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

Functions

add.transparency Man page
as.phylocom Man page
as.picante Man page
as.spacodi Man page
check.distmat Man page
cophen Man page
debug Man page
get.descendants.of.node Man page
get.desc.of.node Man page
match.spacodi.data Man page
phy.deresolve Man page
phy.dotplot Man page
phy.nodetimes Man page
prune.sp Man page
reorderspacodiobj Man page
resamp.1a Man page
resamp.1s Man page
resamp.2s Man page
resamp.2x Man page
resamp.3i Man page
resamp.3t Man page
resamp.3x Man page
resamp.phy Man page
resamp.test Man page
spacodi Man page
spacodi.all.nodes Man page
spacodi.by.nodes Man page
spacodi.calc Man page
spacodi.data Man page
spacodi.exp.nodes Man page
spacodi.permutplot Man page
spacodi.treeplot Man page
sp.example Man page
withinrange Man page
write.spacodi.data Man page

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

Please suggest features or report bugs with the GitHub issue tracker.

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