tests/testthat/test_missing.R

In bcm-uga/pcadapt: Fast Principal Component Analysis for Outlier Detection

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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)