tests/testthat/test-growth-fishbase.R

In atlantistools: Process and Visualise Output from Atlantis Models

context("test extraction of data from fishbase.")

df1 <- get_growth_fishbase("Scyliorhinus canicula")

test_that("test extraction for Small-spotted catshark", {
  expect_equal(dim(df1), c(4, 16))
  expect_equivalent(df1$linf[3], 87.4)
  expect_equivalent(df1$k[2], 0.15)
  expect_equivalent(df1$locality[1], "Central Adriatic, 100-200 m depth")
})

# df2 <- get_growth_fishbase("Anguilla anguilla")
#
# test_that("test extraction for eel", {
#   expect_equal(dim(df2), c(43, 17))
#   expect_equivalent(df2$linf[10], 50.1)
#   expect_equivalent(df2$k[19],  0.078)
#   expect_equivalent(df2$locality[4], "Monaci lagoon")
# })

refs <- unique(c(df1$main_ref, df1$data_ref))
df3 <- get_ref_fishbase(ref_id = na.omit(refs))

test_that("test extraction of references for sprat", {
  expect_true(stringr::str_detect(df3$ref[df3$ref_id == 1231], "Zupanovic, S., 1961. Contribution"))
  expect_true(stringr::str_detect(df3$ref[df3$ref_id == 81067], "Ivory, P., F. Jeal and C.P. Nolan, 2005. Age determination"))
})

# use this for internal testing only
# fish <- read.csv("Z:/my_data_alex/fish_species_names_from_ibts.csv", stringsAsFactors = FALSE)[, 1]
# url <- get_growth_fishbase(fish)
# test_url <- urls$ref_url
# use the following ids to test the function. the have 1-5 listed references.
# 1, 2, 3, 16, 697

# use this to check the package.
test_url <- "/popdyn/FishPopGrowthSummary.php?ID=861&pref=312&sex=unsexed&loo=56.80000&k=0.53000&id2=845&genusname=Scyliorhinus&speciesname=canicula&fc=183&gm_loo=75.682521749986&gm_lm=49.520370700602&gm_m=0.184&gm_k=0.20812285885834&vautoctr=2040&gm_lm_rl=0.62928533390764"

tests <- purrr::map_chr(test_url, ~paste0("http://www.fishbase.se/", .)) %>%
  purrr::map(., xml2::read_html) %>%
  purrr::map(., rvest::html_text)

test_that("test extraction of references for sprat", {
  expect_true(all(stringr::str_detect(tests, "Main Ref. :")))
  expect_true(all(stringr::str_detect(tests, "Data Ref. :")))
  expect_true(all(stringr::str_detect(tests, "Data Type :")))
  expect_equal(url_to_refid(test_url), c(312, 1231))
})

# test NA handling
df <- suppressWarnings(get_growth_fishbase(c("Alosa agone", "Scyliorhinus canicula")))

test_that("error and NA handling", {
  expect_error(get_growth_fishbase("Alosa agone"), "None of the species have information about growth.")
  expect_equal(sum(is.na(df[df$species == "Alosa agone", ])), 15)
  expect_equal(nrow(is.na(df[df$species == "Alosa agone", ])), 1)
})