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EvolEcolGroup · Jul 12, 2024 · f752cac · f752cac
2 parents 1c929f5 + 7fabea4
commit f752cac
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diff --git a/data-raw/make_data/create_lacerta_data.R b/data-raw/make_data/create_lacerta_data.R
@@ -1,3 +1,6 @@
+### THIS IS NOW OBSOLETE AS THE DATASETS ARE GENERATED IN THE OVERVIEW VIGNETTE
+
+
 # download presences
 library(rgbif)
 # download file
@@ -50,13 +53,7 @@ land_mask <- crop(land_mask, iberia_poly)
 # and mask to the polygon
 land_mask <- mask(land_mask, iberia_poly)
 gdal(warn = 3)
-writeCDF(land_mask, "./inst/extdata/lacerta_land_mask.nc",
-  compression = 9, split = TRUE, overwrite = TRUE
-)
-# fix time axis (this is a workaround if we open the file with sf)
-nc_in <- ncdf4::nc_open("./inst/extdata/lacerta_land_mask.nc", write = TRUE)
-ncdf4::ncatt_put(nc_in, varid = "time", attname = "axis", attval = "T")
-ncdf4::nc_close(nc_in)
+terra::saveRDS(land_mask, "./inst/extdata/lacerta_land_mask.rds")
 
 
 climate_vars <- get_vars_for_dataset("WorldClim_2.1_10m")
@@ -67,13 +64,14 @@ climate_present <- pastclim::region_slice(
   crop = iberia_poly
 )
 
-writeCDF(climate_present, "./inst/extdata/lacerta_climate_present_10m.nc",
-  compression = 9, split = TRUE, overwrite = TRUE
-)
+terra::saveRDS(climate_present, "./inst/extdata/lacerta_climate_present_10m.rds")
+#writeCDF(climate_present, "./inst/extdata/lacerta_climate_present_10m.nc",
+#  compression = 9, split = TRUE, overwrite = TRUE
+#)
 # fix time axis (this is a workaround if we open the file with sf)
-nc_in <- ncdf4::nc_open("./inst/extdata/lacerta_climate_present_10m.nc", write = TRUE)
-ncdf4::ncatt_put(nc_in, varid = "time", attname = "axis", attval = "T")
-ncdf4::nc_close(nc_in)
+#nc_in <- ncdf4::nc_open("./inst/extdata/lacerta_climate_present_10m.nc", write = TRUE)
+#ncdf4::ncatt_put(nc_in, varid = "time", attname = "axis", attval = "T")
+#ncdf4::nc_close(nc_in)
 
 
 vars_uncor <- c("bio15", "bio05", "bio13", "bio06")
@@ -84,13 +82,14 @@ climate_future <- pastclim::region_slice(
   dataset = "WorldClim_2.1_HadGEM3-GC31-LL_ssp245_10m",
   crop = iberia_poly
 )
-writeCDF(climate_future, "./inst/extdata/lacerta_climate_future_10m.nc",
-  compression = 9, split = TRUE, overwrite = TRUE
-)
+terra::saveRDS(climate_future, "./inst/extdata/lacerta_climate_future_10m.rds")
+#writeCDF(climate_future, "./inst/extdata/lacerta_climate_future_10m.nc",
+#  compression = 9, split = TRUE, overwrite = TRUE
+#)
 # fix time axis (this is a workaround if we open the file with sf)
-nc_in <- ncdf4::nc_open("./inst/extdata/lacerta_climate_future_10m.nc", write = TRUE)
-ncdf4::ncatt_put(nc_in, varid = "time", attname = "axis", attval = "T")
-ncdf4::nc_close(nc_in)
+#nc_in <- ncdf4::nc_open("./inst/extdata/lacerta_climate_future_10m.nc", write = TRUE)
+#ncdf4::ncatt_put(nc_in, varid = "time", attname = "axis", attval = "T")
+#ncdf4::nc_close(nc_in)
 
