spacodiR: Spatial and Phylogenetic Analysis of Community Diversity
Version 0.13.0115

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("spacodiR")

Popular man pages

as.phylocom: converting between data formats for community phylogenetics
as.spacodi: converting between data formats for community phylogenetics
phy.nodetimes: finding splitting times for nodes
resamp.2x: randomizing a community phylogenetics matrix: '2x' of Hardy...
spacodi.calc: measuring spatial and phylogenetic structuring of diversity...
spacodi.treeplot: EXPERIMENTAL: plotting diversity turnover on trees
sp.example: example data for spacodiR
See all...

All man pages Function index File listing

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

Files

MD5
src
src/Xatools.h
src/spacodi.c
src/Makevars.win
src/Makevars
src/cophen.cpp
R
R/temporalAnalysis.R
R/spacodi.calc.R
R/spacodi-internal.R
R/plotting.R
R/phylogeneticUtilities.R
R/dataResampling.R
R/dataManipulation.R
R/cophen.R
NAMESPACE
man
man/write.spacodi.data.Rd
man/spacodi.treeplot.Rd
man/spacodi.permutplot.Rd
man/spacodi.calc.Rd
man/spacodi.by.nodes.Rd
man/spacodi-package.Rd
man/spacodi-internal.Rd
man/sp.example.Rd
man/resamp.test.Rd
man/resamp.phy.Rd
man/resamp.3x.Rd
man/resamp.3t.Rd
man/resamp.3i.Rd
man/resamp.2x.Rd
man/resamp.2s.Rd
man/resamp.1s.Rd
man/resamp.1a.Rd
man/phy.nodetimes.Rd
man/phy.dotplot.Rd
man/phy.deresolve.Rd
man/match.spacodi.data.Rd
man/as.spacodi.Rd
man/as.picante.Rd
man/as.phylocom.Rd
DESCRIPTION
data
data/sp.example.rda
data/debug.rda
ChangeLog
spacodiR documentation built on May 19, 2017, 8:49 p.m.

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

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