Integrating Phylogenies and Ecology

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Documentation for package ‘picante’ version 1.8.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

picante-package	picante: Integrating Phylogenies and Ecology
color.plot.phylo	Color tip labels based on trait
comdist	Calculates inter-community mean pairwise distance
comdistnn	Calculates inter-community mean nearest taxon distance
comdistnt	Calculates inter-community mean nearest taxon distance
comm.phylo.cor	Correlations between species co-occurrence and phylogenetic distances
comm.phylo.qr	Quantile regression slopes between species co-occurrence and phylogenetic distances
cor.table	Table of correlations and P-values
df2vec	Picante utility functions
ead	Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
evol.distinct	Species' evolutionary distinctiveness
expected.pd	Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
internal2tips	Picante utility functions
IvesGodfray	Host-parasitoid food web data
Kcalc	K statistic of phylogenetic signal
match.comm.dist	Match taxa in phylogeny and data
match.phylo.comm	Match taxa in phylogeny and data
match.phylo.data	Match taxa in phylogeny and data
matrix2sample	Convert community data matrix to Phylocom sample
mnnd	Mean nearest taxon distance
mntd	Mean nearest taxon 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
PCD	Phylogenetic Community Dissimilarity
pcd	Phylogenetic Community Dissimilarity
pd	Calculate Faith's Phylogenetic Diversity
phyEstimate	Phylogenetic estimation of traits for unobserved taxa
phyEstimateDisc	Phylogenetic estimation of traits for unobserved taxa
phylocom	Phylocom default data
phylosignal	Measure phylogenetic signal
phylosor	Phylogenetic index of beta-diversity PhyloSor
phylosor.rnd	Null PhyloSor values of phylogenetic beta-diversity
phylostruct	Permutations to Test for Phylogenetic Signal in Community Composition
pic.variance	Picante utility functions
picante	picante: Integrating Phylogenies and Ecology
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
psv.spp	Phylogenetic Species Diversity Metrics
randomizeMatrix	Null models for community data matrix randomization
raoD	Rao's quadratic entropy
readsample	Read Phylocom sample
sample2matrix	Convert Phylocom sample to community data matrix
ses.mnnd	Standardized effect size of MNTD
ses.mntd	Standardized effect size of MNTD
ses.mpd	Standardized effect size of MPD
ses.pd	Standardized effect size of PD
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
sppregs.plot	Regressions to Separate Phylogenetic Attraction and Repulsion
tax.distinctiveness	Taxonomic distinctiveness sensu Vane-Wright or May
taxaShuffle	Picante utility functions
tipShuffle	Picante utility functions
traitgram	Draw phylogeny with nodes at trait positions
unifrac	Unweighted UniFrac distance between communities
variance.pd	Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
writesample	Write a Phylocom community sample file
writetraits	Write a Phylocom traits formatted file