays);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_schedule_vector
+void targeted_event_schedule_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, double delay);
+RcppExport SEXP _individual_targeted_event_schedule_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< double >::type delay(delaySEXP);
+    targeted_event_schedule_vector(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_schedule_multi_delay
+void targeted_event_schedule_multi_delay(const Rcpp::XPtr<TargetedEvent> event, const Rcpp::XPtr<individual_index_t> target, const std::vector<double> delay);
+RcppExport SEXP _individual_targeted_event_schedule_multi_delay(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
+    targeted_event_schedule_multi_delay(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_schedule_multi_delay_vector
+void targeted_event_schedule_multi_delay_vector(const Rcpp::XPtr<TargetedEvent> event, std::vector<size_t> target, const std::vector<double> delay);
+RcppExport SEXP _individual_targeted_event_schedule_multi_delay_vector(SEXP eventSEXP, SEXP targetSEXP, SEXP delaySEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type target(targetSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type delay(delaySEXP);
+    targeted_event_schedule_multi_delay_vector(event, target, delay);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_get_target
+Rcpp::XPtr<individual_index_t> targeted_event_get_target(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_get_target(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(targeted_event_get_target(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// targeted_event_resize
+void targeted_event_resize(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_resize(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    targeted_event_resize(event);
+    return R_NilValue;
+END_RCPP
+}
+// targeted_event_checkpoint
+Rcpp::List targeted_event_checkpoint(const Rcpp::XPtr<TargetedEvent> event);
+RcppExport SEXP _individual_targeted_event_checkpoint(SEXP eventSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    rcpp_result_gen = Rcpp::wrap(targeted_event_checkpoint(event));
+    return rcpp_result_gen;
+END_RCPP
+}
+// targeted_event_restore
+void targeted_event_restore(const Rcpp::XPtr<TargetedEvent> event, Rcpp::List state);
+RcppExport SEXP _individual_targeted_event_restore(SEXP eventSEXP, SEXP stateSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<TargetedEvent> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type state(stateSEXP);
+    targeted_event_restore(event, state);
+    return R_NilValue;
+END_RCPP
+}
+// process_listener
+void process_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<listener_t> listener);
+RcppExport SEXP _individual_process_listener(SEXP eventSEXP, SEXP listenerSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<listener_t> >::type listener(listenerSEXP);
+    process_listener(event, listener);
+    return R_NilValue;
+END_RCPP
+}
+// process_targeted_listener
+void process_targeted_listener(const Rcpp::XPtr<Event> event, const Rcpp::XPtr<targeted_listener_t> listener, const Rcpp::XPtr<individual_index_t> target);
+RcppExport SEXP _individual_process_targeted_listener(SEXP eventSEXP, SEXP listenerSEXP, SEXP targetSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<Event> >::type event(eventSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<targeted_listener_t> >::type listener(listenerSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<individual_index_t> >::type target(targetSEXP);
+    process_targeted_listener(event, listener, target);
+    return R_NilValue;
+END_RCPP
+}
+// create_integer_variable
+Rcpp::XPtr<IntegerVariable> create_integer_variable(const std::vector<int>& values);
+RcppExport SEXP _individual_create_integer_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<int>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_integer_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_values
+const std::vector<int>& integer_variable_get_values(Rcpp::XPtr<IntegerVariable> variable);
+RcppExport SEXP _individual_integer_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_modulo_differences
+individual_index_t integer_variable_get_modulo_differences(Rcpp::XPtr<IntegerVariable> variable, const int value, const int difference);
+RcppExport SEXP _individual_integer_variable_get_modulo_differences(SEXP variableSEXP, SEXP valueSEXP, SEXP differenceSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< const int >::type difference(differenceSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_modulo_differences(variable, value, difference));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_values_at_index
+std::vector<int> integer_variable_get_values_at_index(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_variable_get_values_at_index(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_values_at_index_vector
+std::vector<int> integer_variable_get_values_at_index_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_index_of_set_vector
+Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values_set);
+RcppExport SEXP _individual_integer_variable_get_index_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type values_set(values_setSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_vector(variable, values_set));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_index_of_set_scalar
+Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int values_set);
+RcppExport SEXP _individual_integer_variable_get_index_of_set_scalar(SEXP variableSEXP, SEXP values_setSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type values_set(values_setSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_set_scalar(variable, values_set));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_index_of_range
+Rcpp::XPtr<individual_index_t> integer_variable_get_index_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
+RcppExport SEXP _individual_integer_variable_get_index_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_index_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_size_of_set_vector
+size_t integer_variable_get_size_of_set_vector(Rcpp::XPtr<IntegerVariable> variable, const std::vector<int> values_set);
+RcppExport SEXP _individual_integer_variable_get_size_of_set_vector(SEXP variableSEXP, SEXP values_setSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<int> >::type values_set(values_setSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_vector(variable, values_set));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_size_of_set_scalar
+size_t integer_variable_get_size_of_set_scalar(Rcpp::XPtr<IntegerVariable> variable, const int value);
+RcppExport SEXP _individual_integer_variable_get_size_of_set_scalar(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type value(valueSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_set_scalar(variable, value));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_get_size_of_range
+size_t integer_variable_get_size_of_range(Rcpp::XPtr<IntegerVariable> variable, const int a, const int b);
+RcppExport SEXP _individual_integer_variable_get_size_of_range(SEXP variableSEXP, SEXP aSEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const int >::type a(aSEXP);
+    Rcpp::traits::input_parameter< const int >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_variable_get_size_of_range(variable, a, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_variable_queue_fill
+void integer_variable_queue_fill(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value);
+RcppExport SEXP _individual_integer_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
+    integer_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_update
+void integer_variable_queue_update(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    integer_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_update_bitset
+void integer_variable_queue_update_bitset(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_extend
+void integer_variable_queue_extend(Rcpp::XPtr<IntegerVariable> variable, std::vector<int> values);
+RcppExport SEXP _individual_integer_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<int> >::type values(valuesSEXP);
+    integer_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_shrink
+void integer_variable_queue_shrink(Rcpp::XPtr<IntegerVariable> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    integer_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_variable_queue_shrink_bitset
+void integer_variable_queue_shrink_bitset(Rcpp::XPtr<IntegerVariable> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<IntegerVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// fixed_probability_multinomial_process_internal
+Rcpp::XPtr<process_t> fixed_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const double rate, const std::vector<double> destination_probabilities);
+RcppExport SEXP _individual_fixed_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rateSEXP, SEXP destination_probabilitiesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
+    Rcpp::traits::input_parameter< const double >::type rate(rateSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
+    rcpp_result_gen = Rcpp::wrap(fixed_probability_multinomial_process_internal(variable, source_state, destination_states, rate, destination_probabilities));
+    return rcpp_result_gen;
+END_RCPP
+}
+// multi_probability_multinomial_process_internal
+Rcpp::XPtr<process_t> multi_probability_multinomial_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string source_state, const std::vector<std::string> destination_states, const Rcpp::XPtr<DoubleVariable> rate_variable, const std::vector<double> destination_probabilities);
+RcppExport SEXP _individual_multi_probability_multinomial_process_internal(SEXP variableSEXP, SEXP source_stateSEXP, SEXP destination_statesSEXP, SEXP rate_variableSEXP, SEXP destination_probabilitiesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type source_state(source_stateSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::string> >::type destination_states(destination_statesSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<double> >::type destination_probabilities(destination_probabilitiesSEXP);
+    rcpp_result_gen = Rcpp::wrap(multi_probability_multinomial_process_internal(variable, source_state, destination_states, rate_variable, destination_probabilities));
+    return rcpp_result_gen;
+END_RCPP
+}
+// multi_probability_bernoulli_process_internal
+Rcpp::XPtr<process_t> multi_probability_bernoulli_process_internal(Rcpp::XPtr<CategoricalVariable> variable, const std::string from, const std::string to, const Rcpp::XPtr<DoubleVariable> rate_variable);
