Integrating Phylogenies and Ecology
Color tip labels based on trait
Calculates inter-community mean pairwise distance
Calculates inter-community mean nearest taxon distance
Correlations between species co-occurrence and phylogenetic distances
Quantile regression slopes between species co-occurrence and phylogene...
Table of correlations and P-values
Match taxa in phylogeny and data
Species' evolutionary distinctiveness
Expected PD, PD Variance, and Edge Abundance Distribution of a phyloge...
K statistic of phylogenetic signal
Convert community data matrix to Phylocom sample
Mean nearest taxon distance
Mean pairwise distance
Calculates phylogenetic signal for data.frame of traits
Phylogenetic Bipartite Linear Model
Phylogenetic Community Dissimilarity
Calculate Faith's Phylogenetic Diversity
Phylogenetic estimation of traits for unobserved taxa
Measure phylogenetic signal
Phylogenetic index of beta-diversity PhyloSor
Null PhyloSor values of phylogenetic beta-diversity
Permutations to Test for Phylogenetic Signal in Community Composition
picante: Integrating Phylogenies and Ecology
Prune tree to match community data or trait data
Phylogenetic Species Diversity Metrics
Null models for community data matrix randomization
Rao's quadratic entropy
Read Phylocom sample
Convert Phylocom sample to community data matrix
Standardized effect size of MNTD
Standardized effect size of MPD
Standardized effect size of PD
Phylogenetic Species Richness Sample-Based Rarefaction Curve
Species co-occurrence distances
Regressions to Separate Phylogenetic Attraction and Repulsion
Taxonomic distinctiveness sensu Vane-Wright or May
Draw phylogeny with nodes at trait positions
Unweighted UniFrac distance between communities
Picante utility functions
Write a Phylocom community sample file
Write a Phylocom traits formatted file
Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.