Nothing
prefix <- tempdir()
# prefix <- "tests/testthat/" # nolint
library(data.table)
test_that(
desc = "correct functioning of BiasCorrection, data type 1",
code = {
local_edition(3)
local_reproducible_output(rstudio = TRUE)
plotdir <- paste0(prefix, "/plotdir/")
csvdir <- paste0(prefix, "/csvdir/")
b1 <- biascorrection(
experimental = "./testdata/exp_type_1.csv",
calibration = "./testdata/cal_type_1.csv",
samplelocusname = "Testlocus",
minmax = FALSE,
correct_method = "hyperbolic",
selection_method = "SSE",
type = 1,
plotdir = plotdir,
csvdir = csvdir,
logfilename = paste0(prefix, "/log.txt"),
seed = 1234,
parallel = FALSE
)
expect_length(list.files(plotdir), 50)
expect_length(list.files(csvdir), 13)
options(rBiasCorrection.nls_implementation = "GN.guess")
b2 <- biascorrection(
experimental = "./testdata/exp_type_1.csv",
calibration = "./testdata/cal_type_1.csv",
samplelocusname = "Testlocus",
minmax = FALSE,
correct_method = "hyperbolic",
selection_method = "SSE",
type = 1,
plotdir = plotdir,
csvdir = csvdir,
logfilename = paste0(prefix, "/log.txt"),
seed = 1234,
parallel = FALSE
)
expect_equal(
object = b1$final_results,
expected = b2$final_results,
tolerance = 1e-3
)
options(rBiasCorrection.nls_implementation = "LM")
b3 <- biascorrection(
experimental = "./testdata/exp_type_1.csv",
calibration = "./testdata/cal_type_1.csv",
samplelocusname = "Testlocus",
minmax = FALSE,
correct_method = "hyperbolic",
selection_method = "SSE",
type = 1,
plotdir = plotdir,
csvdir = csvdir,
logfilename = paste0(prefix, "/log.txt"),
seed = 1234,
parallel = FALSE
)
expect_equal(
object = b1$final_results,
expected = b3$final_results,
tolerance = 2e-1
)
# reset
options(rBiasCorrection.nls_implementation = "GN.paper")
# cleanup
expect_silent(clean_up(plotdir = plotdir,
csvdir = csvdir))
expect_true(file.remove(paste0(prefix, "/log.txt")))
})
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