dist.xxx: Make co-existence matrices based on phylogeny (and/or)...

In pez: Phylogenetics for the Environmental Sciences

Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap

Description

Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap

Usage

comm.dist(x)

## S3 method for class 'matrix'
comm.dist(x)

## S3 method for class 'comparative.comm'
comm.dist(x)

traits.dist(x, dist.func = dist.func.default, ...)

## S3 method for class 'comparative.comm'
traits.dist(x, dist.func = dist.func.default, alltogether = TRUE, ...)

## Default S3 method:
traits.dist(x, dist.func = dist.func.default, ...)

## S3 method for class 'data.frame'
traits.dist(x, dist.func = dist.func.default, ...)

dist.func.default(x)

phylo.dist(x, ...)

## S3 method for class 'phylo'
phylo.dist(x, ...)

## S3 method for class 'comparative.comm'
phylo.dist(x, ...)

funct.phylo.dist(x, phyloWeight, p = 2, ...)

pianka.dist(x, ...)

## S3 method for class 'matrix'
pianka.dist(x, env = NULL, ...)

## S3 method for class 'comparative.comm'
pianka.dist(x, alltogether = TRUE, ...)

Arguments

x	an object
dist.func	a function for computing distances. The default, dist.func.default, returns a Euclidean distance of the scaled and centred data.
...	not used
alltogether	should one multivariate distance matrix be computed for all traits at once (DEFAULT; alltogether = TRUE) or for each trait at a time (alltogether = FALSE)?
phyloWeight	phylogenetic weighting parameter (referred to as a in Cadotte et al. (2013)
p	exponent giving the exponent to use for combining functional and phylogenetic distances (the default, p = 2, gives a Euclidean combination).
env	environmental variable to be used to calculate the distance matrix

Details

comm.dist returns the 1 - co-existence of species. Look at how this is calcualted; it incorporates abundances, and if you don't want it to do so simply call it on a presence/absensence (1/0) matrix.

traits.dist returns the functional trait distance of species

phylo.dist returns the phylogenetic (cophenetic) distance of species

funct.phylo.dist returns the combined phylogenetic and trait distances of species, based on the traitgram approach of Cadotte et al. (2013).

Make functional phylogenetic distance matrix

pianka.dist returns the environemntal tolerances distance matrices of species. Based on Pianka's distance (i.e., niche overlap based on environmental variables at co-occuring sites), as defined in Cavender-Bares et al. (2004) - likely not the original reference!

References

Cadotte M.A., Albert C.H., & Walker S.C. The ecology of differences: assessing community assembly with trait and evolutionary distances. Ecology Letters 16(10): 1234–1244.

Cavender-Bares J., Ackerly D.D., Baum D.A. & Bazzaz F.A. (2004) Phylogenetic overdispersion in Floridian oak communities. The Americant Naturalist 163(6): 823–843.

pez documentation built on Sept. 1, 2022, 1:09 a.m.