tests/testthat/test_occs_paleoDb.R

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

# #### COMPONENT occs:  Obtain Occurrence Data
# #### MODULE: Query Database (Past)
# context("paleoDb")
#
# ##Set parameters
#
# #species name
# spName <- "Didelphis virginiana"
# spNameError <- "Panthera onc"
# genus <- "panthera"
# #maximum number of occurrences to download
# occNum <- 100
# # For PaleobioDB only Holocene is allowed.
# timeInterval <- "Holocene"
#
# # run function if no Windows
# if (Sys.info()['sysname'] != "Windows") {
#    occsPaleo <- occs_paleoDb(spName, occNum, timeInterval, logger = NULL)
# }
#
#
# ###Test that errors check
#   ### test if the error messages appear when they are supposed to
# test_that("error checks", {
#   # paleobioDB failing in Windows
#   skip_on_os("windows")
#   # the user doesn't input any species name
#   expect_error(occs_paleoDb( occNum, occNum, timeInterval),
#                'Please input both genus and species names of ONE species.',
#                fixed = TRUE)
#   # the user inputs just one name (genus or epithet)
#   expect_error(occs_paleoDb(spName = genus,occNum, timeInterval),
#                'Please input both genus and species names of ONE species.',
#                fixed = TRUE)
#   # the species' name has spelling errors, or it is not found in the database
#   expect_error(occs_paleoDb(spName = spNameError, occNum, timeInterval),
#                paste0(hlSpp(spNameError),
#                       "No records found, please check the spelling."),
#                fixed = TRUE)
# })
#
# ###Test of warnings:
# ##Function has one warning for records without coordinates, this is forbidden by
# ##the database
# ##thus making the case impossible. If it was possible it would look like this:
# # test_that("warnings checks", {
# # # the species is found in the database, but it does not have coordinates (Log & lat)
# # expect_warning(occs_paleoDb(spName = "impossible species", occNum = 1,
# #                             timeInterval),
# #                paste0(hlSpp("impossible species"),
# #                       "No records with coordinates found in paleobioDB."),
# #                fixed = TRUE)
# # })
#
# # test output features
# test_that("output type checks", {
#   # paleobioDB failing in Windows
#   skip_on_os("windows")
#   # skip on CRAN
#   skip_on_cran()
#   #output is a list
#   expect_is(occsPaleo, "list")
#   #List has two elements
#   expect_equal(length(occsPaleo), 2)
# })
# test_that("output data checks", {
#   # paleobioDB failing in Windows
#   skip_on_os("windows")
#   # skip on CRAN
#   skip_on_cran()
#   # if the original database has records without coordinates OR duplicates:
#   if ((TRUE %in% duplicated(occsPaleo$orig[,c('longitude','latitude')]) == TRUE) |
#       (NA %in% occsPaleo$orig[,c('longitude','latitude')]) == TRUE){
#     # the cleaned table must have fewer records than the original one
#     expect_true((nrow(occsPaleo$orig)) > (nrow(occsPaleo$cleaned)))
#   } else { # if not,
#     # both tables should have the same number of records
#     expect_true((nrow(occsPaleo$orig)) == (nrow(occsPaleo$cleaned)))
#   }
#   # there are not "NA" values in longitude OR latitude columns in the cleaned table
#   expect_false(NA %in% occsPaleo$cleaned$latitude) |
#     (NA %in% occsPaleo$cleaned$longitude)
#   # there are not duplicate values in longitude AND latitude columns in the cleaned table
#   expect_false(TRUE %in% duplicated(occsPaleo$cleaned[, c('longitude','latitude')]))
#   # downloaded species corresponds to queried species. T
#   expect_match(unique(occsPaleo$cleaned$scientific_name),
#                spName, ignore.case = TRUE, all = TRUE)
# })
# ##Check headers for both original and cleaned tables
# keyPaleoHeaders <- c("occID", "scientific_name", "longitude", "latitude",
#                      # "early_interval", "late_interval",
#                      "country", "collection_no", "record_type",
#                      "early_age", "late_age")
#
# test_that("headers check", {
#   # paleobioDB failing in Windows
#   skip_on_os("windows")
#   #
#   expect_false('FALSE' %in%  (keyPaleoHeaders %in% names(occsPaleo$orig)))
#   # the headers in the cleaned table are the ones specified in the function
#   expect_equal(names(occsPaleo$cleaned),c(keyPaleoHeaders,"pop"))
# })
#
#