spacodiR: Spatial and Phylogenetic Analysis of Community Diversity

群集の多様性を空間・系統的に解析する

> library(spacodiR)

Loading required package: picante
Loading required package: nlme
Loading required package: colorspace
Loading required package: Rcpp

バージョン: 0.13.115

関数名 概略
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