tests/testthat/test-community_generate.R

In diazrenata/birdsize: Estimate Avian Body Size Distributions

test_that("error catching works", {
  bbs_data <- demo_route_raw |>
    filter_bbs_survey()

  no_AOU <- bbs_data |>
    dplyr::select(-AOU)

  expect_error(community_generate(no_AOU), regexp = "At least one of `AOU`, `scientific_name`, or `mean_size` is required")

  no_abundance <- bbs_data |>
    dplyr::select(-speciestotal)

  expect_error(community_generate(no_abundance), regexp = "abundance column is required. If the name is not `speciestotal` specify using the `abundance_column_name` argument")

  misnamed_abundance <- bbs_data |>
    dplyr::rename(abund = speciestotal)

  expect_error(community_generate(misnamed_abundance), regexp = "abundance column is required. If the name is not `speciestotal` specify using the `abundance_column_name` argument")
})
test_that("simulation from AOU works", {
  bbs_data <- demo_route_raw |>
    filter_bbs_survey()

  short_bbs_data <- bbs_data |>
    dplyr::filter(year == 2019)

  set.seed(22)
  bbs_data_sims <- community_generate(short_bbs_data)

  expect_true(nrow(bbs_data_sims) == sum(short_bbs_data$speciestotal))
  expect_false(anyNA(bbs_data_sims))
})

test_that("simulation from AOU works with nonstandard abund name", {
  bbs_data <- demo_route_raw |>
    filter_bbs_survey()

  short_bbs_data <- bbs_data |>
    dplyr::filter(year == 2019) |>
    dplyr::rename(abund = speciestotal)

  set.seed(22)
  bbs_data_sims <- community_generate(short_bbs_data, abundance_column_name = "abund")

  expect_true(nrow(bbs_data_sims) == sum(short_bbs_data$abund))
  expect_false(anyNA(bbs_data_sims))
  expect_true(all(bbs_data_sims$sd_method == "AOU lookup"))
})

test_that("simulation from species name works", {
  bbs_data <- demo_route_raw |>
    filter_bbs_survey()

  short_bbs_data <- bbs_data |>
    dplyr::filter(year == 2019) |>
    dplyr::left_join(dplyr::select(birdsize::sd_table, AOU, scientific_name)) |>
    dplyr::select(-AOU)

  set.seed(22)
  bbs_data_sims <- community_generate(short_bbs_data)

  expect_true(nrow(bbs_data_sims) == sum(short_bbs_data$speciestotal))
  expect_false(anyNA(bbs_data_sims))
  expect_true(all(bbs_data_sims$sd_method == "Scientific name lookup"))
})



test_that("simulation from mean size works", {
  bbs_data <- demo_route_raw |>
    filter_bbs_survey()

  short_bbs_data <- bbs_data |>
    dplyr::filter(year == 2019) |>
    dplyr::left_join(dplyr::select(birdsize::sd_table, AOU, mean_mass)) |>
    dplyr::select(-AOU) |>
    dplyr::rename(mean_size = mean_mass)

  set.seed(22)
  bbs_data_sims <- community_generate(short_bbs_data)

  expect_true(nrow(bbs_data_sims) == sum(short_bbs_data$speciestotal))
  expect_true(all(is.na(bbs_data_sims$AOU)))
  expect_true(all(is.na(bbs_data_sims$scientific_name)))
  expect_true(all(bbs_data_sims$sd_method == "SD estimated from mean"))
})


test_that("simulation from mean and sd size works", {
  bbs_data <- demo_route_raw |>
    filter_bbs_survey()

  short_bbs_data <- bbs_data |>
    dplyr::filter(year == 2019) |>
    dplyr::left_join(dplyr::select(birdsize::sd_table, AOU, mean_mass, mean_sd)) |>
    dplyr::select(-AOU) |>
    dplyr::rename(
      mean_size = mean_mass,
      sd_size = mean_sd
    )

  set.seed(22)
  bbs_data_sims <- community_generate(short_bbs_data)

  expect_true(nrow(bbs_data_sims) == sum(short_bbs_data$speciestotal))
  expect_true(all(is.na(bbs_data_sims$AOU)))
  expect_true(all(is.na(bbs_data_sims$scientific_name)))
  expect_true(all(bbs_data_sims$sd_method == "Mean and SD provided"))
})


test_that("simulation from toy df works", {
  toy_df <- data.frame(
    speciestotal = c(10, 10, 5, 5, 5),
    mean_size = c(100, 50, 45, 20, 10),
    sim_species_id = c(1:5)
  )

  set.seed(22)
  toy_sims <- community_generate(toy_df)

  # expect_true(ncol(toy_sims) == 10)
  expect_true(nrow(toy_sims) == sum(toy_df$speciestotal))
  expect_true(all(is.na(toy_sims$AOU)))
  expect_true(all(is.na(toy_sims$scientific_name)))
  expect_false(any(is.na(toy_sims$sim_species_id)))
  expect_true(all(round(toy_sims$individual_mass[1:5]) == c(96, 118, 107, 102, 99)))
  expect_true(all(toy_sims$sd_method == "SD estimated from mean"))
})