picante: R tools for integrating phylogenies and ecology

Share:

Phylocom integration, community analyses, null-models, traits and evolution in R

Author
Steven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly <dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K. Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R. Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O. Webb <cwebb@oeb.harvard.edu>
Date of publication
2013-10-18 01:29:45
Maintainer
Steven W. Kembel <steve.kembel@gmail.com>
License
GPL-2
Version
1.6-1

View on R-Forge

Man pages

color.plot.phylo
Color tip labels based on trait
comdist
Calculates inter-community mean pairwise distance
comdistnt
Calculates inter-community mean nearest taxon distance
comm.phylo.cor
Correlations between species co-occurrence and phylogenetic...
comm.phylo.qr
Quantile regression slopes between species co-occurrence and...
cor.table
Table of correlations and P-values
data.checking
Match taxa in phylogeny and data
evol.distinct
Species' evolutionary distinctiveness
expected.pd
Expected PD, PD Variance, and Edge Abundance Distribution of...
IvesGodfray
Host-parasitoid food web data
Kcalc
K statistic of phylogenetic signal
matrix2sample
Convert community data matrix to Phylocom sample
mntd
Mean nearest taxon distance
mpd
Mean pairwise distance
multiPhylosignal
Calculates phylogenetic signal for data.frame of traits
pblm
Phylogenetic Bipartite Linear Model
pcd
Phylogenetic Community Dissimilarity
pd
Calculate Faith's Phylogenetic Diversity
pglmm
Phylogenetic Generalized Linear Mixed Model
phyEstimate
Phylogenetic estimation of traits for unobserved taxa
phylocom
Phylocom default data
phylosignal
Measure phylogenetic signal
phylosor
Phylogenetic index of beta-diversity PhyloSor
phylosor.rnd
Null PhyloSor values of phylogenetic beta-diversity
phylostruct
Permutations to Test for Phylogenetic Signal in Community...
picante-package
picante: R tools for integrating phylogenies and ecology
pruning
Prune tree to match community data or trait data
psd
Phylogenetic Species Diversity Metrics
randomizeSample
Null models for community data matrix randomization
raoD
Rao's quadratic entropy
readsample
Read Phylocom sample
sample2matrix
Convert Phylocom sample to community data matrix
ses.mntd
Standardized effect size of MNTD
ses.mpd
Standardized effect size of MPD
ses.pd
Standardized effect size of PD
specaccum.psr
Phylogenetic Species Richness Sample-Based Rarefaction Curve
species.dist
Species co-occurrence distances
sppregs
Regressions to Separate Phylogenetic Attraction and Repulsion
tax.distinctiveness
Taxonomic distinctiveness sensu Vane-Wright or May
traitgram
Draw phylogeny with nodes at trait positions
unifrac
Unweighted UniFrac distance between communities
utility
Picante utility functions
writesample
Write a Phylocom community sample file
writetraits
Write a Phylocom traits formatted file

Files in this package

picante/DESCRIPTION
picante/NAMESPACE
picante/R
picante/R/color.plot.phylo.R
picante/R/cor.table.R
picante/R/data.checking.R
picante/R/evol.distinct.R
picante/R/evolve.trait.R
picante/R/expected.pd.R
picante/R/get.nodes.R
picante/R/node.desc.R
picante/R/node.number.R
picante/R/pblm.R
picante/R/pblmpredict.R
picante/R/pcd.R
picante/R/pglmm.R
picante/R/phyEstimate.R
picante/R/phylobeta.R
picante/R/phylocom.R
picante/R/phylodiversity.R
picante/R/phylosignal.R
picante/R/phylosor.R
picante/R/phylostruct.R
picante/R/pruning.R
picante/R/randomizeSample.R
picante/R/raoD.R
picante/R/specaccum.psr.R
picante/R/species.dist.R
picante/R/sppregs.R
picante/R/tax.distinctiveness.R
picante/R/traitgram.R
picante/R/utility.R
picante/build
picante/build/vignette.rds
picante/data
picante/data/IvesGodfray.rda
picante/data/phylocom.rda
picante/inst
picante/inst/CITATION
picante/inst/doc
picante/inst/doc/picante-intro.R
picante/inst/doc/picante-intro.Rnw
picante/inst/doc/picante-intro.pdf
picante/man
picante/man/IvesGodfray.Rd
picante/man/Kcalc.Rd
picante/man/color.plot.phylo.Rd
picante/man/comdist.Rd
picante/man/comdistnt.Rd
picante/man/comm.phylo.cor.Rd
picante/man/comm.phylo.qr.Rd
picante/man/cor.table.Rd
picante/man/data.checking.Rd
picante/man/evol.distinct.Rd
picante/man/expected.pd.Rd
picante/man/matrix2sample.Rd
picante/man/mntd.Rd
picante/man/mpd.Rd
picante/man/multiPhylosignal.Rd
picante/man/pblm.Rd
picante/man/pcd.Rd
picante/man/pd.Rd
picante/man/pglmm.Rd
picante/man/phyEstimate.Rd
picante/man/phylocom.Rd
picante/man/phylosignal.Rd
picante/man/phylosor.Rd
picante/man/phylosor.rnd.Rd
picante/man/phylostruct.Rd
picante/man/picante-package.Rd
picante/man/pruning.Rd
picante/man/psd.Rd
picante/man/randomizeSample.Rd
picante/man/raoD.Rd
picante/man/readsample.Rd
picante/man/sample2matrix.Rd
picante/man/ses.mntd.Rd
picante/man/ses.mpd.Rd
picante/man/ses.pd.Rd
picante/man/specaccum.psr.Rd
picante/man/species.dist.Rd
picante/man/sppregs.Rd
picante/man/tax.distinctiveness.Rd
picante/man/traitgram.Rd
picante/man/unifrac.Rd
picante/man/utility.Rd
picante/man/writesample.Rd
picante/man/writetraits.Rd
picante/src
picante/src/picante.c