tests/testthat/test-formatOcc.R

In LimaRAF/plantR: Managing Species Records from Biological Collections

# occs <- read.csv("example.csv")
# occs <- formatDwc(splink_data = occs)
# occs_format <- formatOcc(occs)
#
# test_that("formatOcc works", {
#   #setdiff(names(occs), names(occs_format))
#   setdiff(names(occs_format), names(occs))
#   # check that all columns are still there
#   expect_equal(setdiff(names(occs), names(occs_format)), character(0))
#   # check that the columns were created
#   new_cols <- c("collectionCode.new",
#                 "collectionObs",
#                 "recordedBy.new",
#                 "recordNumber.new",
#                 "year.new",
#                 "identifiedBy.new",
#                 "yearIdentified.new",
#                 "recordedBy.aux",
#                 "identifiedBy.aux",
#                 "last.name")
#   expect_equal(setdiff(names(occs_format), names(occs)), new_cols)
# })
#
# occs_loc <- formatLoc(occs_format)
# test_that("formatLoc works", {
#   expect_equal(setdiff(names(occs_format), names(occs_loc)), character(0))
#   loc_cols <- c("country.new",
#                 "stateProvince.new",
#                 "municipality.new",
#                 "locality.new",
#                 "locality.scrap",
#                 "resol.orig",
#                 "loc",
#                 "loc.correct",
#                 "latitude.gazetteer",
#                 "longitude.gazetteer",
#                 "resolution.gazetteer")
#   expect_equal(setdiff(names(occs_loc), names(occs_format)), loc_cols)
# })
#
# occs_fc <- formatCoord(occs_loc)
# test_that("formatCoord works", {
#   expect_equal(setdiff(names(occs_loc), names(occs_fc)), character(0))
#   coord_cols <- c("coord.check",
#                   "decimalLatitude.new",
#                   "decimalLongitude.new",
#                   "origin.coord",
#                   "precision.coord")
#   expect_equal(setdiff(names(occs_fc), names(occs_loc)), coord_cols)
# })
#
# occs_tax <- formatTax(occs_fc)
#
# test_that("formatTax works", {
#   expect_equal(setdiff(names(occs_fc), names(occs_tax)), character(0))
#   tax_cols <- c("scientificName.new",
#                   "scientificNameStatus",
#                   "suggestedName",
#                   "scientificNameFull",
#                   "tax.notes",
#                   "tax.source",
#                   "family.new")
#
#   expect_equal(setdiff(names(occs_tax), names(occs_fc)), tax_cols)
# })
#
# occs_val_loc <- validateLoc(occs_tax)
#
# test_that("validateLoc works", {
#   expect_equal(setdiff(names(occs_tax), names(occs_val_loc)), character(0))
#   expect_equal(setdiff(names(occs_val_loc), names(occs_tax)), "loc.check")
# })
# #x <- occs_val_loc
# ###AQUI quedó la consola
# test_that("validateCoord works", {
# occs_val_coord <- validateCoord(occs_val_loc)
#   expect_equal(setdiff(names(occs_val_loc), names(occs_val_coord)), character(0))
#   expect_equal(setdiff(names(occs_val_coord), names(occs_val_loc)), "loc.check")
# })
#
# #
# test_that("validateCoord new.col works", {
# occs_val_coord <- validateCoord(occs_val_loc, output = "new.col")
#   expect_equal(setdiff(names(occs_val_loc), names(occs_val_coord)), character(0))
#   expect_equal(setdiff(names(occs_val_coord), names(occs_val_loc)), "loc.check")
# })
# #nothing works
# # Splitting validate coords then
# test_that("checkCoord works", {
#   cC <- checkCoord(occs_val_loc)
#
#   expect_equal(setdiff(names(occs_val_loc), names(cC)), character(0))
#   expect_equal(setdiff(names(cC), names(occs_val_loc)), c("NAME_0", "geo.check"))
# })
#
#   cC <- checkCoord(occs_val_loc, dist.center = T)
# test_that("checkCoord works", {
#
#   expect_equal(setdiff(names(occs_val_loc), names(cC)), character(0))
#   expect_equal(setdiff(names(cC), names(occs_val_loc)), c("NAME_0", "distCentroid_m", "geo.check"))
# })
# x <- cC
#   cB <- checkBorders(cC)
# test_that("checkBorders works", {
#   expect_equal(setdiff(names(cC), names(cB)), character(0))
#   expect_equal(setdiff(names(cB), names(cC)),
#                c("share_border", "border.check"))
# })
#
# test_that("checkBorders same.col works", {
#   cB2 <- checkBorders(cC, output = "same.col")
#   expect_equal(setdiff(names(cC), names(cB)), character(0))
#   expect_equal(setdiff(names(cB), names(cC)),
#                c("share_border", "border.check"))
# })
# #cB$share_border#no need to return share_border
# dplyr::count(cC,geo.check)