tests/testthat/test-relabund.R

In bpbond/nmrrr: Binning and Visualizing NMR Spectra in Environmental Samples

test_that("relabund works", {

  # Handles bad method
  expect_error(nmr_relabund(dat = 1, method = "not_valid"),
    regexp = "Available methods"
  )

  # AUC: expected data format
  spectra_test <- nmr_import_spectra(
    path = "compdata/spectra_mnova",
    method = "mnova", quiet = TRUE
  )
  spectra_binset <- nmr_assign_bins(
    dat = spectra_test,
    binset = bins_Clemente2012
  )
  x <- nmr_relabund(dat = spectra_binset, method = "AUC")

  expect_s3_class(x, "data.frame")
  expect_named(x, expected = c("sampleID", "group", "relabund"))
  expect_type(x$sampleID, "character")
  expect_type(x$group, "character")
  expect_type(x$relabund, "double")

  # ...each group should sum to ~100
  vals <- sapply(split(x$relabund, x$sampleID), sum)
  expect_true(all(vals - 100.0 < 1e-6))

  # peaks: handles bad data
  expect_error(nmr_relabund(dat = spectra_binset, method = "peaks"),
    regexp = "No 'Area' column"
  )

  # peaks/single: expected data format
  single_dir <- "compdata/peaks_mnova_single"
  single_test <- nmr_import_peaks(
    path = single_dir,
    method = "single column", quiet = TRUE
  )
  single_binset <- nmr_assign_bins(
    dat = single_test,
    binset = bins_Clemente2012
  )
  x <- nmr_relabund(dat = single_binset, method = "peaks")

  expect_s3_class(x, "data.frame")
  expect_named(x, expected = c("sampleID", "group", "relabund"))
  expect_type(x$sampleID, "character")
  expect_type(x$group, "character")
  expect_type(x$relabund, "double")

  # ...each group should sum to ~100
  vals <- sapply(split(x$relabund, x$sampleID), sum)
  expect_true(all(vals - 100.0 < 1e-6))
})