Tools for integrating phylogenies and ecology

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Documentation for package ‘picante’ version 0.4-0

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picante-package Picante: Phylocom Integration, Community Analyses, Null-models, Traits, and Evolution in R
color.plot.phylo Color tip labels based on trait
comm.phylo.cor Correlations between species co-occurrence and phylogenetic distances
cor.table Table of correlations and P-values
df2vec Picante utility functions
evolve.brownian Trait evolution under Brownian motion
internal2tips Picante utility functions
Kcalc K statistic of phylogenetic signal
matrix2sample Convert community data matrix to Phylocom sample
mnnd Mean nearest neighbour distance
mpd Mean pairwise distance
multiPhylosignal Calculates phylogenetic signal for data.frame of traits
node.age Picante utility functions
pblm Phylogenetic Bipartite Linear Model
pblmpredict Phylogenetic Bipartite Linear Model
pd Calculate Faith's Phylogenetic Diversity
phylocom Phylocom default data
phylosignal Measure phylogenetic signal
phylostruct Permutations to Test for Phylogenetic Signal in Community Composition
pic.circular Phylogenetic independent contrasts for circular data
pic.variance Picante utility functions
picante Picante: Phylocom Integration, Community Analyses, Null-models, Traits, and Evolution in R
prune.missing Prune tree to match community data or trait data
prune.sample Prune tree to match community data or trait data
psc Phylogenetic Species Diversity Metrics
psd Phylogenetic Species Diversity Metrics
pse Phylogenetic Species Diversity Metrics
psr Phylogenetic Species Diversity Metrics
psv Phylogenetic Species Diversity Metrics
randomizeSample Null models for community data matrix randomization
readsample Read Phylocom sample
sample2matrix Convert Phylocom sample to community data matrix
ses.mnnd Standardized effect size of MNND
ses.mpd Standardized effect size of mpd
sortColumns Picante utility functions
sortRows Picante utility functions
specaccum.psr Phylogenetic Species Richness Sample-Based Rarefaction Curve
species.dist Species co-occurrence distances
sppregs Regressions to Separate Phylogenetic Attraction and Repulsion
taxaShuffle Picante utility functions
writesample Write a Phylocom community sample file
writetraits Write a Phylocom traits formatted file