limiting: Calculate which factors limit predicted habitat suitability
In johnbaums/rmaxent: Tools for working with Maxent in R

Description Usage Arguments Value References Examples

Calculate a limiting factor surface corresponding to projections of a Maxent model.

1	limiting(x, me)

`x`	A `RasterStack` containing predictors grids for predictors used in the Maxent model specified at `me`.
`me`	A a `MaxEnt` fitted model object (from `dismo::maxent`).

A Raster object indicating the most limiting factor at each grid cell. This is defined, for each grid cell, as the variable whose value is most responsible for decreasing suitability at that cell. The decrease in suitability is calculated, for each predictor in turn, relative to the suitability (logistic prediction) that would be achieved if that predictor took the value equal to the mean at occurrence sites (median for categorical variables). The predictor associated with the largest decrease in suitability is the most limiting factor.

Elith, J., Kearney, M. and Phillips, S. (2010), The art of modelling range-shifting species. Methods in Ecology and Evolution, 1: 330-342. doi: 10.1111/j.2041-210X.2010.00036.x

# This uses the ?dismo::maxent example. Only run if maxent.jar exists.
if(require(dismo) && require(rJava) && 
   file.exists(system.file('java/maxent.jar', package='dismo'))) {
  fnames <- list.files(system.file('ex', package='dismo'), '\\.grd$', 
                       full.names=TRUE)
  predictors <- stack(fnames)
  occurrence <- system.file('ex/bradypus.csv', package='dismo')
  occ <- read.table(occurrence, header=TRUE, sep=',')[,-1]
  me <- maxent(predictors, occ, factors='biome')
  limiting(predictors, me)
}