tests/testthat/test_check_depth.R

In iobis/obistools: Data Enhancement and Quality Control of Marine Species Observations

library(obistools)
context("check depth")


test_that("check_depth detects invalid or impossible depth values", {
  if(Sys.getenv("TZ") == "") {
    Sys.setenv(TZ="Europe/Brussels") # handle warning
  }
  # Overview of all test cases:
  # empty dataframe
  # Min D > Max D
  # Min D | Max D missing
  # Min D | Max D empty
  # Min D | Max D not numeric and not ''
  # Min D | Max D > bathy (and check depthmargin)
  # Min D | Max D < 0 & shoredist > 0 (and check shoremargin)
  # report: TRUE/FALSE

  t1 <- data.frame(decimalLongitude = 0, decimalLatitude = 0,
    minimumDepthInMeters = c("4936", "4938", "4935", "-20"),
    maximumDepthInMeters = c("4936", "4937", "5000", "-10"))
  d1 <- check_depth(t1, depthmargin = 0, shoremargin = NA, report = FALSE)
  expect_equal(2, nrow(d1))
  expect_equal(c("4938", "4935"), as.character(d1$minimumDepthInMeters))
  r <- check_depth(t1, depthmargin = 0, shoremargin = NA, report = TRUE)
  expect_equal(4, nrow(r))
  expect_equal(3, sum(grepl("depth.*?margin", r$message)))
  expect_equal(1, sum(grepl("greater than maximum", r$message)))

  r2 <- check_depth(t1, depthmargin = 0, shoremargin = 1e6, report = TRUE)
  expect_equal(r, r2)

  r <- check_depth(t1, depthmargin = 1000, shoremargin = NA, report = TRUE)
  expect_equal(1, nrow(r))
  expect_equal(0, sum(grepl("depth.*?margin", r$message)))
  expect_equal(1, sum(grepl("greater than maximum", r$message)))

  r <- check_depth(t1, depthmargin = 0, shoremargin = 0, report = TRUE)
  expect_equal(6, nrow(r))
  expect_equal(3, sum(grepl("depth.*?margin", r$message)))
  expect_equal(1, sum(grepl("greater than maximum", r$message)))
  expect_equal(2, sum(grepl("shoredistance.*?margin", r$message)))
  expect_equal(2, sum(grepl("negative", r$message)))

  # missing column
  t <- data.frame(decimalLongitude=c(0), decimalLatitude=c(0), minimumDepthInMeters=c("10"))
  d <- check_depth(t, depthmargin = 0, shoremargin = 0, report = FALSE)
  expect_equal(0, nrow(d))
  r <- check_depth(t, depthmargin = 0, shoremargin = 0, report = TRUE)
  expect_equal(1, sum(grepl("missing", r$message)))

  # missing column + an error
  t <- data.frame(decimalLongitude=c(0), decimalLatitude=c(0), minimumDepthInMeters=c("10", "10000"))
  d <- check_depth(t, depthmargin = 0, shoremargin = 0, report = FALSE)
  expect_equal(1, nrow(d))
  r <- check_depth(t, depthmargin = 0, shoremargin = 0, report = TRUE)
  expect_equal(1, sum(grepl("missing", r$message)))
  expect_equal(1, sum(grepl("depth.*?margin", r$message)))
  expect_equal(2, nrow(r))

  t <- data.frame(decimalLongitude=c(0), decimalLatitude=c(0), minimumDepthInMeters=c("", "", ""), maximumDepthInMeters="4")
  r <- check_depth(t, depthmargin = 0, shoremargin = 0, report = TRUE)
  expect_equal(1, sum(grepl("empty", r$message)))
  t$minimumDepthInMeters <- c("", "a", "1")
  expect_warning({
    r <- check_depth(t, depthmargin = 0, shoremargin = 0, report = TRUE)
    expect_equal(1, sum(grepl("not numeric", r$message)))
  }, "NAs")
})

test_that("Issue 42", {
  skip_if_not_installed("robis")
  pol <- robis::occurrence("Polychaeta", geometry = "POLYGON ((6.50391 54.59753, 6.45996 53.14677, 8.26172 53.17312, 8.08594 54.54658, 6.50391 54.59753))")
  problems <- check_depth(pol, report=FALSE)
  testthat::expect_gt(nrow(problems), 5)
  problems <- check_depth(pol, report=TRUE)
  testthat::expect_gt(nrow(problems), 5)

  problems_margin10 <- check_depth(pol, depthmargin=10, report=TRUE)
  testthat::expect_lt(nrow(problems_margin10), nrow(problems))
})

# test_that("External bathymetry raster is used", {
#   x <- raster::raster(nrow=10, ncol=10,
#                       xmn=-4.5, xmx=5.5, ymn=-4.5, ymx=5.5,
#                       crs="+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0",
#                       resolution=1)
#   set.seed(42)
#   raster::values(x) <- runif(100, min = 0, max = 1000)
#   x[55] <- 7
#   x[10] <- NA
#
#   t1 <- data.frame(decimalLongitude=c(0,0,5,30), decimalLatitude=c(0,0,5,30),
#                    minimumDepthInMeters = c("5", "10", "20", "25"),
#                    maximumDepthInMeters = c("5", "10", "20", "25"))
#
#   d1 <- check_depth(t1, report = FALSE, depthmargin = 0, shoremargin = NA, bathymetry = x)
#   r1 <- check_depth(t1, report = TRUE, depthmargin = 0, shoremargin = NA, bathymetry = x)
#
#   expect_true(!1 %in% unique(r1$row))
#   expect_true(all(2:4 %in% unique(r1$row)))
#   expect_true(all(c("decimalLongitude", "decimalLatitude", "minimumDepthInMeters", "maximumDepthInMeters") %in% unique(r1$field)))
#   expect_true(any(c("error", "warning") %in% unique(r1$level)))
# })

test_that("support for tibble", {
  skip_if_not_installed("dplyr")
  t1 <- data.frame(decimalLongitude=0, decimalLatitude=0,
                   minimumDepthInMeters = c("4936", "4938", "4935", "-20"),
                   maximumDepthInMeters = c("4936", "4937", "5000", "-10"))
  r1 <- check_depth(t1, depthmargin = 0, shoremargin = NA, report = TRUE)
  t2 <- dplyr::as_tibble(t1)
  r2 <- check_depth(t2, depthmargin = 0, shoremargin = NA, report = TRUE)
  expect_equal(r2, r1)
  expect_equal(nrow(r2), 4)
})