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Export EOO and AOO as spatial files (shapefile or GeoPackage)

Source: R/export.R
export_ranges.Rd

Writes the Extent of Occurrence (EOO) polygons and the Area of Occupancy (AOO) polygons produced by assess_species() to disk, with the area, habitat-conversion and provisional-category attributes attached to each feature (one feature per species by default). Handy for opening the results in QGIS/ArcGIS or sharing them.

Usage

export_ranges(
  assessment,
  dir = tempdir(),
  layer_prefix = "mappingAS",
  what = c("both", "eoo", "aoo"),
  format = c("shapefile", "gpkg"),
  crs = 4326,
  aoo_as = c("cells", "union"),
  class_csv = TRUE,
  zip = FALSE,
  quiet = TRUE
)

Arguments

assessment

A geoconv_assessment object from assess_species().

dir

Output directory (created if it does not exist). Default tempdir(); pass an explicit path to keep the files.

layer_prefix

File/layer name prefix. Default "mappingAS".

what

Which ranges to export: "both" (default), "eoo" or "aoo".

format

"shapefile" (default; one file set per range, i.e. *_EOO.shp and *_AOO.shp) or "gpkg" (a single GeoPackage holding both layers).

crs

Output CRS (default 4326, WGS84). Anything accepted by sf::st_crs() also works (an EPSG code or a proj string).

aoo_as

"cells" (default; one feature per occupied 2-km grid cell, each with a cell_id) or "union" (one dissolved feature per species).

class_csv

If TRUE (default), also writes <prefix>_classes.csv with the full per-class MapBiomas breakdown (every class) for the EOO and AOO of each species; included in the zip when zip = TRUE. Skipped if MapBiomas was not computed.

zip

If TRUE, the written files are bundled into a single .zip inside dir and the path to that zip is returned (most useful for the shapefile format, which has several sidecar files). Default FALSE.

quiet

Passed to sf::st_write(). Default TRUE.

Value

(Invisibly) a character vector with the file paths written, or the path to the .zip when zip = TRUE.

Details

Because the ESRI Shapefile format limits field names to 10 characters, the attribute fields use compact names (see the Attribute fields section). A GeoPackage (format = "gpkg") stores both ranges as two layers (eoo, aoo) inside a single file and has no such limitation.

Attribute fields

species; eoo_km2 or aoo_km2 (and n_cells for AOO); conv_pct (percent converted/anthropic within that range); nat_pct (percent natural); cat_B1 or cat_B2 (provisional size-only category); prov_cat; mb_year; mb_coll (MapBiomas year and collection). Conversion fields are NA when MapBiomas was not computed.

Examples

occ <- read_occurrences(system.file("extdata", "example_occurrences.csv",
                                    package = "mappingAS"))
res <- assess_species(occ, mapbiomas = FALSE, verbose = FALSE)

d <- file.path(tempdir(), "mappingAS_ranges")
dir.create(d, showWarnings = FALSE)

# Two shapefiles (EOO + AOO) written to a temporary directory:
export_ranges(res, dir = d)

# A single GeoPackage with both layers:
export_ranges(res, dir = d, format = "gpkg")

# \donttest{
# Everything bundled into one .zip (good for downloads):
export_ranges(res, dir = d, zip = TRUE)
# }