tests/testthat/test-fst.R

In thijsjanzen/isoSIM: Simulate Linkage Disequilibrium Along Chromosomes in Isofemale Lines

context("fst")

testthat::test_that("fst", {
  pop_size <- 100
  number_of_founders <- 20
  run_time <- 1
  morgan <- 1

  pop1 <- create_population(pop_size, number_of_founders,
                            run_time, morgan, 42)

  pop2 <- create_population(pop_size, number_of_founders,
                            run_time, morgan, 24)

  pop2 <- increase_ancestor(pop2, number_of_founders)

  testthat::expect_true(verify_population(pop1))
  testthat::expect_true(verify_population(pop2))

  number_of_markers <- 100
  sampled_individuals <- 10
  v1 <- calculate_fst(pop1, pop2,
                      sampled_individuals,
                      number_of_markers, random_markers = TRUE)

  v2 <- calculate_fst(pop1, pop2,
                      sampled_individuals,
                      number_of_markers, random_markers = FALSE)

  testthat::expect_equal(v1, v2, tolerance = 0.05)

  pop_size <- 100
  number_of_founders <- 10
  run_time <- 10000
  morgan <- 1
  overlap <- 0.0

  pop1 <- create_population(pop_size, number_of_founders,
                            run_time, morgan, 42)

  pop2 <- create_population(pop_size, number_of_founders,
                            run_time, morgan, 24)
  pop2 <- increase_ancestor(pop2, number_of_founders)

  testthat::expect_true(verify_population(pop1))
  testthat::expect_true(verify_population(pop2))

  number_of_markers <- 100
  v1 <- calculate_fst(pop1, pop2,
                      number_of_markers, random_markers = TRUE)

  testthat::expect_equal(1.0, v1, tolerance = 0.01)
})

testthat::test_that("random markers", {
  set.seed(42)
  create_random_markers(1e3)
  create_random_markers(1e6)
})