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spacodiR (version 0.13.0115)

Spatial and Phylogenetic Analysis of Community Diversity

Description

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

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Version

Install

install.packages('spacodiR')

Monthly Downloads

48

Version

0.13.0115

License

GPL (>= 2)

Maintainer

Jonathan Eastman

Last Published

January 16th, 2013

Functions in spacodiR (0.13.0115)

spacodi.by.nodes

conducting randomization tests of turnover in diversity through time
resamp.test

statistical comparison of sets of values by randomization
resamp.3x

randomizing a community phylogenetics matrix: '3x' of Hardy (2008)
sp.example

example data for spacodiR
resamp.1s

randomizing a community phylogenetics matrix: '1s' of Hardy (2008)
resamp.1a

randomizing a community phylogenetics matrix: '1a' of Hardy (2008)
write.spacodi.data

saving community phylogenetics datasets to a file
spacodi.permutplot

EXPERIMENTAL: plotting observed and expected community structure across branching times of a phylogeny
resamp.phy

partial phylogeny randomization for tips
resamp.2x

randomizing a community phylogenetics matrix: '2x' of Hardy (2008)
as.picante

converting between data formats for community phylogenetics
resamp.2s

randomizing a community phylogenetics matrix: '2s' of Hardy (2008)
as.phylocom

converting between data formats for community phylogenetics
as.spacodi

converting between data formats for community phylogenetics
phy.deresolve

collapse phylogenetic nodes into multichotomies
resamp.3t

randomizing a community phylogenetics matrix: '3t' of Hardy (2008)
phy.nodetimes

finding splitting times for nodes
spacodi-internal

internal SPACoDi functions
spacodi.calc

measuring spatial and phylogenetic structuring of diversity in communities
resamp.3i

randomizing a community phylogenetics matrix: '3i' of Hardy (2008)
spacodi

main: Spatial and Phylogenetic Analysis of Community Diversity
match.spacodi.data

pruning a tree to match datasets used in SPACoDi
spacodi.treeplot

EXPERIMENTAL: plotting diversity turnover on trees
phy.dotplot

EXPERIMENTAL: plotting members of communities (or plots) on a phylogeny