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picante (version 0.7-1)

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

0.7-1

License

GPL-2

Maintainer

Steven Kembel

Last Published

July 3rd, 2009

Functions in picante (0.7-1)

multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
comdistnt

Calculates inter-community mean nearest taxon distance
pic3

Independent contrasts
utility

Picante utility functions
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
phylosignal

Measure phylogenetic signal
pic.circular

Phylogenetic independent contrasts for circular data
pblm

Phylogenetic Bipartite Linear Model
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
psd

Phylogenetic Species Diversity Metrics
picante-package

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

Color tip labels based on trait
prune.sample

Prune tree to match community data or trait data
traitgram

Draw phylogeny with nodes at trait positions
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
writetraits

Write a Phylocom traits formatted file
species.dist

Species co-occurrence distances
evolve.brownian

Trait evolution under Brownian motion
randomizeSample

Null models for community data matrix randomization
mntd

Mean nearest taxon distance
mpd

Mean pairwise distance
pd

Calculate Faith's Phylogenetic Diversity
ses.mpd

Standardized effect size of mpd
Kcalc

K statistic of phylogenetic signal
ses.mntd

Standardized effect size of MNTD
writesample

Write a Phylocom community sample file
phylocom

Phylocom default data
phylosor

Phylogenetic index of beta-diversity PhyloSor
comm.phylo.qr

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

Permutations to Test for Phylogenetic Signal in Community Composition
comdist

Calculates inter-community mean pairwise distance
cor.table

Table of correlations and P-values
readsample

Read Phylocom sample
ses.pd

Standardized effect size of PD
sample2matrix

Convert Phylocom sample to community data matrix
matrix2sample

Convert community data matrix to Phylocom sample
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve