R: Integrating Phylogenies and Ecology

# Integrating Phylogenies and Ecology

## Documentation for package ‘picante’ version 1.8.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## 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