ENMTools (version 1.0.5)

enmtools.ecospat.bg: enmtools.ecospat.bg, Runs an ecospat background/similarity test using enmtool.species objects.

Description

enmtools.ecospat.bg, Runs an ecospat background/similarity test using enmtool.species objects.

Usage

enmtools.ecospat.bg(
  species.1,
  species.2,
  env,
  nreps = 99,
  layers = NULL,
  test.type = "asymmetric",
  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.

test.type

Symmetric or asymmetric test. An asymmetric test is bguivalent to the "one.sided" option in the ecospat documentation, while a symmetric one would be two-sided.

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.

...

Further arguments to be passed to check.bg

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

# NOT RUN {
install.extras(repos='http://cran.us.r-project.org')
data(iberolacerta.clade)
data(euro.worldclim)
monticola <- iberolacerta.clade$species$monticola
cyreni <- iberolacerta.clade$species$cyreni
enmtools.ecospat.bg(monticola, cyreni, euro.worldclim[[1:2]], nback = 500)
# }