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picante (version 0.4-0)

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

0.4-0

License

GPL-2

Maintainer

Steve Kembel

Last Published

June 10th, 2020

Functions in picante (0.4-0)

color.plot.phylo

Color tip labels based on trait
phylocom

Phylocom default data
mnnd

Mean nearest neighbour distance
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
pic.circular

Phylogenetic independent contrasts for circular data
Kcalc

K statistic of phylogenetic signal
species.dist

Species co-occurrence distances
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
randomizeSample

Null models for community data matrix randomization
phylosignal

Measure phylogenetic signal
prune.sample

Prune tree to match community data or trait data
matrix2sample

Convert community data matrix to Phylocom sample
mpd

Mean pairwise distance
sample2matrix

Convert Phylocom sample to community data matrix
pblm

Phylogenetic Bipartite Linear Model
readsample

Read Phylocom sample
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
utility

Picante utility functions
evolve.brownian

Trait evolution under Brownian motion
psd

Phylogenetic Species Diversity Metrics
pd

Calculate Faith's Phylogenetic Diversity
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
ses.mnnd

Standardized effect size of MNND
cor.table

Table of correlations and P-values
picante-package

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

Write a Phylocom community sample file
writetraits

Write a Phylocom traits formatted file