tests/testthat/test_read_individual_genomes.R

In rscherrer/speciomer: Import Speciome Data into R

root <- system.file("extdata", "sim-indiv-genomes", package = "speciomer")

test_that("Read individual genomes", {

  data <- read_individual_genomes(root)
  expect_true("haplotype1" %in% colnames(data))
  population_sizes <- read_binary(paste0(root, "/population_sizes.dat"))
  nloci <- sum(read_parameters(root)[["nvertices"]])
  expect_equal(nrow(data), sum(population_sizes) *  nloci)

})

test_that("Read individual genomes with individual metadata", {

  data <- suppressMessages(read_individual_genomes(root, "individual_ecotypes"))
  expect_true("ecotype" %in% colnames(data))

})

test_that("Read individual genomes with locus metadata", {

  data <- suppressMessages(read_individual_genomes(root, locus_variables = "locus_Fst"))
  expect_true("Fst" %in% colnames(data))

})

test_that("Read individual genomes with genetic architecture only", {

  data <- suppressMessages(read_individual_genomes(root, locus_architecture = TRUE))
  expect_true("effect" %in% colnames(data))

})