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
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
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.by.nodes        conducting randomization tests of turnover in
                        diversity through time
spacodi.calc            measuring spatial and phylogenetic structuring
                        of diversity in communities
spacodi.permutplot      EXPERIMENTAL: plotting observed and expected
                        community structure across branching times of a
                        phylogeny
spacodi.treeplot        EXPERIMENTAL: plotting diversity turnover on
                        trees
write.spacodi.data      saving community phylogenetics datasets to a
                        file