+RcppExport SEXP _individual_multi_probability_bernoulli_process_internal(SEXP variableSEXP, SEXP fromSEXP, SEXP toSEXP, SEXP rate_variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type from(fromSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type to(toSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<DoubleVariable> >::type rate_variable(rate_variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(multi_probability_bernoulli_process_internal(variable, from, to, rate_variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// infection_age_process_internal
+Rcpp::XPtr<process_t> infection_age_process_internal(Rcpp::XPtr<CategoricalVariable> state, const std::string susceptible, const std::string exposed, const std::string infectious, const Rcpp::XPtr<IntegerVariable> age, const int age_bins, const double p, const double dt, const Rcpp::NumericMatrix mixing);
+RcppExport SEXP _individual_infection_age_process_internal(SEXP stateSEXP, SEXP susceptibleSEXP, SEXP exposedSEXP, SEXP infectiousSEXP, SEXP ageSEXP, SEXP age_binsSEXP, SEXP pSEXP, SEXP dtSEXP, SEXP mixingSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<CategoricalVariable> >::type state(stateSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type susceptible(susceptibleSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type exposed(exposedSEXP);
+    Rcpp::traits::input_parameter< const std::string >::type infectious(infectiousSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::XPtr<IntegerVariable> >::type age(ageSEXP);
+    Rcpp::traits::input_parameter< const int >::type age_bins(age_binsSEXP);
+    Rcpp::traits::input_parameter< const double >::type p(pSEXP);
+    Rcpp::traits::input_parameter< const double >::type dt(dtSEXP);
+    Rcpp::traits::input_parameter< const Rcpp::NumericMatrix >::type mixing(mixingSEXP);
+    rcpp_result_gen = Rcpp::wrap(infection_age_process_internal(state, susceptible, exposed, infectious, age, age_bins, p, dt, mixing));
+    return rcpp_result_gen;
+END_RCPP
+}
+// create_double_ragged_variable
+Rcpp::XPtr<RaggedDouble> create_double_ragged_variable(const std::vector<std::vector<double>>& values);
+RcppExport SEXP _individual_create_double_ragged_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_double_ragged_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_values
+std::vector<std::vector<double>> double_ragged_variable_get_values(Rcpp::XPtr<RaggedDouble> variable);
+RcppExport SEXP _individual_double_ragged_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_values_at_index_bitset
+std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_values_at_index_vector
+std::vector<std::vector<double>> double_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_length
+std::vector<size_t> double_ragged_variable_get_length(Rcpp::XPtr<RaggedDouble> variable);
+RcppExport SEXP _individual_double_ragged_variable_get_length(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_length_at_index_bitset
+std::vector<size_t> double_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_get_length_at_index_vector
+std::vector<size_t> double_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_double_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(double_ragged_variable_get_length_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// double_ragged_variable_queue_fill
+void double_ragged_variable_queue_fill(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value);
+RcppExport SEXP _individual_double_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
+    double_ragged_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_update
+void double_ragged_variable_queue_update(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>>& value, std::vector<size_t> index);
+RcppExport SEXP _individual_double_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>>& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    double_ragged_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_update_bitset
+void double_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedDouble> variable, const std::vector<std::vector<double>> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<double>> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_ragged_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_extend
+void double_ragged_variable_queue_extend(Rcpp::XPtr<RaggedDouble> variable, std::vector<std::vector<double>>& values);
+RcppExport SEXP _individual_double_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<std::vector<double>>& >::type values(valuesSEXP);
+    double_ragged_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_shrink
+void double_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedDouble> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_double_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    double_ragged_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// double_ragged_variable_queue_shrink_bitset
+void double_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedDouble> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_double_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedDouble> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    double_ragged_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// create_integer_ragged_variable
+Rcpp::XPtr<RaggedInteger> create_integer_ragged_variable(const std::vector<std::vector<int>>& values);
