| 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 |
