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picante (version 1.1-0)
R tools for integrating phylogenies and ecology
Description
Phylocom integration, community analyses, null-models, traits and evolution in R
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Install
install.packages('picante')
Monthly Downloads
5,136
Version
1.1-0
License
GPL-2
Maintainer
Steven Kembel
Last Published
April 10th, 2010
Functions in picante (1.1-0)
Search all functions
sample2matrix
Convert Phylocom sample to community data matrix
mpd
Mean pairwise distance
unifrac
Unweighted UniFrac distance between communities
comdist
Calculates inter-community mean pairwise distance
randomizeMatrix
Null models for community data matrix randomization
pblm
Phylogenetic Bipartite Linear Model
phylosor
Phylogenetic index of beta-diversity PhyloSor
utility
Picante utility functions
evol.distinct
Species' evolutionary distinctiveness
species.dist
Species co-occurrence distances
phylostruct
Permutations to Test for Phylogenetic Signal in Community Composition
specaccum.psr
Phylogenetic Species Richness Sample-Based Rarefaction Curve
readsample
Read Phylocom sample
phylosor.rnd
Null PhyloSor values of phylogenetic beta-diversity
comdistnt
Calculates inter-community mean nearest taxon distance
Kcalc
K statistic of phylogenetic signal
ses.mntd
Standardized effect size of MNTD
prune.sample
Prune tree to match community data or trait data
tax.distinctiveness
Taxonomic distinctiveness sensu Vane-Wright or May
pic.circular
Phylogenetic independent contrasts for circular data
match.phylo.data
Match taxa in phylogeny and data
writesample
Write a Phylocom community sample file
psd
Phylogenetic Species Diversity Metrics
phylocom
Phylocom default data
ses.pd
Standardized effect size of PD
sppregs
Regressions to Separate Phylogenetic Attraction and Repulsion
mntd
Mean nearest taxon distance
IvesGodfray
Host-parasitoid food web data
raoD
Rao's quadratic entropy
multiPhylosignal
Calculates phylogenetic signal for data.frame of traits
picante-package
picante: R tools for integrating phylogenies and ecology
matrix2sample
Convert community data matrix to Phylocom sample
pd
Calculate Faith's Phylogenetic Diversity
comm.phylo.qr
Quantile regression slopes between species co-occurrence and phylogenetic distances
ses.mpd
Standardized effect size of MPD
pic3
Independent contrasts
writetraits
Write a Phylocom traits formatted file
cor.table
Table of correlations and P-values
phylosignal
Measure phylogenetic signal
comm.phylo.cor
Correlations between species co-occurrence and phylogenetic distances
traitgram
Draw phylogeny with nodes at trait positions
color.plot.phylo
Color tip labels based on trait
evolve.brownian
Trait evolution under Brownian motion
