prune.sample
(Package: picante) :
Prune tree to match community data or trait data
Prune a phylogenetic tree to include only species present in a community data set or with non-missing trait data
● Data Source:
CranContrib
● Keywords: manip
● Alias: prune.missing, prune.sample
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comm.phylo.cor
(Package: picante) :
Correlations between species co-occurrence and phylogenetic distances
Calculates measures of community phylogenetic structure (correlation between co-occurrence and phylogenetic distance) to patterns expected under various null models
● Data Source:
CranContrib
● Keywords: univar
● Alias: comm.phylo.cor
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comm.phylo.qr
(Package: picante) :
Quantile regression slopes between species co-occurrence and phylogenetic distances
Calculates measures of community phylogenetic structure (quantile regression between co-occurrence and phylogenetic distance) to patterns expected under various null models
● Data Source:
CranContrib
● Keywords: univar
● Alias: comm.phylo.qr
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traitgram
(Package: picante) :
Draw phylogeny with nodes at trait positions
Draws a phylogeny where x position of nodes and tips corresponds to value of a continuous trait variable, and y position corresponds to node depth (i.e. age).
● Data Source:
CranContrib
● Keywords: univar
● Alias: traitgram
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Calculates evolutionary distinctiveness measures for a suite of species by: a) equal splits (Redding and Mooers 2006) b) fair proportions (Isaac et al., 2007). Returns a datafram with species identifiers and species scores.
● Data Source:
CranContrib
● Keywords:
● Alias: evol.distinct
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utility
(Package: picante) :
Picante utility functions
Picante utility functions for tree and data manipulation
● Data Source:
CranContrib
● Keywords: manip
● Alias: df2vec, internal2tips, node.age, pic.variance, sortColumns, sortRows, taxaShuffle, tipShuffle
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Plots a phylogeny with tip labels colored to indicate continuous or discrete trait values
● Data Source:
CranContrib
● Keywords: color
● Alias: color.plot.phylo
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expected.pd
(Package: picante) :
Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
Calculates the expected phylogenetic diversity (Faith's PD) and variance of PD under binomial sampling with a fixed probability of each tip being sampled, and the Edge-length Abundance Distribution of a phylogeny.
● Data Source:
CranContrib
● Keywords: univar
● Alias: ead, expected.pd, variance.pd
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ses.mpd
(Package: picante) :
Standardized effect size of MPD
Standardized effect size of mean pairwise distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Relative Index (NRI).
● Data Source:
CranContrib
● Keywords: univar
● Alias: ses.mpd
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specaccum.psr
(Package: picante) :
Phylogenetic Species Richness Sample-Based Rarefaction Curve
Finds a sample-based rarefaction curve for phylogentic species richness for a set of samples.
● Data Source:
CranContrib
● Keywords: univar
● Alias: specaccum.psr
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