env.overlap: Calculates overlap between models in environment space using...

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

Calculates overlap between models in environment space using latin hypercube sampling

Description

Calculates overlap between models in environment space using latin hypercube sampling

Usage

env.overlap(
  model.1,
  model.2,
  env,
  tolerance = 0.001,
  max.reps = 10,
  cor.method = "spearman",
  chunk.size = 1e+05,
  recal.model.1 = NA,
  recal.model.2 = NA,
  verbose = FALSE
)

Arguments

model.1	An enmtools.model object model object that can be projected using the predict() function
model.2	Another enmtools.model object or other model object that can be projected using the predict() function
env	A raster, raster stack of environmental data, or a list of minima and maxima for the environmental space to evaluate models over
tolerance	How close do successive overlap metrics have to be before we decide we're close enough to the final answer
max.reps	Maximum number of attempts that will be made to find suitable starting conditions
cor.method	Which method to use for calculating correlations between models
chunk.size	How many combinations of environmental variables to try at a time. If your niche breadth in environment space is small, increasing this value may help you get a result.
recal.model.1	Optional. The output of enmtools.recalibrate for model 1, which needs to have been run with "recalibrate = TRUE".
recal.model.2	Optional. The output of enmtools.recalibrate for model 2, which needs to have been run with "recalibrate = TRUE".
verbose	Controls printing of various messages progress reports. Defaults to FALSE.

Value

A list of values measuring the overlap between models in environment space, as well as some plots depicting change of the estimates as a function of how many samples were used, which are included as a sort of convergence diagnostic.

Examples

cyreni <- iberolacerta.clade$species$cyreni
monticola <- iberolacerta.clade$species$monticola
cyreni.glm <- enmtools.glm(cyreni, euro.worldclim, f = pres ~ bio1 + bio12, nback = 500)
monticola.glm <- enmtools.glm(monticola, euro.worldclim, f = pres ~ bio1 + bio12, nback = 500)
env.overlap(cyreni.glm, monticola.glm, euro.worldclim)

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