 #####
 # from the vignette, we save

diff --git a/data/lacerta.rda b/data/lacerta.rda
diff --git a/data/lacerta_ensemble.rda b/data/lacerta_ensemble.rda
diff --git a/data/lacerta_rep_ens.rda b/data/lacerta_rep_ens.rda
diff --git a/data/lacertidae_background.rda b/data/lacertidae_background.rda
diff --git a/inst/extdata/lacerta_climate_future_10m.nc b/inst/extdata/lacerta_climate_future_10m.nc
diff --git a/inst/extdata/lacerta_climate_future_10m.rds b/inst/extdata/lacerta_climate_future_10m.rds
diff --git a/inst/extdata/lacerta_climate_present_10m.nc b/inst/extdata/lacerta_climate_present_10m.nc
diff --git a/inst/extdata/lacerta_climate_present_10m.rds b/inst/extdata/lacerta_climate_present_10m.rds
diff --git a/inst/extdata/lacerta_coords.RDS b/inst/extdata/lacerta_coords.RDS
diff --git a/inst/extdata/lacerta_land_mask.nc b/inst/extdata/lacerta_land_mask.nc
diff --git a/inst/extdata/lacerta_land_mask.rds b/inst/extdata/lacerta_land_mask.rds
diff --git a/tests/testthat/test_clamp_predictors.R b/tests/testthat/test_clamp_predictors.R
@@ -1,12 +1,12 @@
 test_that("clamping_predictor works on SpatRasters",{
   # get current climate and subset to 3 variables
-  climate_present <- terra::rast(system.file("extdata/lacerta_climate_present_10m.nc",
+  climate_present <- terra::readRDS(system.file("extdata/lacerta_climate_present_10m.rds",
                                 package = "tidysdm"
   ))
   climate_present <- climate_present[[c("bio05","bio13","bio06","bio15")]]
   lacerta_env <- bind_cols(terra::extract(climate_present, lacerta[,c(3,2)], ID = FALSE))
   # now get future climate
-  climate_future <- terra::rast(system.file("extdata/lacerta_climate_future_10m.nc",
+  climate_future <- terra::readRDS(system.file("extdata/lacerta_climate_future_10m.rds",
                                      package = "tidysdm"
   ))
   climate_future <- climate_future [[names(climate_present)]]

diff --git a/tests/testthat/test_extrapol_mess.R b/tests/testthat/test_extrapol_mess.R
@@ -1,6 +1,6 @@
 test_that("mess_predictor works on SpatRasters",{
   # now get future climate
-  climate_future <- terra::rast(system.file("extdata/lacerta_climate_future_10m.nc",
+  climate_future <- terra::readRDS(system.file("extdata/lacerta_climate_future_10m.rds",
                                      package = "tidysdm"
   ))
   mess_rast <- extrapol_mess(climate_future, training = lacerta_thin, .col= class)

diff --git a/tests/testthat/test_filter_collinear.R b/tests/testthat/test_filter_collinear.R
@@ -43,7 +43,7 @@ test_that("filter collinear variables with cor_caret", {
 
 
   # test method on SpatRaster
-  climate_present <- terra::rast(system.file("extdata/lacerta_climate_present_10m.nc",
+  climate_present <- terra::readRDS(system.file("extdata/lacerta_climate_present_10m.rds",
                                       package = "tidysdm"
   ))
   cor_spatraster_ken <- filter_collinear(climate_present, cor_type = "kendall")

diff --git a/tests/testthat/test_overlap_niche.R b/tests/testthat/test_overlap_niche.R
@@ -1,9 +1,9 @@
 test_that("niche_overlap quantifies difference between rasters",{
-climate_present <- terra::rast(system.file("extdata/lacerta_climate_present_10m.nc",
+climate_present <- terra::readRDS(system.file("extdata/lacerta_climate_present_10m.rds",
                                            package = "tidysdm"
 ))
 
-climate_future <- terra::rast(system.file("extdata/lacerta_climate_future_10m.nc",
+climate_future <- terra::readRDS(system.file("extdata/lacerta_climate_future_10m.rds",
                                           package = "tidysdm"
 ))
 lacerta_present<-predict_raster(lacerta_ensemble, climate_present)