library(breedTools)
context("Testing each of 2 main functions (in different ways) with a subset of Yorkshire data")
load("dat_for_breedTools_test.RData")
test <- solve_composition(Y8K_sample, X8K)
test_that("solve_composition returns proper class", {
expect_is(test, "matrix")
})
test_that("solve_composition computes expected column means", {
expect_equal(unname(round(colMeans(test)[1], 5)), 0.01225)
expect_equal(unname(round(colMeans(test)[2], 5)), 0.01745)
expect_equal(unname(round(colMeans(test)[3], 5)), 0.03085)
expect_equal(unname(round(colMeans(test)[4], 5)), 0.93945)
expect_equal(unname(round(colMeans(test)[5], 5)), 0.39806)
})
test_w_ped <- solve_composition(Y8K_sample, X8K,
ped = yorkshirePed)
test_that("sim_composition with ped option returns proper class", {
expect_is(test_w_ped, "matrix")
})
test_that("solve_composition with ped option computes expected column means", {
expect_equal(unname(round(colMeans(test_w_ped)[1], 5)), 0.04142)
expect_equal(unname(round(colMeans(test_w_ped)[2], 5)), 0.00399)
expect_equal(unname(round(colMeans(test_w_ped)[3], 5)), 0.02582)
expect_equal(unname(round(colMeans(test_w_ped)[4], 5)), 0.92878)
expect_equal(unname(round(colMeans(test_w_ped)[5], 5)), 0.27156)
})
test_w_ped_mia <- solve_composition(Y8K_sample, X8K,
ped = yorkshirePed,
mia = TRUE)
test_that("mia argument gives expected allele codings and output", {
expect_equal(ncol(test_w_ped_mia), ncol(Y8K_sample))
expect_true(names(table(test_w_ped_mia))[1] %in% c("?", "0", "0.5", "1"))
expect_true(names(table(test_w_ped_mia))[2] %in% c("?", "0", "0.5", "1"))
expect_true(names(table(test_w_ped_mia))[3] %in% c("?", "0", "0.5", "1"))
expect_true(names(table(test_w_ped_mia))[4] %in% c("?", "0", "0.5", "1"))
})
test_w_group <- solve_composition(Y8K_sample, X8K,
groups = list("Yorkshire" = rownames(Y8K_sample)[1:50],
"Landrace" = rownames(Y8K_sample)[51:100]))
test_that("sim_composition with group option returns proper class", {
expect_is(test_w_group, "list")
})
test_that("sim_composition stops since only one breed is provided", {
expect_error(sim_composition(Y8K_sample, X8K, rep = 5, par1 = list("Yorkshire" = rownames(Y8K_sample))),
"There must be at least two breeds to choose from")
})
test_that("sim_composition returns proper class", {
expect_is(sim_composition(Y8K_sample, X8K, rep = 5,
par1 = list("Yorkshire" = rownames(Y8K_sample)[1:50],
"Landrace" = rownames(Y8K_sample)[51:100])),
"matrix")
})
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