tests/testthat/test_unmarked.r

In CornellLabofOrnithology/auk: eBird Data Extraction and Processing in R

library(dplyr)
context("unmarked utilities")

test_that("filter_repeat_visits works", {
  f_ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
  f_smpl <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
  ebd_zf <- auk_zerofill(x = f_ebd, sampling_events = f_smpl,
                         species = "Collared Kingfisher",
                         collapse = TRUE)
  
  # no annual_closure, no number of days
  expect_error(filter_repeat_visits(ebd_zf, annual_closure = FALSE))
  
  # no annual_closure, number of days given
  occ <- filter_repeat_visits(ebd_zf, annual_closure = FALSE, n_days = 30)
  expect_is(occ, "data.frame")
  expect_true(all(c("site", "closure_id", "n_observations") %in% names(occ)))
  expect_gte(min(occ$n_observations), 2)
  expect_lte(max(occ$n_observations), 10)
  # check closure period
  days_bt_first_last_obs <- occ %>% 
    group_by(site) %>% 
    mutate(drange = as.integer(diff(range(observation_date)))) %>% 
    pull(drange) %>% 
    max()
  expect_lte(days_bt_first_last_obs, 30)
  occ_10 <- filter_repeat_visits(ebd_zf, annual_closure = FALSE, n_days = 10)
  days_bt_first_last_obs <- occ_10 %>% 
    group_by(site) %>% 
    mutate(drange = as.integer(diff(range(observation_date)))) %>% 
    pull(drange) %>% 
    max()
  expect_lte(days_bt_first_last_obs, 10)
  
  # annual_closure, no number of days
  occ <- filter_repeat_visits(ebd_zf, annual_closure = TRUE,
                              site_vars = "locality_id",
                              min_obs = 4, max_obs = 8)
  closure_obs <- occ %>% 
    count(locality_id, year = format(observation_date, "%Y")) %>% 
    pull(n)
  expect_lte(max(closure_obs), 8)
  expect_gte(min(closure_obs), 4)
  
  n_years <- occ %>% 
    group_by(closure_id) %>% 
    summarise(n_years = n_distinct(format(observation_date, "%Y"))) %>% 
    pull(n_years)
  expect_equal(max(n_years), 1)
  expect_equal(min(n_years), 1)
})

test_that("format_unmarked works", {
  skip_if_not_installed("unmarked")
  f_ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
  f_smpl <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
  ebd_zf <- auk_zerofill(x = f_ebd, sampling_events = f_smpl,
                         species = "Collared Kingfisher",
                         collapse = TRUE)
  occ <- filter_repeat_visits(ebd_zf)
  occ_wide <- format_unmarked_occu(occ,
                                   response = "species_observed",
                                   site_covs = c("latitude", "longitude"),
                                   obs_covs = c("effort_distance_km",
                                                "duration_minutes"))
  occ_um <- unmarked::formatWide(occ_wide, type = "unmarkedFrameOccu")
  
  expect_is(occ_wide, "data.frame")
  expect_is(occ_um, "unmarkedFrameOccu")
  expect_named(occ_um@siteCovs, c("latitude", "longitude"))
  expect_named(occ_um@obsCovs, c("effort_distance_km", "duration_minutes"))
  expect_equal(nrow(occ_um@y), n_distinct(occ$site))
  expect_equal(nrow(occ_um@y), nrow(occ_wide))
})