enmtools.aoc {ENMTools}

Takes an overlap matrix and a tree and runs permutation tests to determine the statistical significance of the relationship between overlap and time

Description

Takes an overlap matrix and a tree and runs permutation tests to determine the statistical significance of the relationship between overlap and time

Usage

enmtools.aoc(
  clade,
  env = NULL,
  overlap.source,
  nreps = 100,
  f = NULL,
  overlap.matrix = NULL,
  metric = "D",
  ...
)

Arguments

clade

An enmtools.clade object containing species data and a phylogeny

env

Environmental layers for use when overlap is calculated using niche models.

overlap.source

The source of the overlaps to calculate. Choices are "bc", "dm", "gam", "glm", "mx", "range", and "point"

nreps

A number of reps to do

f

The model to be used for GLM and GAM comparisons

overlap.matrix

A matrix of overlaps to use, for option overlap.source = "matrix"

metric

The overlap metric to use. For ENM sources, this can be any combination of "D", "I", "cor", "env.D", "env.I", and "env.cor". for range and point overlap this argument is ignored.

...

Arguments to be passed to modeling functions for ENM-based overlaps.

Value

A list containing a data frame of coefficients from the empirical regression of overlap on time along with the coefficients from all Monte Carlo replicates, along with plots and p values for the accompanying statistical tests.