| picante-package | picante: Integrating Phylogenies and Ecology |
| color.plot.phylo | Color tip labels based on trait |
| comdist | Calculates inter-community mean pairwise distance |
| comdistnn | Calculates inter-community mean nearest taxon distance |
| comdistnt | Calculates inter-community mean nearest taxon distance |
| comm.phylo.cor | Correlations between species co-occurrence and phylogenetic distances |
| comm.phylo.qr | Quantile regression slopes between species co-occurrence and phylogenetic distances |
| cor.table | Table of correlations and P-values |
| df2vec | Picante utility functions |
| ead | Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny |
| evol.distinct | Species' evolutionary distinctiveness |
| expected.pd | Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny |
| internal2tips | Picante utility functions |
| IvesGodfray | Host-parasitoid food web data |
| Kcalc | K statistic of phylogenetic signal |
| match.comm.dist | Match taxa in phylogeny and data |
| match.phylo.comm | Match taxa in phylogeny and data |
| match.phylo.data | Match taxa in phylogeny and data |
| matrix2sample | Convert community data matrix to Phylocom sample |
| mnnd | Mean nearest taxon distance |
| mntd | Mean nearest taxon distance |
| mpd | Mean pairwise distance |
| multiPhylosignal | Calculates phylogenetic signal for data.frame of traits |
| node.age | Picante utility functions |
| pblm | Phylogenetic Bipartite Linear Model |
| pblmpredict | Phylogenetic Bipartite Linear Model |
| PCD | Phylogenetic Community Dissimilarity |
| pcd | Phylogenetic Community Dissimilarity |
| pd | Calculate Faith's Phylogenetic Diversity |
| phyEstimate | Phylogenetic estimation of traits for unobserved taxa |
| phyEstimateDisc | 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 Composition |
| pic.variance | Picante utility functions |
| picante | picante: Integrating Phylogenies and Ecology |
| prune.missing | Prune tree to match community data or trait data |
| prune.sample | Prune tree to match community data or trait data |
| psc | Phylogenetic Species Diversity Metrics |
| psd | Phylogenetic Species Diversity Metrics |
| pse | Phylogenetic Species Diversity Metrics |
| psr | Phylogenetic Species Diversity Metrics |
| psv | Phylogenetic Species Diversity Metrics |
| psv.spp | Phylogenetic Species Diversity Metrics |
| randomizeMatrix | 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.mnnd | Standardized effect size of MNTD |
| ses.mntd | Standardized effect size of MNTD |
| ses.mpd | Standardized effect size of MPD |
| ses.pd | Standardized effect size of PD |
| sortColumns | Picante utility functions |
| sortRows | Picante utility functions |
| specaccum.psr | Phylogenetic Species Richness Sample-Based Rarefaction Curve |
| species.dist | Species co-occurrence distances |
| sppregs | Regressions to Separate Phylogenetic Attraction and Repulsion |
| sppregs.plot | Regressions to Separate Phylogenetic Attraction and Repulsion |
| tax.distinctiveness | Taxonomic distinctiveness sensu Vane-Wright or May |
| taxaShuffle | Picante utility functions |
| tipShuffle | Picante utility functions |
| traitgram | Draw phylogeny with nodes at trait positions |
| unifrac | Unweighted UniFrac distance between communities |
| variance.pd | Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny |
| writesample | Write a Phylocom community sample file |
| writetraits | Write a Phylocom traits formatted file |