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| add.transparency | internal SPACoDi functions |
| as.phylocom | converting between data formats for community phylogenetics |
| as.picante | converting between data formats for community phylogenetics |
| as.spacodi | converting between data formats for community phylogenetics |
| check.distmat | internal SPACoDi functions |
| cophen | internal SPACoDi functions |
| debug | internal SPACoDi functions |
| get.desc.of.node | internal SPACoDi functions |
| get.descendants.of.node | internal SPACoDi functions |
| match.spacodi.data | pruning a tree to match datasets used in SPACoDi |
| phy.deresolve | collapse phylogenetic nodes into multichotomies |
| phy.dotplot | EXPERIMENTAL: plotting members of communities (or plots) on a phylogeny |
| phy.nodetimes | finding splitting times for nodes |
| prune.sp | internal SPACoDi functions |
| reorderspacodiobj | internal SPACoDi functions |
| resamp.1a | randomizing a community phylogenetics matrix: '1a' of Hardy (2008) |
| resamp.1s | randomizing a community phylogenetics matrix: '1s' of Hardy (2008) |
| resamp.2s | randomizing a community phylogenetics matrix: '2s' of Hardy (2008) |
| resamp.2x | randomizing a community phylogenetics matrix: '2x' of Hardy (2008) |
| resamp.3i | randomizing a community phylogenetics matrix: '3i' of Hardy (2008) |
| resamp.3t | randomizing a community phylogenetics matrix: '3t' of Hardy (2008) |
| resamp.3x | randomizing a community phylogenetics matrix: '3x' of Hardy (2008) |
| resamp.phy | partial phylogeny randomization for tips |
| resamp.test | statistical comparison of sets of values by randomization |
| sp.example | example data for spacodiR |
| spacodi | main: Spatial and Phylogenetic Analysis of Community Diversity |
| spacodi.all.nodes | internal SPACoDi functions |
| spacodi.by.nodes | conducting randomization tests of turnover in diversity through time |
| spacodi.calc | measuring spatial and phylogenetic structuring of diversity in communities |
| spacodi.data | example data for spacodiR |
| spacodi.exp.nodes | internal SPACoDi functions |
| spacodi.permutplot | EXPERIMENTAL: plotting observed and expected community structure across branching times of a phylogeny |
| spacodi.treeplot | EXPERIMENTAL: plotting diversity turnover on trees |
| withinrange | internal SPACoDi functions |
| write.spacodi.data | saving community phylogenetics datasets to a file |