spacodiR: Spatial and Phylogenetic Analysis of Community Diversity

SPACoDi is primarily designed to characterise the structure and phylogenetic diversity of communities using abundance or presence-absence data of species among community plots.

AuthorJonathan Eastman, Timothy Paine, and Olivier Hardy
Date of publication2013-01-16 10:08:49
MaintainerJonathan Eastman <jonathan.eastman@gmail.com>
LicenseGPL (>= 2)
Version0.13.0115

View on CRAN

Man pages

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...

phy.nodetimes: finding splitting times for nodes

resamp.1a: randomizing a community phylogenetics matrix: '1a' of Hardy...

resamp.1s: randomizing a community phylogenetics matrix: '1s' of Hardy...

resamp.2s: randomizing a community phylogenetics matrix: '2s' of Hardy...

resamp.2x: randomizing a community phylogenetics matrix: '2x' of Hardy...

resamp.3i: randomizing a community phylogenetics matrix: '3i' of Hardy...

resamp.3t: randomizing a community phylogenetics matrix: '3t' of Hardy...

resamp.3x: randomizing a community phylogenetics matrix: '3x' of Hardy...

resamp.phy: partial phylogeny randomization for tips

resamp.test: statistical comparison of sets of values by randomization

spacodi.by.nodes: conducting randomization tests of turnover in diversity...

spacodi.calc: measuring spatial and phylogenetic structuring of diversity...

spacodi-internal: internal SPACoDi functions

spacodi-package: main: Spatial and Phylogenetic Analysis of Community...

spacodi.permutplot: EXPERIMENTAL: plotting observed and expected community...

spacodi.treeplot: EXPERIMENTAL: plotting diversity turnover on trees

sp.example: example data for spacodiR

write.spacodi.data: saving community phylogenetics datasets to a file

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.