spacodiR: Spatial and Phylogenetic Analysis of Community Diversity

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

Author
Jonathan Eastman, Timothy Paine, and Olivier Hardy
Date of publication
2013-01-16 10:08:49
Maintainer
Jonathan Eastman <jonathan.eastman@gmail.com>
License
GPL (>= 2)
Version
0.13.0115

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

Files in this package

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