+RcppExport SEXP _individual_create_integer_ragged_variable(SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type values(valuesSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_integer_ragged_variable(values));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_values
+std::vector<std::vector<int>> integer_ragged_variable_get_values(Rcpp::XPtr<RaggedInteger> variable);
+RcppExport SEXP _individual_integer_ragged_variable_get_values(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_values_at_index_bitset
+std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_values_at_index_vector
+std::vector<std::vector<int>> integer_ragged_variable_get_values_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_values_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_values_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_length
+std::vector<size_t> integer_ragged_variable_get_length(Rcpp::XPtr<RaggedInteger> variable);
+RcppExport SEXP _individual_integer_ragged_variable_get_length(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_length_at_index_bitset
+std::vector<size_t> integer_ragged_variable_get_length_at_index_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_bitset(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_get_length_at_index_vector
+std::vector<size_t> integer_ragged_variable_get_length_at_index_vector(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_get_length_at_index_vector(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    rcpp_result_gen = Rcpp::wrap(integer_ragged_variable_get_length_at_index_vector(variable, index));
+    return rcpp_result_gen;
+END_RCPP
+}
+// integer_ragged_variable_queue_fill
+void integer_ragged_variable_queue_fill(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value);
+RcppExport SEXP _individual_integer_ragged_variable_queue_fill(SEXP variableSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
+    integer_ragged_variable_queue_fill(variable, value);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_update
+void integer_ragged_variable_queue_update(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>>& value, std::vector<size_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_update(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>>& >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t> >::type index(indexSEXP);
+    integer_ragged_variable_queue_update(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_update_bitset
+void integer_ragged_variable_queue_update_bitset(Rcpp::XPtr<RaggedInteger> variable, const std::vector<std::vector<int>> value, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_update_bitset(SEXP variableSEXP, SEXP valueSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< const std::vector<std::vector<int>> >::type value(valueSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_ragged_variable_queue_update_bitset(variable, value, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_extend
+void integer_ragged_variable_queue_extend(Rcpp::XPtr<RaggedInteger> variable, std::vector<std::vector<int>>& values);
+RcppExport SEXP _individual_integer_ragged_variable_queue_extend(SEXP variableSEXP, SEXP valuesSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<std::vector<int>>& >::type values(valuesSEXP);
+    integer_ragged_variable_queue_extend(variable, values);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_shrink
+void integer_ragged_variable_queue_shrink(Rcpp::XPtr<RaggedInteger> variable, std::vector<size_t>& index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_shrink(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< std::vector<size_t>& >::type index(indexSEXP);
+    integer_ragged_variable_queue_shrink(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// integer_ragged_variable_queue_shrink_bitset
+void integer_ragged_variable_queue_shrink_bitset(Rcpp::XPtr<RaggedInteger> variable, Rcpp::XPtr<individual_index_t> index);
+RcppExport SEXP _individual_integer_ragged_variable_queue_shrink_bitset(SEXP variableSEXP, SEXP indexSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RaggedInteger> >::type variable(variableSEXP);
+    Rcpp::traits::input_parameter< Rcpp::XPtr<individual_index_t> >::type index(indexSEXP);
+    integer_ragged_variable_queue_shrink_bitset(variable, index);
+    return R_NilValue;
+END_RCPP
+}
+// create_render_vector
+Rcpp::XPtr<RenderVector> create_render_vector(std::vector<double> data);
+RcppExport SEXP _individual_create_render_vector(SEXP dataSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< std::vector<double> >::type data(dataSEXP);
+    rcpp_result_gen = Rcpp::wrap(create_render_vector(data));
+    return rcpp_result_gen;
+END_RCPP
+}
+// render_vector_update
+void render_vector_update(Rcpp::XPtr<RenderVector> v, size_t index, double value);
+RcppExport SEXP _individual_render_vector_update(SEXP vSEXP, SEXP indexSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
+    Rcpp::traits::input_parameter< size_t >::type index(indexSEXP);
+    Rcpp::traits::input_parameter< double >::type value(valueSEXP);
+    render_vector_update(v, index, value);
+    return R_NilValue;
+END_RCPP
+}
+// render_vector_data
+std::vector<double> render_vector_data(Rcpp::XPtr<RenderVector> v);
+RcppExport SEXP _individual_render_vector_data(SEXP vSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<RenderVector> >::type v(vSEXP);
+    rcpp_result_gen = Rcpp::wrap(render_vector_data(v));
