tests/testthat/test_xylookup.R

In sharksmhi/tryout: Automatic quality control of physical, chemical and marine biological data generated by the SHARK system

library(testthat)
context("xylookup")

check_skip <- function() {
  skip_on_cran()
}

test_data <- function(x=c(1,2,3), y=c(51,52,53)) {
  check_skip()
  data.frame(decimalLongitude=x, decimalLatitude=y)
}

test_that("lookup_xy returns correct data", {
  results <- lookup_xy(test_data(), asdataframe = FALSE)
  expect_equal(length(results), 3)
  r1 <- results[[1]]
  expect_equal(sort(names(r1)), c("grids", "shoredistance"))
  expect_true("bathymetry" %in% names(r1$grids))
})

test_that("lookup_xy results filtering works", {
  results <- lookup_xy(test_data(), areas = TRUE)
  expect_equal(nrow(results), 3)
  expect_true(all(c("shoredistance", "bathymetry", "sssalinity", "sstemperature", "obis") %in% colnames(results)))
  results <- lookup_xy(test_data(), areas = FALSE, grids = FALSE, shoredistance = TRUE)
  expect_equal(results[1,,drop=F]$shoredistance, 1604)
  expect_false(any(c("bathymetry", "obis") %in% colnames(results)))
  results <- lookup_xy(test_data(), areas = FALSE, grids = TRUE, shoredistance = FALSE)
  expect_false(any(c("shoredistance", "obis") %in% colnames(results)))
  expect_equal(results[1,,drop=F]$bathymetry, 2)
})

test_that("lookup_xy empty areas works", {
  results <- lookup_xy(test_data(x=90,y=60), areas = TRUE, shoredistance = FALSE, grids = FALSE)
  expect_equal(nrow(results), 1)
  expect_equal(ncol(results), 0)
})

test_that("lookup_xy duplicate coordinates works", {
  results <- lookup_xy(test_data(x=c(90,90,0,1,2,1),y=c(60,60,0,4,3,4)), asdataframe = FALSE)
  expect_equal(length(results), 6)
  expect_equal(results[[1]],results[[2]])
  expect_equal(results[[4]],results[[6]])

  results <- lookup_xy(test_data(x=c(90,90,0,1,2,1),y=c(60,60,0,4,3,4)), asdataframe = TRUE)
  expect_equal(nrow(results), 6)
  expect_equal(as.list(results[1,]),as.list(results[2,]))
  expect_equal(as.list(results[4,]),as.list(results[6,]))
})

test_that("lookup_xy mix of valid and invalid coordinates works", {
  data <- test_data(x=c(90,"90",NA,-181,2,181,0),y=c(-91,60,0,4,91,4,0))
  expect_error(lookup_xy(data, asdataframe = FALSE))
  expect_error(lookup_xy(data, asdataframe = TRUE))

  data <- test_data(x=c(90,NA,-181,2,181,0),y=c(-91,0,4,91,4,0))
  results <- lookup_xy(data, asdataframe = FALSE)
  expect_equal(length(results), 6)
  expect_equal(results[[1]], NULL)
  expect_equal(sort(names(results[[6]])), c("grids", "shoredistance"))

  results <- lookup_xy(data, asdataframe = TRUE)
  expect_equal(nrow(results), 6)
  expect_equal(sum(is.na(results$shoredistance)), 5)
  expect_false(is.na(results$shoredistance[6]))
})

test_that("lookup_xy no data works", {
  data <- test_data(x=numeric(0),y=numeric(0))
  expect_equal(length(lookup_xy(data, asdataframe = FALSE)), 0)
  expect_equal(nrow(lookup_xy(data, asdataframe = TRUE)), 0)
  data <- test_data(x=as.numeric(c(NA, NA)),y=as.numeric(c(NA, NA)))
  expect_equal(length(lookup_xy(data, asdataframe = FALSE)), 2)
  expect_equal(nrow(lookup_xy(data, asdataframe = TRUE)), 2)
})

test_that("wrong url fails", {
  options(obistools_xylookup_url = "http://api.iobis.org/thisdoesnotexist")
  on.exit(options(obistools_xylookup_url = NULL))
  data <- test_data(x=0,y=0)
  expect_error(lookup_xy(data))
})

test_that("lookup_xy only areas works", {
  data <- test_data(x=c(0,1),y=c(0,0))
  result <- lookup_xy(data, shoredistance = FALSE, grids = FALSE, areas = TRUE)
  expect_equal(nrow(result), 2)
  expect_equal(ncol(result), 1)
})

test_that("lookup_xy areas distance works", {
  data <- test_data(x=c(0,1),y=c(0,0))
  result <- lookup_xy(data, shoredistance = FALSE, grids = FALSE, areas = TRUE)
  expect_equal(nrow(result), 2)
  expect_equal(ncol(result), 1)
  expect_gte(nrow(result[1,][[1]]), 3)
  result0 <- lookup_xy(data, shoredistance = FALSE, grids = FALSE, areas = 0)
  expect_equal(result, result0)
  result <- lookup_xy(data, shoredistance = FALSE, grids = FALSE, areas = 1000000)
  expect_gte(nrow(result[1,][[1]]), nrow(result0[1,][[1]]))
})



test_that("lookup_xy works for Calanus: issue 48", {
  skip_if_not_installed("robis")
  skip("Very SLOOOOW test, only run on major releases")
  library(robis)

  calfin <- occurrence("Calanus finmarchicus", fields = c("decimalLongitude", "decimalLatitude"))
  data <- lookup_xy(calfin, shoredistance = FALSE, grids = TRUE, areas = FALSE)
  expect_gt(nrow(data), 200000)
})