Takes an overlap matrix and a tree and runs permutation tests to determine the statistical significance of the relationship between overlap and time
enmtools.aoc(
clade,
env = NULL,
overlap.source,
nreps = 100,
f = NULL,
overlap.matrix = NULL,
metric = "D"
)An enmtools.clade object containing species data and a phylogeny
Environmental layers for use when overlap is calculated using niche models.
The source of the overlaps to calculate. Choices are "bc", "dm", "gam", "glm", "mx", "range", and "point"
A number of reps to do
The model to be used for GLM and GAM comparisons
A matrix of overlaps to use, for option overlap.source = "matrix"
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.
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.