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picante (version 1.6-1)

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

5,136

Version

1.6-1

License

GPL-2

Maintainer

Steven W Kembel

Last Published

November 1st, 2013

Functions in picante (1.6-1)

ses.mntd

Standardized effect size of MNTD
IvesGodfray

Host-parasitoid food web data
phylocom

Phylocom default data
evol.distinct

Species' evolutionary distinctiveness
Kcalc

K statistic of phylogenetic signal
comdistnt

Calculates inter-community mean nearest taxon distance
expected.pd

Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
mntd

Mean nearest taxon distance
comdist

Calculates inter-community mean pairwise distance
phylosor

Phylogenetic index of beta-diversity PhyloSor
readsample

Read Phylocom sample
phyEstimate

Phylogenetic estimation of traits for unobserved taxa
pcd

Phylogenetic Community Dissimilarity
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
sample2matrix

Convert Phylocom sample to community data matrix
matrix2sample

Convert community data matrix to Phylocom sample
pblm

Phylogenetic Bipartite Linear Model
species.dist

Species co-occurrence distances
prune.sample

Prune tree to match community data or trait data
mpd

Mean pairwise distance
pd

Calculate Faith's Phylogenetic Diversity
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
ses.mpd

Standardized effect size of MPD
tax.distinctiveness

Taxonomic distinctiveness sensu Vane-Wright or May
color.plot.phylo

Color tip labels based on trait
randomizeMatrix

Null models for community data matrix randomization
pglmm

Phylogenetic Generalized Linear Mixed Model
writesample

Write a Phylocom community sample file
comm.phylo.qr

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

Rao's quadratic entropy
traitgram

Draw phylogeny with nodes at trait positions
unifrac

Unweighted UniFrac distance between communities
utility

Picante utility functions
phylosignal

Measure phylogenetic signal
psd

Phylogenetic Species Diversity Metrics
ses.pd

Standardized effect size of PD
picante-package

picante: R tools for integrating phylogenies and ecology
sppregs

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

Correlations between species co-occurrence and phylogenetic distances
writetraits

Write a Phylocom traits formatted file
match.phylo.data

Match taxa in phylogeny and data
cor.table

Table of correlations and P-values
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity