inst/tinytest/test_gdm.R

In fitzLab-AL/gdm: Generalized Dissimilarity Modeling

#library(gdm)
#library(terra)

#sppTab <- southwest[, c("species", "site", "Lat", "Long")]

#rastFile <- system.file("./extdata/swBioclims.grd", package="gdm")
#envRast <- terra::rast(rastFile)


# test formatsitepair function --------------------------------------------

# expect warning because of using raster inputs
# expect_warning({
#
#   sitePairRast <- formatsitepair(
#     sppTab,
#     2,
#     XColumn = "Long",
#     YColumn = "Lat",
#     sppColumn = "species",
#     siteColumn = "site",
#     predData = envRast
#   )
#
# })

#sitePairRast <- na.omit(sitePairRast)

# build the model ---------------------------------------------------------

# expect_silent({
#
#   gdmRastMod <- gdm(sitePairRast, geo = TRUE)
#
# })

# # test predict function ---------------------------------------------------
# futureRast <- envRast
# futureRast[[3]] <- futureRast[[3]] * 0.75
#
# # check prediction is done silently i.e. no errors/warnings
# expect_silent({
#
#  pred_raster <- gdm:::predict.gdm(
#     object = gdmRastMod,
#     data = envRast,
#     time = TRUE,
#     predRasts = futureRast,
#     filename = tempfile(fileext = ".tif")
#   )
#
# })
#
# # read the prediction created by gdm version 1.5.x
# pred_v1.5 <- terra::rast(
#   system.file("./extdata/test_data/pred_3_75.tif", package="gdm")
# )
#
# # round as file compression might lose some precision
# diff <- round(terra::global(pred_raster - pred_v1.5, "mean", na.rm = TRUE)[1,1], 5)
#
# expect_true(
#   diff == 0
# )

#
# # test transform function -------------------------------------------------
#
# # check gdm.transform is done silently i.e. no errors/warnings
# expect_silent({
#
#   trans_raster <- gdm.transform(
#     model = gdmRastMod,
#     data = envRast,
#     filename = tempfile(fileext = ".tif")
#   )
#
# })
#
# # read the transformed vars created by gdm version 1.5.x
# trans_v1.5 <- terra::rast(
#   system.file("./extdata/test_data/gdm_trans_vars.grd", package="gdm")
# )
#
# # round as file compression might lose some precision
# diff <- round(terra::global(trans_raster - trans_v1.5, "mean", na.rm = TRUE)[, 1], 5)
#
# # expect all difference be zero
# expect_true(
#   all(diff == 0)
# )
#