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picante (version 0.6-1)

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

4,131

Version

0.6-1

License

GPL-2

Maintainer

Steven Kembel

Last Published

March 19th, 2009

Functions in picante (0.6-1)

cor.table

Table of correlations and P-values
randomizeSample

Null models for community data matrix randomization
evolve.brownian

Trait evolution under Brownian motion
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
matrix2sample

Convert community data matrix to Phylocom sample
color.plot.phylo

Color tip labels based on trait
pic.circular

Phylogenetic independent contrasts for circular data
ses.mpd

Standardized effect size of mpd
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
writetraits

Write a Phylocom traits formatted file
psd

Phylogenetic Species Diversity Metrics
ses.mnnd

Standardized effect size of MNND
Kcalc

K statistic of phylogenetic signal
pd

Calculate Faith's Phylogenetic Diversity
sample2matrix

Convert Phylocom sample to community data matrix
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
utility

Picante utility functions
prune.sample

Prune tree to match community data or trait data
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
pblm

Phylogenetic Bipartite Linear Model
species.dist

Species co-occurrence distances
writesample

Write a Phylocom community sample file
phylosor

Phylogenetic index of beta-diversity PhyloSor
mnnd

Mean nearest neighbour distance
mpd

Mean pairwise distance
readsample

Read Phylocom sample
phylocom

Phylocom default data
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
phylosignal

Measure phylogenetic signal
picante-package

Picante: Phylocom Integration, Community Analyses, Null-models, Traits, and Evolution in R