createPresAb: Create pseudo absences and combine with the scheme occurrence...

In robboyd/soaR:

Create pseudo absences and combine with the scheme occurrence data.

Description

This function creates pseudo absences according to the "target group" approach (Phillips 2009). The aim is to generate pseudo absences with similar environmental bias as the occurrence data. Pseudo absences are created for individual species, but the function works at the group level because absences are inferred from the presences of non-focal species in the same group.

Create environmental layers in ascii for a specified region and spatial resolution

Usage

createPresAb(
  inPath,
  taxon,
  species,
  minYear,
  maxYear,
  nAbs,
  matchPres = FALSE,
  recThresh
)

createPresAb(
  inPath,
  taxon,
  species,
  minYear,
  maxYear,
  nAbs,
  matchPres = FALSE,
  recThresh
)

Arguments

inPath	String. Path to species data extracted using extract_records.
taxon	String. Taxonomic group. Must match one of the groups in inPath.
species	String. Focal species' name (must be in chosen taxonomic group)
minYear	Numeric.
maxYear	Numeric. Threshold number of records below which species' are dropped.
nAbs	Numeric. Number of pseudo absences to produce. Note that this is overriden if matchPres = TRUE.
matchPres	Logical. If true, will produce absences such that there are an equal number to presences. Defaults to false
recThresh	Numeric. Lower threshold number of records; species with fewer records are dropped.
dat	String. data.frame with occurrence records for all species in the group of interest. Could be the output of formatData. Must have column names "species", "eastings" and "northings".
matchpres	Logical. If TRUE this overrides nAbs and creates pseudo absences in equal number to the occurrence data.
res	Numeric. Spatial resolution in decimal degrees (defaults to 0.5)

Value

A list with n elements, where n is the number of species in the group. Each element contains two dataframes, one with the coordinates of the presence data, and a second with the coordinates of the pseudo absences. The coordinate reference system is OSGB36.

robboyd/soaR documentation built on April 24, 2022, 9:44 a.m.