tests/testthat/test-get-dat.R

In pbs-assess/gfdata: Data Extraction for DFO PBS Groundfish Stocks

context("test-get-spp-dat")

.dir <- here::here("tests", "test-cache")
dir.create(.dir, showWarnings = FALSE)

test_that("get species data functions work at PBS", {
  # skip_on_cran()
  skip_on_travis()
  skip_on_appveyor()
  tryCatch(get_ssids(), error = function(e) skip("No database access"))

  expect_error(get_survey_sets("lingcod", ssid = 99999))

  d <- get_survey_sets("lingcod", 16)
  expect_gte(d$catch_weight[[1]], 0)
  d <- dplyr::filter(d, year %in% 2018)
  expect_known_value(d, file = file.path(.dir, "get_survey_sets.rds"))

  d <- get_survey_samples("lingcod", 16)
  expect_type(d$survey_id, "integer")
  d <- dplyr::filter(d, year %in% 2016) %>%
    # could be later aged:
    select(-age, -ageing_method_code, -species_ageing_group)
  expect_known_value(d, file = file.path(.dir, "get_survey_samples.rds"))

  d <- get_commercial_samples("lingcod")
  expect_gte(d$year[[1]], 1900L)

  d <- get_catch("lingcod")
  expect_gte(nrow(d), 1L)

  d <- get_cocaught_species(610, "groundfish trawl", "bottom trawl")
  expect_gt(nrow(d), 1L)
  expect_match(class(d$total_landed_kg), "numeric")

  d <- get_hake_catch()
  expect_false(is.null(sum(d$landed_kg)))
  expect_match(class(d$discarded_kg), "numeric")

  d <- get_cpue_historical("442")
  expect_equal(d$species_common_name[[1]], "YELLOWEYE ROCKFISH")
  expect_equal(class(d$landed_kg), "numeric")

  d <- get_cpue_spatial("lingcod")
  expect_gte(d$fishing_event_id[[1]], 1)
  expect_equal(class(d$cpue), "numeric")

  d <- get_cpue_spatial_ll("lingcod")
  expect_match(class(d$landed_round_kg), "numeric")
  expect_gte(nrow(d), 1L)

  d <- get_cpue_index("bottom trawl", min_cpue_year = 2015)
  expect_gt(sum(d$landed_kg, d$discarded_kg), 0)

  d <- get_age_precision("lingcod")
  expect_equal(d$species_code[[1L]], "467")

  d <- get_survey_index("lingcod", ssid = 1)
  expect_type(d$num_pos_sets, "integer")

  d <- get_management(396)
  expect_match(d$species_common_name, "pacific ocean perch")

  d <- get_sara_dat()
  expect_type(d$sara_status, "character")

  d <- get_ll_hook_data(442, c(39, 40))
  expect_type(d$count_non_target_species, "integer")
  expect_gt(sum(d$count_target_species), 1)

})