+    return rcpp_result_gen;
+END_RCPP
+}
+// execute_process
+void execute_process(Rcpp::XPtr<process_t> process, size_t timestep);
+RcppExport SEXP _individual_execute_process(SEXP processSEXP, SEXP timestepSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<process_t> >::type process(processSEXP);
+    Rcpp::traits::input_parameter< size_t >::type timestep(timestepSEXP);
+    execute_process(process, timestep);
+    return R_NilValue;
+END_RCPP
+}
+// variable_get_size
+size_t variable_get_size(Rcpp::XPtr<Variable> variable);
+RcppExport SEXP _individual_variable_get_size(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
+    rcpp_result_gen = Rcpp::wrap(variable_get_size(variable));
+    return rcpp_result_gen;
+END_RCPP
+}
+// variable_update
+void variable_update(Rcpp::XPtr<Variable> variable);
+RcppExport SEXP _individual_variable_update(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
+    variable_update(variable);
+    return R_NilValue;
+END_RCPP
+}
+// variable_resize
+void variable_resize(Rcpp::XPtr<Variable> variable);
+RcppExport SEXP _individual_variable_resize(SEXP variableSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::XPtr<Variable> >::type variable(variableSEXP);
+    variable_resize(variable);
+    return R_NilValue;
+END_RCPP
+}
+
+// validate (ensure exported C++ functions exist before calling them)
+static int _individual_RcppExport_validate(const char* sig) { 
+    static std::set<std::string> signatures;
+    if (signatures.empty()) {
+        signatures.insert("void(*dummy)()");
+    }
+    return signatures.find(sig) != signatures.end();
+}
+
+// registerCCallable (register entry points for exported C++ functions)
+RcppExport SEXP _individual_RcppExport_registerCCallable() { 
+    R_RegisterCCallable("individual", "_individual_dummy", (DL_FUNC)_individual_dummy_try);
+    R_RegisterCCallable("individual", "_individual_RcppExport_validate", (DL_FUNC)_individual_RcppExport_validate);
+    return R_NilValue;
+}
+
+RcppExport SEXP run_testthat_tests(SEXP);
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_individual_create_bitset", (DL_FUNC) &_individual_create_bitset, 1},
+    {"_individual_bitset_copy", (DL_FUNC) &_individual_bitset_copy, 1},
+    {"_individual_bitset_insert", (DL_FUNC) &_individual_bitset_insert, 2},
+    {"_individual_bitset_remove", (DL_FUNC) &_individual_bitset_remove, 2},
+    {"_individual_bitset_clear", (DL_FUNC) &_individual_bitset_clear, 1},
+    {"_individual_bitset_size", (DL_FUNC) &_individual_bitset_size, 1},
+    {"_individual_bitset_max_size", (DL_FUNC) &_individual_bitset_max_size, 1},
+    {"_individual_bitset_and", (DL_FUNC) &_individual_bitset_and, 2},
+    {"_individual_bitset_not", (DL_FUNC) &_individual_bitset_not, 2},
+    {"_individual_bitset_or", (DL_FUNC) &_individual_bitset_or, 2},
+    {"_individual_bitset_copy_from", (DL_FUNC) &_individual_bitset_copy_from, 2},
+    {"_individual_bitset_xor", (DL_FUNC) &_individual_bitset_xor, 2},
+    {"_individual_bitset_set_difference", (DL_FUNC) &_individual_bitset_set_difference, 2},
+    {"_individual_bitset_sample", (DL_FUNC) &_individual_bitset_sample, 2},
+    {"_individual_bitset_sample_vector", (DL_FUNC) &_individual_bitset_sample_vector, 2},
+    {"_individual_bitset_to_vector", (DL_FUNC) &_individual_bitset_to_vector, 1},
+    {"_individual_filter_bitset_integer", (DL_FUNC) &_individual_filter_bitset_integer, 2},
+    {"_individual_filter_bitset_bitset", (DL_FUNC) &_individual_filter_bitset_bitset, 2},
+    {"_individual_filter_bitset_logical", (DL_FUNC) &_individual_filter_bitset_logical, 2},
+    {"_individual_bitset_choose", (DL_FUNC) &_individual_bitset_choose, 2},
+    {"_individual_bitset_count_and_cpp", (DL_FUNC) &_individual_bitset_count_and_cpp, 2},
+    {"_individual_create_categorical_variable", (DL_FUNC) &_individual_create_categorical_variable, 2},
+    {"_individual_categorical_variable_get_size", (DL_FUNC) &_individual_categorical_variable_get_size, 1},
+    {"_individual_categorical_variable_queue_update", (DL_FUNC) &_individual_categorical_variable_queue_update, 3},
+    {"_individual_categorical_variable_get_index_of", (DL_FUNC) &_individual_categorical_variable_get_index_of, 2},
+    {"_individual_categorical_variable_get_size_of", (DL_FUNC) &_individual_categorical_variable_get_size_of, 2},
+    {"_individual_categorical_variable_get_categories", (DL_FUNC) &_individual_categorical_variable_get_categories, 1},
+    {"_individual_categorical_variable_queue_update_vector", (DL_FUNC) &_individual_categorical_variable_queue_update_vector, 3},
+    {"_individual_categorical_variable_update", (DL_FUNC) &_individual_categorical_variable_update, 1},
+    {"_individual_categorical_variable_queue_extend", (DL_FUNC) &_individual_categorical_variable_queue_extend, 2},
+    {"_individual_categorical_variable_queue_shrink", (DL_FUNC) &_individual_categorical_variable_queue_shrink, 2},
+    {"_individual_categorical_variable_queue_shrink_bitset", (DL_FUNC) &_individual_categorical_variable_queue_shrink_bitset, 2},
+    {"_individual_categorical_variable_get_values", (DL_FUNC) &_individual_categorical_variable_get_values, 1},
+    {"_individual_categorical_variable_get_values_with_index", (DL_FUNC) &_individual_categorical_variable_get_values_with_index, 2},
+    {"_individual_dummy", (DL_FUNC) &_individual_dummy, 0},
