iucn_species_gpkg() splits IUCN shape files into separate gpkg files
for each species, and returns their paths. This allows for parallel processing
in downstream analysis, and avoids the need to read large shape files again.
Use iucn_spatial_species() and iucn_spatial_features()
for quick skimming of the whole dataset, and determine which species to analyze.
Usage
iucn_spatial_species(iucn_source = NULL)
iucn_species_gpkg(iucn_source = NULL, overwrite = FALSE)Arguments
- iucn_source
Path to the directory containing IUCN shape files.
iucn_source_path()is used ifNULLis given (default).- overwrite
Whether to overwrite existing cache files.
Value
iucn_spatial_species() returns a data.frame extracted from iucn_spatial_features().
iucn_species_gpkg() returns a data.frame with two columns,
"sci_name" and "source", to be used for quantify_vector_kgc().
Examples
if (FALSE) { # \dontrun{
options(habistats.iucn_source = "path/to/your/data")
habistats::iucn_source_path()
} # }
old = options(habistats.cache_dir = "~/.cache/habistats-example")
habistats::cache_dir()
#> ~/.cache/habistats-example
habistats::iucn_spatial_species()
#> # A tibble: 4 × 11
#> kingdom phylum class order_ family genus sci_name category marine terrestria
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <lgl> <lgl>
#> 1 METALLICA CHORD… MAMM… CARNI… CANID… Stra… Strato … LC FALSE TRUE
#> 2 METALLICA CHORD… AVES PASSE… CORVI… Diva Diva sa… LC FALSE TRUE
#> 3 METALLICA TRACH… MAGN… CUCUR… CUCUR… Kai Kai kis… LC FALSE TRUE
#> 4 METALLICA CHORD… MAMM… CINGU… CHLAM… Elp Elp tar… EW FALSE TRUE
#> # ℹ 1 more variable: freshwater <lgl>
habistats::iucn_species_gpkg()
#> # A tibble: 4 × 2
#> sci_name source
#> <chr> <fs::path>
#> 1 Strato arctica …A/MAMMALIA/CARNIVORA/CANIDAE/Strato/Strato_arctica/source.gpkg
#> 2 Diva satanica …ATA/AVES/PASSERIFORMES/CORVIDAE/Diva/Diva_satanica/source.gpkg
#> 3 Kai kiske …OLIOPSIDA/CUCURBITALES/CUCURBITACEAE/Kai/Kai_kiske/source.gpkg
#> 4 Elp tarkus …A/MAMMALIA/CINGULATA/CHLAMYPHORIDAE/Elp/Elp_tarkus/source.gpkg
options(old) # reset for this example, not needed in real use