################################################################################
context("MISSING_VALUES")
res <- list()
tol <- 1e-5
for (ext in c("bed", "lfmm", "pcadapt")) {
file_path <- system.file("extdata",
paste0("missing.", ext),
package = "pcadapt")
if (ext == "bed") {
tmp_file <- file_path
} else {
tmp_file <- tempfile(fileext = paste0(".", ext))
file.copy(file_path, tmp_file)
}
x <- read.pcadapt(tmp_file, type = ext)
res[[ext]] <- pcadapt(x, K = 5)
}
testthat::expect_equal(res[["bed"]]["scores"], res[["lfmm"]]["scores"],
tolerance = tol)
testthat::expect_equal(res[["bed"]]["scores"], res[["pcadapt"]]["scores"],
tolerance = tol)
testthat::expect_equal(res[["lfmm"]]["scores"], res[["pcadapt"]]["scores"],
tolerance = tol)
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