+    {"_individual_create_double_variable", (DL_FUNC) &_individual_create_double_variable, 1},
+    {"_individual_double_variable_get_values", (DL_FUNC) &_individual_double_variable_get_values, 1},
+    {"_individual_double_variable_get_values_at_index", (DL_FUNC) &_individual_double_variable_get_values_at_index, 2},
+    {"_individual_double_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_variable_get_values_at_index_vector, 2},
+    {"_individual_double_variable_get_index_of_range", (DL_FUNC) &_individual_double_variable_get_index_of_range, 3},
+    {"_individual_double_variable_get_size_of_range", (DL_FUNC) &_individual_double_variable_get_size_of_range, 3},
+    {"_individual_double_variable_queue_fill", (DL_FUNC) &_individual_double_variable_queue_fill, 2},
+    {"_individual_double_variable_queue_update", (DL_FUNC) &_individual_double_variable_queue_update, 3},
+    {"_individual_double_variable_queue_update_bitset", (DL_FUNC) &_individual_double_variable_queue_update_bitset, 3},
+    {"_individual_double_variable_queue_extend", (DL_FUNC) &_individual_double_variable_queue_extend, 2},
+    {"_individual_double_variable_queue_shrink", (DL_FUNC) &_individual_double_variable_queue_shrink, 2},
+    {"_individual_double_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_variable_queue_shrink_bitset, 2},
+    {"_individual_create_event", (DL_FUNC) &_individual_create_event, 0},
+    {"_individual_create_targeted_event", (DL_FUNC) &_individual_create_targeted_event, 1},
+    {"_individual_event_base_tick", (DL_FUNC) &_individual_event_base_tick, 1},
+    {"_individual_event_base_get_timestep", (DL_FUNC) &_individual_event_base_get_timestep, 1},
+    {"_individual_event_base_set_timestep", (DL_FUNC) &_individual_event_base_set_timestep, 2},
+    {"_individual_event_base_should_trigger", (DL_FUNC) &_individual_event_base_should_trigger, 1},
+    {"_individual_event_schedule", (DL_FUNC) &_individual_event_schedule, 2},
+    {"_individual_event_clear_schedule", (DL_FUNC) &_individual_event_clear_schedule, 1},
+    {"_individual_event_checkpoint", (DL_FUNC) &_individual_event_checkpoint, 1},
+    {"_individual_event_restore", (DL_FUNC) &_individual_event_restore, 2},
+    {"_individual_targeted_event_clear_schedule_vector", (DL_FUNC) &_individual_targeted_event_clear_schedule_vector, 2},
+    {"_individual_targeted_event_clear_schedule", (DL_FUNC) &_individual_targeted_event_clear_schedule, 2},
+    {"_individual_targeted_event_get_scheduled", (DL_FUNC) &_individual_targeted_event_get_scheduled, 1},
+    {"_individual_targeted_event_schedule", (DL_FUNC) &_individual_targeted_event_schedule, 3},
+    {"_individual_targeted_event_queue_shrink_bitset", (DL_FUNC) &_individual_targeted_event_queue_shrink_bitset, 2},
+    {"_individual_targeted_event_queue_shrink", (DL_FUNC) &_individual_targeted_event_queue_shrink, 2},
+    {"_individual_targeted_event_queue_extend", (DL_FUNC) &_individual_targeted_event_queue_extend, 2},
+    {"_individual_targeted_event_queue_extend_with_schedule", (DL_FUNC) &_individual_targeted_event_queue_extend_with_schedule, 2},
+    {"_individual_targeted_event_schedule_vector", (DL_FUNC) &_individual_targeted_event_schedule_vector, 3},
+    {"_individual_targeted_event_schedule_multi_delay", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay, 3},
+    {"_individual_targeted_event_schedule_multi_delay_vector", (DL_FUNC) &_individual_targeted_event_schedule_multi_delay_vector, 3},
+    {"_individual_targeted_event_get_target", (DL_FUNC) &_individual_targeted_event_get_target, 1},
+    {"_individual_targeted_event_resize", (DL_FUNC) &_individual_targeted_event_resize, 1},
+    {"_individual_targeted_event_checkpoint", (DL_FUNC) &_individual_targeted_event_checkpoint, 1},
+    {"_individual_targeted_event_restore", (DL_FUNC) &_individual_targeted_event_restore, 2},
+    {"_individual_process_listener", (DL_FUNC) &_individual_process_listener, 2},
+    {"_individual_process_targeted_listener", (DL_FUNC) &_individual_process_targeted_listener, 3},
+    {"_individual_create_integer_variable", (DL_FUNC) &_individual_create_integer_variable, 1},
+    {"_individual_integer_variable_get_values", (DL_FUNC) &_individual_integer_variable_get_values, 1},
+    {"_individual_integer_variable_get_modulo_differences", (DL_FUNC) &_individual_integer_variable_get_modulo_differences, 3},
+    {"_individual_integer_variable_get_values_at_index", (DL_FUNC) &_individual_integer_variable_get_values_at_index, 2},
+    {"_individual_integer_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_variable_get_values_at_index_vector, 2},
+    {"_individual_integer_variable_get_index_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_index_of_set_vector, 2},
+    {"_individual_integer_variable_get_index_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_index_of_set_scalar, 2},
+    {"_individual_integer_variable_get_index_of_range", (DL_FUNC) &_individual_integer_variable_get_index_of_range, 3},
+    {"_individual_integer_variable_get_size_of_set_vector", (DL_FUNC) &_individual_integer_variable_get_size_of_set_vector, 2},
+    {"_individual_integer_variable_get_size_of_set_scalar", (DL_FUNC) &_individual_integer_variable_get_size_of_set_scalar, 2},
+    {"_individual_integer_variable_get_size_of_range", (DL_FUNC) &_individual_integer_variable_get_size_of_range, 3},
+    {"_individual_integer_variable_queue_fill", (DL_FUNC) &_individual_integer_variable_queue_fill, 2},
