tests/testthat/test-community_overlap.R

In NEON-biodiversity/Ostats: O-Stats, or Pairwise Community-Level Niche Overlap Statistics

library(Ostats)
context("community_overlap")

# Set up data for test.
# Use small mammal data from the vignette.
# For this test we will only use HARV.

dat <- small_mammal_data[small_mammal_data$siteID %in% c('HARV', 'JORN'),
                         c('siteID', 'taxonID', 'mass')]
dat <- dat[!is.na(dat$mass), ]
dat$log_mass <- log10(dat$mass)

trait_harv <- as.matrix(dat[dat$siteID %in% 'HARV', 'log_mass', drop = FALSE])
spp_harv <- factor(dat$taxonID[dat$siteID %in% 'HARV'])

# Test 1. Verify correct output format if raw = FALSE
test_that (
  "community_overlap() returns expected output when raw = FALSE",
  {
    result1 <- community_overlap(traits = trait_harv, sp = spp_harv)
    expected1 <- 0.8946
    expect_equivalent(result1, expected1, tolerance = 0.001)
  }
)

# Test 2. Verify correct output format if raw = TRUE
test_that (
  "community_overlap() returns expected output when raw = TRUE",
  {
    result2 <- community_overlap(traits = trait_harv, sp = spp_harv, raw = TRUE)
    expected2 <- 0.8946
    expect_equivalent(result2[['value']], expected2, tolerance = 0.001)
    expect_s3_class(result2[['raw']], 'data.frame')
    expect_length(result2[['raw']][['overlap']], 10)
  }
)