adding get_values to CategoricalVariable and making a new function for IntegrerVariable

[JasonRWood]

This PR adds the get_values function to variables of the type CategoricalVariable and a new function called get_modulo_differences to variables of the type IntegerVariable.

get_modulo_differences is designed to be used in future work where individuals within host dynamics may only want to be updated every N timesteps.

get_values has been added to CategoricalVariable to be able to follow the changes that occur for a given individual more easily.

[giovannic]

Wonderful. I would add some simple tests to protect this code from future changes. Something like:

in test-categoricalvariable.R

test_that("CategoricalVariables returns correct values", {
  categories = c('S', 'S', 'R', 'I')

  # standard case
  variable <- CategoricalVariable$new(SIR, categories)
  expect_equal(categories$get_values(), categories)

  # empty case
  variable <- CategoricalVariable$new(SIR, c())
  expect_equal(variable$get_values(), c())
})

test_that("CategoricalVariables returns correct values after update", {
  categories = c('S', 'S', 'R', 'I')

  # standard case
  variable <- CategoricalVariable$new(SIR, categories)
  variable$queue_update(1, 'I')
  variable$.update()
  expect_equal(variable$get_values(), c('I', 'S', 'R', 'I'))
})

# perhaps in here: https://github.com/mrc-ide/individual/blob/dev/tests/testthat/test-categoricalvariable-resize.R
test_that("CategoricalVariables returns correct values after resize", {
  categories = c('S', 'S', 'R', 'I')

  # standard case
  variable <- CategoricalVariable$new(SIR, categories)
  x$queue_extend(values = rep('I', 2))
  x.resize()
  expect_equal(variable$get_values(), c(categories, rep('I', 2)))
})

And for integer variable tests

test_that("IntegerVariables returns correct modulo differences", {
  #...
  expect_equal(variable$get_modulo_differences(x, d)$to_vector(), expected_modulo_differences)
})

test_that("IntegerVariables errors for invalid modulo differences", {
  #...
  expect_error(variable$get_modulo_differences(x, -1))
  expect_error(variable$get_modulo_differences(wrong_sized_values, d))
})

And finally, please run devtools::document() in the root directory and commit the updated documentation so that it appears on the website when this merges!

[giovannic]

I've approved, but please remove the comment and extra unnecessary checks before merging (I've pointed them out as suggestions). Thank you!

[giovannic]

Interesting, why is all this diffed?

[giovannic]

My guess is that your git is changing all the hiddne line endings

I would recommend this in the future: git config --system core.autocrlf false

Stack overflow for context

[JasonRWood]

Thanks for the fix