write.spacodi.data
(Package: spacodiR) :
saving community phylogenetics datasets to a file
write.spacodi.data generates community phylogenetic datasets to be used in the external program SPACoDi
● Data Source:
CranContrib
● Keywords:
● Alias: write.spacodi.data
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spacodi.treeplot
(Package: spacodiR) :
EXPERIMENTAL: plotting diversity turnover on trees
spacodi.treeplot is used to plot departures from expectations for diversity turnover on a phylogeny
● Data Source:
CranContrib
● Keywords:
● Alias: spacodi.treeplot
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spacodi.permutplot
(Package: spacodiR) :
EXPERIMENTAL: plotting observed and expected community structure across branching times of a phylogeny
spacodi.permutplot is a function used to plot departures from null expectations of diversity turnover, nodewise for a phylogeny.
● Data Source:
CranContrib
● Keywords:
● Alias: spacodi.permutplot
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spacodi.calc
(Package: spacodiR) :
measuring spatial and phylogenetic structuring of diversity in communities
Considering species-, phylogenetic-, or trait-diversities, this function measures diversity structuring of community samples.
● Data Source:
CranContrib
● Keywords:
● Alias: spacodi.calc
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spacodi.by.nodes
(Package: spacodiR) :
conducting randomization tests of turnover in diversity through time
spacodi.by.nodes is a function for testing the null expectation of uniform diversity turnover across nodes of a phylogeny.
● Data Source:
CranContrib
● Keywords:
● Alias: spacodi.by.nodes
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spacodi
(Package: spacodiR) :
main: Spatial and Phylogenetic Analysis of Community Diversity
spacodiR is primarily designed to characterise the structure and phylogenetic diversity of communities using abundance or presence-absence data of species among community plots. For estimation of community structure, see spacodi.calc. More information on SPACoDi can be found at http://ebe.ulb.ac.be/ebe/Software.html
● Data Source:
CranContrib
● Keywords:
● Alias: spacodi
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spacodi-internal are not typically called by the user
● Data Source:
CranContrib
● Keywords:
● Alias: add.transparency, check.distmat, cophen, debug, get.desc.of.node, get.descendants.of.node, prune.sp, reorderspacodiobj, spacodi.all.nodes, spacodi.exp.nodes, withinrange
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sp.example
(Package: spacodiR) :
example data for spacodiR
spacodi-package provides example community phylogenetics data, a phylogeny, and trait data
● Data Source:
CranContrib
● Keywords:
● Alias: sp.example, spacodi.data
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resamp.test
(Package: spacodiR) :
statistical comparison of sets of values by randomization
compares means by bootstrap resampling of differences between empirical distributions
● Data Source:
CranContrib
● Keywords:
● Alias: resamp.test
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resamp.phy
(Package: spacodiR) :
partial phylogeny randomization for tips
resamp.phy is used to shuffle tips subtended by a set of internal nodes determining by divergence time or specified by the user
● Data Source:
CranContrib
● Keywords:
● Alias: resamp.phy
●
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providing 
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