gammatest
(Package: phytools) :
Gamma test of Pybus & Harvey (2000)
Conducts γ-test of Pybus & Harvey (2000).
● Data Source:
CranContrib
● Keywords: comparative method, diversification, phylogenetics
● Alias: gammatest
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genSeq
(Package: phytools) :
Simulate a DNA alignment on the tree under a model
Simulates DNA sequence on tree under the specified model. Uses sim.history internally.
● Data Source:
CranContrib
● Keywords: phylogenetics, simulation
● Alias: genSeq
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expm
(Package: phytools) :
Matrix exponential
Wrapper for MatrixExp that retains row/column names.
● Data Source:
CranContrib
● Keywords: math
● Alias: expm
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phyl.resid
(Package: phytools) :
Phylogenetic size-correction via GLS regression
This function fits one or multiple phylogenetic regressions (depending on the number of columns in Y) and computes the residuals. Designed for phylogenetic size correction using GLS regression (e.g., Revell 2009; Evolution).
● Data Source:
CranContrib
● Keywords: comparative method, least squares, maximum likelihood, phylogenetics, statistics
● Alias: phyl.resid
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anc.ML
(Package: phytools) :
Ancestral character estimation using likelihood
This function estimates the evolutionary parameters and ancestral states for Brownian evolution using likelihood. It is also possible (for model="BM") to allow for missing data for some tip taxa.
● Data Source:
CranContrib
● Keywords: comparative method, maximum likelihood, phylogenetics
● Alias: anc.ML
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fitMk
(Package: phytools) :
Fits Mk model
This function fits a so-called Mk model for discrete character evolution. It is primarily designed to be used inside of make.simmap.
● Data Source:
CranContrib
● Keywords: comparative method, maximum likelihood, phylogenetics
● Alias: fitMk, plot.fitMk, plot.gfit
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rep.phylo
(Package: phytools) :
Replicate a tree or set of trees
S3 method rep for object of class "phylo" or "multiPhylo". repPhylo is just an alias for rep.phylo and rep.multiPhylo.
● Data Source:
CranContrib
● Keywords: phylogenetics, utilities
● Alias: rep.multiPhylo, rep.phylo, repPhylo
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dotTree
(Package: phytools) :
Creates a phylogenetic dot plot
Creates a plot in which different sized dots/circles represent different tip values for a quantitative trait.
● Data Source:
CranContrib
● Keywords: phylogenetics, plotting
● Alias: dot.legend, dotTree
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estDiversity
(Package: phytools) :
Estimate diversity at each node of the tree
This function estimates the lineage density at each node in the tree based on a biogeographic model (based on Mahler et al. 2010).
● Data Source:
CranContrib
● Keywords: comparative method, maximum likelihood, phylogenetics
● Alias: estDiversity
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This function scales a tree with a mapped discrete character to an arbitrary total height, preserving the relative time spent in each state along each edge.
● Data Source:
CranContrib
● Keywords: phylogenetics, utilities
● Alias: rescaleSimmap
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