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picante (version 1.4-1)

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

1.4-1

License

GPL-2

Maintainer

Steven Kembel

Last Published

September 4th, 2012

Functions in picante (1.4-1)

phylosor

Phylogenetic index of beta-diversity PhyloSor
mpd

Mean pairwise distance
cor.table

Table of correlations and P-values
phylosignal

Measure phylogenetic signal
tax.distinctiveness

Taxonomic distinctiveness sensu Vane-Wright or May
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
phylocom

Phylocom default data
color.plot.phylo

Color tip labels based on trait
writetraits

Write a Phylocom traits formatted file
comm.phylo.qr

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

Phylogenetic Generalized Linear Mixed Model
pic.circular

Phylogenetic independent contrasts for circular data
pic3

Independent contrasts
comdist

Calculates inter-community mean pairwise distance
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
writesample

Write a Phylocom community sample file
species.dist

Species co-occurrence distances
picante-package

picante: R tools for integrating phylogenies and ecology
IvesGodfray

Host-parasitoid food web data
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
ses.mpd

Standardized effect size of MPD
pd

Calculate Faith's Phylogenetic Diversity
readsample

Read Phylocom sample
utility

Picante utility functions
ses.pd

Standardized effect size of PD
psd

Phylogenetic Species Diversity Metrics
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
traitgram

Draw phylogeny with nodes at trait positions
Kcalc

K statistic of phylogenetic signal
mntd

Mean nearest taxon distance
prune.sample

Prune tree to match community data or trait data
unifrac

Unweighted UniFrac distance between communities
evol.distinct

Species' evolutionary distinctiveness
matrix2sample

Convert community data matrix to Phylocom sample
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
randomizeMatrix

Null models for community data matrix randomization
ses.mntd

Standardized effect size of MNTD
pblm

Phylogenetic Bipartite Linear Model
comdistnt

Calculates inter-community mean nearest taxon distance
raoD

Rao's quadratic entropy
sample2matrix

Convert Phylocom sample to community data matrix
match.phylo.data

Match taxa in phylogeny and data
pcd

Phylogenetic Community Dissimilarity