Find the areas of the land masses relevant to the taxon of interest with two options: a database of island names and areas, or a user-provided shapefile.
Arguments
- occs
The dataframe that is returned by
ssarp::find_land(). If using a custom occurrence record dataframe, ensure that it has the following columns: "acceptedScientificName", "genericName", "specificEpithet", "decimalLongitude", "decimalLatitude", "First", "Second", "Third", "datasetKey". The "datasetKey" column is important for GBIF records and identifies the dataset to which the occurrence record belongs. Custom dataframes without this style of data organization should fill the column with placeholder values.- area_custom
A dataframe including names of land masses and their associated areas. This dataframe should be provided when the user would like to bypass using the built-in database of island names and areas. Please ensure that the custom dataframe includes the land mass's area in a column called "AREA" and the name in a column called "Name". (Optional)
- shapefile
A shapefile (.shp) containing spatial information for the geographic locations of interest. (Optional)
- names
If the user would like to restrict which polygons in the shapefile are included in the returned occurrence record dataframe, they can be specified here as a vector. If the user does not provide a vector, all of the non-NA names in the shapefile will be included (as found in shapefile$name). (Optional)
Details
The first method is to reference a built-in dataset of island names and areas to find the areas of the landmasses relevant to the taxon of interest. The user may also decide to input their own custom dataframe including names of relevant land masses and their associated areas to bypass using ssarp's built-in dataset.
The second method is to reference a user-supplied shapefile containing spatial information for the landmasses of interest in order to determine their areas.
While the word "landmasses" was used heavily in this documentation, users supplying their own custom area dataframe or shapefile are encouraged to use this function in the ssarp workflow to create species- and speciation- area relationships for island-like systems such as lakes, fragmented habitat, and mountain peaks.
Examples
# The GBIF key for the Anolis genus is 8782549
# Read in example dataset filtered from:
# dat <- rgbif::occ_search(taxonKey = 8782549,
# hasCoordinate = TRUE,
# limit = 10000)
dat <- read.csv(system.file("extdata",
"ssarp_Example_Dat.csv",
package = "ssarp"))
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.char, ...): no lines available in input
occs <- find_land(occurrences = dat)
#> Error: object 'dat' not found
areas <- find_areas(occs = occs)
#> Error: object 'occs' not found