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picante (version 1.5-1)

R tools for integrating phylogenies and ecology

Description

Phylocom integration, community analyses, null-models, traits and evolution in R

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Version

Install

install.packages('picante')

Monthly Downloads

4,766

Version

1.5-1

License

GPL-2

Maintainer

Steven Kembel

Last Published

October 2nd, 2012

Functions in picante (1.5-1)

species.dist

Species co-occurrence distances
prune.sample

Prune tree to match community data or trait data
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
mpd

Mean pairwise distance
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
ses.mntd

Standardized effect size of MNTD
ses.pd

Standardized effect size of PD
evol.distinct

Species' evolutionary distinctiveness
pblm

Phylogenetic Bipartite Linear Model
IvesGodfray

Host-parasitoid food web data
matrix2sample

Convert community data matrix to Phylocom sample
psd

Phylogenetic Species Diversity Metrics
ses.mpd

Standardized effect size of MPD
phylosor

Phylogenetic index of beta-diversity PhyloSor
pglmm

Phylogenetic Generalized Linear Mixed Model
comdist

Calculates inter-community mean pairwise distance
writesample

Write a Phylocom community sample file
phylocom

Phylocom default data
raoD

Rao's quadratic entropy
Kcalc

K statistic of phylogenetic signal
picante-package

picante: R tools for integrating phylogenies and ecology
color.plot.phylo

Color tip labels based on trait
pic3

Independent contrasts
match.phylo.data

Match taxa in phylogeny and data
comm.phylo.qr

Quantile regression slopes between species co-occurrence and phylogenetic distances
comdistnt

Calculates inter-community mean nearest taxon distance
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
writetraits

Write a Phylocom traits formatted file
traitgram

Draw phylogeny with nodes at trait positions
tax.distinctiveness

Taxonomic distinctiveness sensu Vane-Wright or May
randomizeMatrix

Null models for community data matrix randomization
utility

Picante utility functions
sample2matrix

Convert Phylocom sample to community data matrix
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
pcd

Phylogenetic Community Dissimilarity
unifrac

Unweighted UniFrac distance between communities
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
readsample

Read Phylocom sample
cor.table

Table of correlations and P-values
pd

Calculate Faith's Phylogenetic Diversity
expected.pd

Expected PD and Edge Abundance Distribution of a phylogeny
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
phylosignal

Measure phylogenetic signal
mntd

Mean nearest taxon distance