prepData: Prepare SWD files of occurrence and background environmental...

In peterbat1/fitMaxnet: Fit MaxEnt Niche Models Using maxnet

Prepare SWD files of occurrence and background environmental data

Description

Load a set of environmental covariate to be used to spatially project a fitted maxnet model and build pairs of SWD-format files

Usage

prepData(
  taxonName,
  occData,
  excludedVars = NULL,
  boundsPoly,
  envDataPath,
  outputPath,
  appendDate = FALSE,
  trace = FALSE
)

Arguments

taxonName	String (character object) giving the taxonomic name of the entity for which data is being supplied.
occData	A numeric matrix or data.frame with at least two columns holding latitude and longitude values for occurrence records. Column names are matched against 'lat' (or 'Y") and 'long' (or 'X') in a effort to automagically identify these columns.
excludedVars	A character vector of variable names to be excluded from output files. Default is NULL.
boundsPoly	An sf or SpatialPolygons* object defining the region within which background points will be selected.
envDataPath	String giving the file system path to the folder containing the geoTIFF rasters representing the environmental layers to be used to spatially project a fitted maxnet model
outputPath	String giving the file system path to the folder into which occurrence and background SWD files will be written. See Details for information about the file naming convention.
appendDate	Logical. Should the current system date be appended to output file names? Default is FALSE.
trace	Logical. Emits additional diagnostic messages when TRUE; default is FALSE

Details

Load raster stack of environmental data layers to be used for fitting a maxnet model and, using coordinate values of occurrence records supplied in occData and a background-constraining spatial polygon object, output samples-with-data (SWD) files defined in the original Java implementation of MaxEnt. Two files are produced: an occurrence SWD file, and a background points SWD file which are diferentiated by the file name assigned.

NOTE: No checks are made that the projection of occurrence lat/longs or X/Y values matches the raster layers used for environmental data. You must ensure they match before calling this function.

Value

Invisibly returns NULL but has side-effect of outputting data files

peterbat1/fitMaxnet documentation built on Sept. 17, 2024, 10:50 p.m.