tests/testthat/test-calculate_diversities.R

In hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

# test calculate diversities ---------------------------------------------------
data(P_sojae_survey)
diversities <- calculate_diversities(
  x = P_sojae_survey,
  cutoff = 60,
  control = "susceptible",
  sample = "Isolate",
  gene = "Rps",
  perc_susc = "perc.susc"
)

test_that("calculate_diversities() works properly", {
  expect_s3_class(diversities, "hagis.diversities")
  expect_length(diversities, 9)
  expect_named(
    diversities,
    c(
      "individual_pathotypes",
      "table_of_pathotypes",
      "number_of_samples",
      "number_of_pathotypes",
      "Simple",
      "Gleason",
      "Shannon",
      "Simpson",
      "Evenness"
    )
  )
})

test_that("calculate_diversities() stops if lacking all params", {
  expect_error(
    calculate_diversities(
      x = "y",
      cutoff = 60,
      control = "susceptible",
      sample = "Isolate",
      gene = "Rps",
      perc_susc = "perc.susc"
    ),
    regexp = "You have failed to provide all necessary inputs"
  )
  expect_error(
    calculate_diversities(
      x = P_sojae_survey,
      cutoff = "sixty",
      control = "susceptible",
      sample = "Isolate",
      gene = "Rps",
      perc_susc = "perc.susc"
    ),
    regexp = "You have failed to provide all necessary inputs"
  )
  expect_error(
    calculate_diversities(
      x = P_sojae_survey,
      cutoff = 60,
      control = NULL,
      sample = "Isolate",
      gene = "Rps",
      perc_susc = "perc.susc"
    ),
    regexp = "You have failed to provide all necessary inputs"
  )
  expect_error(
    calculate_diversities(
      x = P_sojae_survey,
      cutoff = 60,
      control = "susceptible",
      sample = NULL,
      gene = "Rps",
      perc_susc = "perc.susc"
    ),
    regexp = "You have failed to provide all necessary inputs"
  )
  expect_error(
    calculate_diversities(
      x = P_sojae_survey,
      cutoff = 60,
      control = "susceptible",
      sample = "isolate",
      gene = NULL,
      perc_susc = "perc.susc"
    ),
    regexp = "You have failed to provide all necessary inputs"
  )
  expect_error(
    calculate_diversities(
      x = P_sojae_survey,
      cutoff = 60,
      control = "susceptible",
      sample = "isolate",
      gene = "Rps",
      perc_susc = 60
    ),
    regexp = "You have failed to provide all necessary inputs"
  )
})


test_that("calculate_diversities() stops if data are not valid", {
  # add non-numeric data to `perc.susc`
  x <- P_sojae_survey[1, ]
  x[, 11] <- "X"

  P_sojae_survey <- rbind(P_sojae_survey, x)
  expect_error(
    calculate_diversities(
      x = P_sojae_survey,
      cutoff = 60,
      control = "susceptible",
      sample = "Isolate",
      gene = "Rps",
      perc_susc = "perc.susc"
    ),
    regexp = "Data in the column `perc_susc` must be numeric."
  )

  rm(P_sojae_survey)
  data(P_sojae_survey)
  # add value < 0 to data
  x <- P_sojae_survey[1, ]
  x[, 11] <- -1

  P_sojae_survey <- rbind(P_sojae_survey, x)
  expect_error(
    calculate_diversities(
      x = P_sojae_survey,
      cutoff = 60,
      control = "susceptible",
      sample = "Isolate",
      gene = "Rps",
      perc_susc = "perc.susc"
    ),
    regexp = "Data in the column `perc_susc` must be non-negative."
  )
})

test_that("print.hagis.diversities() returns a proper summary", {
  x <- utils::capture.output(print(diversities))
  expect_type(x, "character")
  expect_equal(x[[2]], "hagis Diversities")
  expect_equal(x[[4]], "Number of Samples 21")
  expect_equal(x[[5]], "Number of Pathotypes 19 ")
  expect_equal(x[[8]], "Simple   0.9047619 ")
  expect_equal(x[[9]], "Gleason  5.912257 ")
  expect_equal(x[[10]], "Shannon  2.912494 ")
  expect_equal(x[[11]], "Simpson  0.9433107 ")
  expect_equal(x[[12]], "Evenness  0.9891509 ")
  expect_equal(x[[13]], "")
})

test_that("pander.hagis.diversities returns a proper table of indices and
          caption", {
            x <- utils::capture.output(pander::pander(diversities))
            expect_equal(
              head(x),
              c(
                "",
                "-------------------------------------------------",
                " Simple   Gleason   Shannon   Simpson   Evenness ",
                "-------- --------- --------- --------- ----------",
                " 0.9048    5.912     2.912    0.9433     0.9892  ",
                "-------------------------------------------------"
              )
            )
          })