v0.1.18

.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
@@ -43,7 +42,7 @@ 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') }}

.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') }}

.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') }}

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",
@@ -65,7 +65,7 @@ Suggests:
     testthat (>= 2.1.0),
     xml2,
     bench
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 LinkingTo:
   Rcpp,

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)

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.

R/RcppExports.R

@@ -81,6 +81,10 @@ 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)
 }
@@ -125,6 +129,14 @@ 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)
 }
@@ -289,6 +301,10 @@ 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)
 }

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)
+}

R/categorical_variable.R

@@ -43,6 +43,20 @@ 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 = NULL) {
+      stopifnot(is.finite(index))
+      stopifnot(index > 0)
+      if (length(index) == 0){
+        results <- categorical_variable_get_values(self$.variable)
+      }
+      else{
+        results <- categorical_variable_get_values_with_index(self$.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

R/integer_variable.R

@@ -39,6 +39,17 @@ 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){
+      stopifnot(is.finite(value))
+      stopifnot(is.finite(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}

_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:

inst/include/CategoricalVariable.h

@@ -52,6 +52,8 @@ 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>&);
+    virtual std::vector<std::string> get_values();
 };
 
 
@@ -228,5 +230,46 @@ 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;
+}
+//' @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_ */

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

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()) {