tests/testthat/test-junctions.R

In thijsjanzen/GenomeAdmixR: Simulate Admixture of Genomes

test_that("expected_number_junctions", {
  testthat::skip_on_os("solaris")
  cat("test_junctions")

  if (requireNamespace("junctions")) {

    test_expected_junction_number <- function(pop_size,
                                              run_time,
                                              morgan,
                                              replicates) {
      found <- c()
      for (r in 1:replicates) {
        vx <- simulate_admixture(module = ancestry_module(morgan = morgan),
                                 pop_size = pop_size,
                                 total_runtime = run_time)

        junct <- calculate_dist_junctions(vx$population)
        found <- c(found, mean(junct))
      }

      require(junctions)
      expected <- junctions::number_of_junctions(N = pop_size,
                                                 H_0 = 0.5,
                                                 C = morgan,
                                                 t = run_time)

      testthat::expect_equal(mean(found), expected, tolerance = 1)
    }

    used_pop_size <- 1000
    # reduce pop size on CRAN
    if ( !identical(Sys.getenv("NOT_CRAN"), "true") ) {
      used_pop_size <- 100
    }

    test_expected_junction_number(pop_size = used_pop_size, run_time = 20,
                                  morgan = 1, replicates = 100)

    test_expected_junction_number(pop_size = used_pop_size, run_time = 20,
                                  morgan = 0.5, replicates = 100)

    test_expected_junction_number(pop_size = used_pop_size, run_time = 20,
                                  morgan = 3, replicates = 100)

    vx <- simulate_admixture(pop_size = used_pop_size,
                             total_runtime = 5)

    plot_dist_junctions(vx$population)
  }
})