enmtools.ecospat.id: enmtools.ecospat.id, Runs an ecospat identity test using...

In ENMTools: Analysis of Niche Evolution using Niche and Distribution Models

enmtools.ecospat.id, Runs an ecospat identity test using enmtool.species objects.

Description

enmtools.ecospat.id, Runs an ecospat identity test using enmtool.species objects.

Usage

enmtools.ecospat.id(
  species.1,
  species.2,
  env,
  nreps = 99,
  layers = NULL,
  th.sp = 0,
  th.env = 0,
  R = 100,
  nback = 1000,
  bg.source = "default",
  verbose = FALSE
)

Arguments

species.1	An enmtools.species object
species.2	An enmtools.species object
env	A set of environmental layers
nreps	The number of pseudoreplicates to perform
layers	A vector of length 2 containing the names of the layers to be used. If no layer names are provided and there are more than two layers in env, enmtools will perform a pca and use the top two layers from that.
th.sp	Quantile of species densities used as a threshold to exclude low species density values. See documentation for ecospat.grid.clim.dyn.
th.env	Quantile of environmental densities across study sites used as threshold to exclude low environmental density values. See documentation for ecospat.grid.clim.dyn.
R	Resolution of the grid. See documentation for ecospat.grid.clim.dyn.
nback	Number of background points to use for density calculations.
bg.source	Source for drawing background points. If "points", it just uses the background points that are already in the species object. If "range", it uses the range raster. If "env", it draws points at randome from the entire study area outlined by the first environmental layer.
verbose	Controls printing of various messages progress reports. Defaults to FALSE.

Value

A list containing the ecospat output kernel density estimates for each species and their background, as well as the results of hypothesis tests and their accompanying plots.

Examples

#install.extras(repos='http://cran.us.r-project.org')
monticola <- iberolacerta.clade$species$monticola
cyreni <- iberolacerta.clade$species$cyreni
if(check.extras("enmtools.ecospat.id")) {
  enmtools.ecospat.id(monticola, cyreni, euro.worldclim[[1:2]], nback = 500)
}

ENMTools documentation built on April 11, 2023, 6:09 p.m.