Man pages for picante
Integrating Phylogenies and Ecology

color.plot.phyloColor tip labels based on trait
comdistCalculates inter-community mean pairwise distance
comdistntCalculates inter-community mean nearest taxon distance
comm.phylo.corCorrelations between species co-occurrence and phylogenetic...
comm.phylo.qrQuantile regression slopes between species co-occurrence and...
cor.tableTable of correlations and P-values
data.checkingMatch taxa in phylogeny and data
evol.distinctSpecies' evolutionary distinctiveness
expected.pdExpected PD, PD Variance, and Edge Abundance Distribution of...
IvesGodfrayHost-parasitoid food web data
KcalcK statistic of phylogenetic signal
matrix2sampleConvert community data matrix to Phylocom sample
mntdMean nearest taxon distance
mpdMean pairwise distance
multiPhylosignalCalculates phylogenetic signal for data.frame of traits
pblmPhylogenetic Bipartite Linear Model
pcdPhylogenetic Community Dissimilarity
pdCalculate Faith's Phylogenetic Diversity
phyEstimatePhylogenetic estimation of traits for unobserved taxa
phylocomPhylocom default data
phylosignalMeasure phylogenetic signal
phylosorPhylogenetic index of beta-diversity PhyloSor
phylosor.rndNull PhyloSor values of phylogenetic beta-diversity
phylostructPermutations to Test for Phylogenetic Signal in Community...
picante-packagepicante: Integrating Phylogenies and Ecology
pruningPrune tree to match community data or trait data
psdPhylogenetic Species Diversity Metrics
randomizeSampleNull models for community data matrix randomization
raoDRao's quadratic entropy
readsampleRead Phylocom sample
sample2matrixConvert Phylocom sample to community data matrix
ses.mntdStandardized effect size of MNTD
ses.mpdStandardized effect size of MPD
ses.pdStandardized effect size of PD
specaccum.psrPhylogenetic Species Richness Sample-Based Rarefaction Curve
species.distSpecies co-occurrence distances
sppregsRegressions to Separate Phylogenetic Attraction and Repulsion
tax.distinctivenessTaxonomic distinctiveness sensu Vane-Wright or May
traitgramDraw phylogeny with nodes at trait positions
unifracUnweighted UniFrac distance between communities
utilityPicante utility functions
writesampleWrite a Phylocom community sample file
writetraitsWrite a Phylocom traits formatted file
picante documentation built on July 1, 2020, 10:57 p.m.