tests/testthat/test_fossillevel_functions.R

In CoordinateCleaner: Automated Cleaning of Occurrence Records from Biological Collections

context("Fossil cleaning tc_*")

set.seed(1)
#cf_range
minages <- runif(n = 100, min = 0.1, max = 25)
set.seed(1)
maxages <- minages + c(runif(n = 99, min = 0, max = 5), 25)

test <- data.frame(
  species = c(letters[1:9], "z"),
  decimalLongitude = c(runif(
    n = 98, min = 4, max = 16
  ), 75, 7),
  decimalLatitude = c(runif(
    n = 100, min = -5, max = 5
  )),
  min_ma = minages,
  max_ma = maxages
)



# cf_range
test_that("cf_range identifies existing bias", {
  #  skip_on_cran()
  #return value
  expect_is(cf_range(test, value = "flagged", taxon = ""), "logical")
  expect_is(cf_range(test, value = "clean", taxon = ""), "data.frame")
  
  #outlier method
  expect_equal(sum(
    cf_range(
      test,
      value = "flagged",
      method = "quantile",
      taxon = ""
    )
  ), 99)
  expect_equal(sum(cf_range(
    test,
    value = "flagged",
    method = "mad",
    taxon = ""
  )), 99)
  expect_equal(sum(
    cf_range(
      test,
      value = "flagged",
      method = "time",
      taxon = "",
      max_range = 20
    )
  ), 99)
  
  expect_equal(nrow(
    cf_range(
      test,
      value = "clean",
      method = "quantile",
      taxon = "",
      uniq_loc = TRUE
    )
  ), 99)
  expect_equal(nrow(
    cf_range(
      test,
      value = "clean",
      method = "mad",
      taxon = "",
      uniq_loc = TRUE
    )
  ), 99)
  expect_equal(nrow(
    cf_range(
      test,
      value = "clean",
      method = "time",
      taxon = "",
      uniq_loc = FALSE
    )
  ), 100)
  
  expect_equal(nrow(
    cf_range(
      test,
      value = "clean",
      method = "quantile",
      taxon = "species",
      uniq_loc = TRUE
    )
  ), 99)
  
  expect_equal(nrow(
    cf_range(
      test,
      value = "clean",
      method = "quantile",
      taxon = "species",
      uniq_loc = TRUE
    )
  ), 99)
})

#cf_age
test_that("cf_age runs", {
  #  skip_on_cran()
  #return value
  expect_is(cf_age(test, value = "flagged", taxon = ""), "logical")
  expect_is(cf_age(test, value = "clean", taxon = ""), "data.frame")
  
  #outlier method
  expect_equal(sum(
    cf_age(
      test,
      value = "flagged",
      method = "quantile",
      taxon = "",
      replicates = 10
    )
  ), 100)
  expect_equal(sum(
    cf_age(
      test,
      value = "flagged",
      method = "quantile",
      taxon = "",
      uniq_loc = F,
      replicates = 10
    )
  ), 100)
  expect_equal(sum(
    cf_age(
      test,
      value = "flagged",
      method = "quantile",
      taxon = "species",
      uniq_loc = F,
      replicates = 10
    )
  ), 100)
  expect_equal(sum(
    cf_age(
      test,
      value = "flagged",
      method = "mad",
      taxon = "",
      replicates = 10,
      flag_thresh = 0.1,
      mltpl = 10
    )
  ), 100)
  expect_equal(sum(
    cf_age(
      test,
      value = "flagged",
      method = "mad",
      taxon = "species",
      replicates = 10,
      flag_thresh = 0.1,
      mltpl = 10
    )
  ), 100)
  expect_equal(sum(
    cf_age(
      test,
      value = "flagged",
      method = "mad",
      taxon = "",
      uniq_loc = F
    )
  ), 100)
})


#cf_outl
set.seed(1)
minages <- c(runif(n = 11, min = 10, max = 25), 62.5)
test <- data.frame(
  species = c(letters[1:10], rep("z", 2)),
  decimalLongitude = c(runif(
    n = 10, min = 4, max = 16
  ), 75, 7),
  decimalLatitude = c(runif(
    n = 12, min = -5, max = 5
  )),
  min_ma = minages,
  max_ma = c(minages[1:11] +
               runif(
                 n = 11, min = 0, max = 5
               ), 65)
)

test_that("cf_outl identifies existing bias", {
  #  skip_on_cran()
  #return value
  expect_is(cf_outl(test, value = "flagged", taxon = ""), "logical")
  expect_is(cf_outl(test, value = "clean", taxon = ""), "data.frame")
  
  #outlier method
  expect_equal(sum(cf_outl(
    test,
    value = "flagged",
    method = "quantile",
    taxon = ""
  )), 10)
  expect_equal(sum(cf_outl(
    test,
    taxon = "",
    value = "flagged",
    method = "quantile"
  )), 10)
  expect_equal(sum(cf_outl(
    test,
    value = "flagged",
    method = "mad",
    taxon = ""
  )), 10)
  expect_equal(sum(cf_outl(
    test,
    value = "flagged",
    method = "mad",
    taxon = ""
  )), 10)
  
})