+    {"_individual_integer_variable_queue_update", (DL_FUNC) &_individual_integer_variable_queue_update, 3},
+    {"_individual_integer_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_variable_queue_update_bitset, 3},
+    {"_individual_integer_variable_queue_extend", (DL_FUNC) &_individual_integer_variable_queue_extend, 2},
+    {"_individual_integer_variable_queue_shrink", (DL_FUNC) &_individual_integer_variable_queue_shrink, 2},
+    {"_individual_integer_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_variable_queue_shrink_bitset, 2},
+    {"_individual_fixed_probability_multinomial_process_internal", (DL_FUNC) &_individual_fixed_probability_multinomial_process_internal, 5},
+    {"_individual_multi_probability_multinomial_process_internal", (DL_FUNC) &_individual_multi_probability_multinomial_process_internal, 5},
+    {"_individual_multi_probability_bernoulli_process_internal", (DL_FUNC) &_individual_multi_probability_bernoulli_process_internal, 4},
+    {"_individual_infection_age_process_internal", (DL_FUNC) &_individual_infection_age_process_internal, 9},
+    {"_individual_create_double_ragged_variable", (DL_FUNC) &_individual_create_double_ragged_variable, 1},
+    {"_individual_double_ragged_variable_get_values", (DL_FUNC) &_individual_double_ragged_variable_get_values, 1},
+    {"_individual_double_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_bitset, 2},
+    {"_individual_double_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_values_at_index_vector, 2},
+    {"_individual_double_ragged_variable_get_length", (DL_FUNC) &_individual_double_ragged_variable_get_length, 1},
+    {"_individual_double_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_bitset, 2},
+    {"_individual_double_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_double_ragged_variable_get_length_at_index_vector, 2},
+    {"_individual_double_ragged_variable_queue_fill", (DL_FUNC) &_individual_double_ragged_variable_queue_fill, 2},
+    {"_individual_double_ragged_variable_queue_update", (DL_FUNC) &_individual_double_ragged_variable_queue_update, 3},
+    {"_individual_double_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_update_bitset, 3},
+    {"_individual_double_ragged_variable_queue_extend", (DL_FUNC) &_individual_double_ragged_variable_queue_extend, 2},
+    {"_individual_double_ragged_variable_queue_shrink", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink, 2},
+    {"_individual_double_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_double_ragged_variable_queue_shrink_bitset, 2},
+    {"_individual_create_integer_ragged_variable", (DL_FUNC) &_individual_create_integer_ragged_variable, 1},
+    {"_individual_integer_ragged_variable_get_values", (DL_FUNC) &_individual_integer_ragged_variable_get_values, 1},
+    {"_individual_integer_ragged_variable_get_values_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_bitset, 2},
+    {"_individual_integer_ragged_variable_get_values_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_values_at_index_vector, 2},
+    {"_individual_integer_ragged_variable_get_length", (DL_FUNC) &_individual_integer_ragged_variable_get_length, 1},
+    {"_individual_integer_ragged_variable_get_length_at_index_bitset", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_bitset, 2},
+    {"_individual_integer_ragged_variable_get_length_at_index_vector", (DL_FUNC) &_individual_integer_ragged_variable_get_length_at_index_vector, 2},
+    {"_individual_integer_ragged_variable_queue_fill", (DL_FUNC) &_individual_integer_ragged_variable_queue_fill, 2},
+    {"_individual_integer_ragged_variable_queue_update", (DL_FUNC) &_individual_integer_ragged_variable_queue_update, 3},
+    {"_individual_integer_ragged_variable_queue_update_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_update_bitset, 3},
+    {"_individual_integer_ragged_variable_queue_extend", (DL_FUNC) &_individual_integer_ragged_variable_queue_extend, 2},
+    {"_individual_integer_ragged_variable_queue_shrink", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink, 2},
+    {"_individual_integer_ragged_variable_queue_shrink_bitset", (DL_FUNC) &_individual_integer_ragged_variable_queue_shrink_bitset, 2},
+    {"_individual_create_render_vector", (DL_FUNC) &_individual_create_render_vector, 1},
+    {"_individual_render_vector_update", (DL_FUNC) &_individual_render_vector_update, 3},
+    {"_individual_render_vector_data", (DL_FUNC) &_individual_render_vector_data, 1},
+    {"_individual_execute_process", (DL_FUNC) &_individual_execute_process, 2},
+    {"_individual_variable_get_size", (DL_FUNC) &_individual_variable_get_size, 1},
+    {"_individual_variable_update", (DL_FUNC) &_individual_variable_update, 1},
+    {"_individual_variable_resize", (DL_FUNC) &_individual_variable_resize, 1},
+    {"_individual_RcppExport_registerCCallable", (DL_FUNC) &_individual_RcppExport_registerCCallable, 0},
+    {"run_testthat_tests", (DL_FUNC) &run_testthat_tests, 1},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_individual(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}
diff --git a/src/bitset.cpp b/src/bitset.cpp
index aec4f9b..a539c7d 100644
--- a/src/bitset.cpp
+++ b/src/bitset.cpp
@@ -203,3 +203,11 @@ void bitset_choose(
 ) {
     bitset_choose_internal(*b, k);
 }
+
+//[[Rcpp::export]]
+size_t bitset_count_and_cpp(
