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, ...)
## S3 method for class 'default':
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, ...)
dist.func.default, returns a Euclidean distance of the
scaled and centred data.alltogether =
TRUE) or for each trait at a time (alltogether = FALSE)?a in Cadotte et al. (2013)p = 2,
gives a Euclidean combination).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).
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!
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.