Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
comm.dist(x)# S3 method for matrix
comm.dist(x)
# S3 method for comparative.comm
comm.dist(x)
traits.dist(x, dist.func = dist.func.default, ...)
# S3 method for comparative.comm
traits.dist(x, dist.func = dist.func.default, alltogether = TRUE, ...)
# S3 method for default
traits.dist(x, dist.func = dist.func.default, ...)
# S3 method for data.frame
traits.dist(x, dist.func = dist.func.default, ...)
dist.func.default(x)
phylo.dist(x, ...)
# S3 method for phylo
phylo.dist(x, ...)
# S3 method for comparative.comm
phylo.dist(x, ...)
funct.phylo.dist(x, phyloWeight, p = 2, ...)
pianka.dist(x, ...)
# S3 method for matrix
pianka.dist(x, env = NULL, ...)
# S3 method for comparative.comm
pianka.dist(x, alltogether = TRUE, ...)
an object
a function for computing distances. The default,
dist.func.default, returns a Euclidean distance of the
scaled and centred data.
not used
should one multivariate distance matrix be
computed for all traits at once (DEFAULT; alltogether =
TRUE) or for each trait at a time (alltogether = FALSE)?
phylogenetic weighting parameter (referred to as
a in Cadotte et al. (2013)
exponent giving the exponent to use for combining
functional and phylogenetic distances (the default, p = 2,
gives a Euclidean combination).
environmental variable to be used to calculate the distance matrix
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!
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.