+        const Rcpp::XPtr<individual_index_t> a,
+        const Rcpp::XPtr<individual_index_t> b
+) {
+    return a->count_and(*b);
+}
diff --git a/tests/testthat/test-bitset.R b/tests/testthat/test-bitset.R
index 888bdce..b5f6a08 100644
--- a/tests/testthat/test-bitset.R
+++ b/tests/testthat/test-bitset.R
@@ -438,3 +438,41 @@ test_that("bitset is not equal to other types", {
   a$insert(c(1,4,5))
   expect_equal(all.equal(a, c(1,4,5)), "'current' is not a Bitset")
 })
+
+test_that("bitset_count_and can return the the count of overlapping betsets", {
+  a <- Bitset$new(10)$insert(c(1,4,5))
+  b <- Bitset$new(10)$insert(c(4,6,9))
+  c <- Bitset$new(10)$insert(c(4,5,9))
+  d <- Bitset$new(10)$insert(c(1,4,5,9))
+  expect_equal(bitset_count_and(a, b), 1)
+  expect_equal(bitset_count_and(a, c), 2)
+  expect_equal(bitset_count_and(a, d), 3)
+})
+
+test_that("bitset_count_and returns 0 for non-overlapping betsets", {
+  a <- Bitset$new(10)$insert(c(1,4,5))
+  b <- Bitset$new(10)$insert(c(2,6,9))
+  expect_equal(bitset_count_and(a, b), 0)
+})
+
+test_that("bitset_count_and doesn't mutate", {
+  a <- Bitset$new(10)$insert(c(1,4,5))
+  b <- Bitset$new(10)$insert(c(4,6,9))
+  c <- a$copy()
+  d <- b$copy()
+  bitset_count_and(a, b)
+  expect_equal(a, c)
+  expect_equal(b, d)
+})
+
+test_that("bitset_count_and doesn't work for differing sizes", {
+  a <- Bitset$new(10)$insert(c(1,4,5))
+  b <- Bitset$new(15)$insert(c(4,6,9))
+  c <- a$copy()
+  d <- b$copy()
+  expect_error(
+    bitset_count_and(a, b),
+    'Incompatible bitmap sizes'
+  )
+})
+

From 4289227848a6792c89896fa573409ee351553498 Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Tue, 12 Aug 2025 10:25:15 +0100
Subject: [PATCH 10/13] Fix Rcpp bug

---
 R/RcppExports.R     | 2 +-
 src/RcppExports.cpp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/RcppExports.R b/R/RcppExports.R
index 354ab8f..f0788dc 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -511,5 +511,5 @@ variable_resize <- function(variable) {
 
 # Register entry points for exported C++ functions
 methods::setLoadAction(function(ns) {
-    .Call('_individual_RcppExport_registerCCallable', PACKAGE = 'individual')
+    .Call(`_individual_RcppExport_registerCCallable`)
 })
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 4c34b84..63a7f8c 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -424,7 +424,7 @@ RcppExport SEXP _individual_dummy() {
     if (rcpp_isError_gen) {
         SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
         UNPROTECT(1);
-        Rf_error(CHAR(rcpp_msgSEXP_gen));
+        Rf_error("%s", CHAR(rcpp_msgSEXP_gen));
     }
     UNPROTECT(1);
     return rcpp_result_gen;

From 1cd669a629e7397e3b1c6e5417eecf8e3513d746 Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Tue, 12 Aug 2025 10:27:17 +0100
Subject: [PATCH 11/13] Update documentation and namespace

---
 NAMESPACE               |  1 +
 man/bitset_count_and.Rd | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 man/bitset_count_and.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 687b7c4..8017a4d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,7 @@ export(RaggedInteger)
 export(Render)
 export(TargetedEvent)
 export(bernoulli_process)
+export(bitset_count_and)
 export(categorical_count_renderer_process)
 export(filter_bitset)
 export(fixed_probability_multinomial_process)
diff --git a/man/bitset_count_and.Rd b/man/bitset_count_and.Rd
new file mode 100644
index 0000000..58165b6
--- /dev/null
+++ b/man/bitset_count_and.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bitset.R
+\name{bitset_count_and}
+\alias{bitset_count_and}
+\title{Count bitset and}
+\usage{
+bitset_count_and(a, b)
+}
+\arguments{
+\item{a}{a \code{\link{Bitset}}}
+
+\item{b}{another \code{\link{Bitset}}}
+}
+\description{
+This non-modifying function returns the number of intersecting
+elements between two bitsets \code{a} and \code{b}. This should be faster than
+writing \code{a$copy()$and(b)$size()} as it avoids the memory allocations of $copy().
+}

From 088730e2740e4ab8dfd4e33c6d1eaacfe39b4e18 Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Tue, 12 Aug 2025 10:31:42 +0100
Subject: [PATCH 12/13] Update pkgdown

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 1283d2a..b889b3a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -12,6 +12,7 @@ reference:
   - RaggedDouble
   - Bitset
   - filter_bitset
+  - bitset_count_and
 - title: "Events & Rendering"
   desc: "Classes for events and rendering output."
 - contents:

From 79acafd344aa08819890b3243c30bfdbd2fef7df Mon Sep 17 00:00:00 2001
From: Giovanni Charles <giovanni.charles@gmail.com>
Date: Tue, 12 Aug 2025 10:42:13 +0100
Subject: [PATCH 13/13] Bump version and update news for 0.1.18

---
 DESCRIPTION | 2 +-
 NEWS.md     | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 05ef975..c21f32d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: individual
 Title: Framework for Specifying and Simulating Individual Based Models
-Version: 0.1.17
+Version: 0.1.18
 Authors@R: c(
   person(
     given = "Giovanni",
diff --git a/NEWS.md b/NEWS.md
index 8763718..04baa27 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# individual 0.1.18
+
+  * add $get_values to CategoricalVariable
+  * add $get_modulo_differences to IntegerVariable
+  * add bitset_count_and for quick intersection counts
+
 # individual 0.1.17
 
   * Add a `copy_from` method to the `Bitset` class.