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BMhyb (version 2.1.5)

Comparative Methods for Phylogenetic Networks

Description

Analyze the phenotypic evolution of species of hybrid origin on a phylogenetic network. This can detect a burst of variation at the formation of a hybrid as well as an increase or decrease in trait value at a hybridization event. Parameters are estimated by maximum likelihood, and model averaging can be done automatically. Users need to enter a comparative data set and a phylogenetic network.

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Install

install.packages('BMhyb')

Monthly Downloads

23

Version

2.1.5

License

GPL (>= 2)

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Maintainer

DwuengChwuan Jhwueng

Last Published

August 2nd, 2019

Functions in BMhyb (2.1.5)

plot.BMhybResult

Plot BMhyb result
cichlid

Cichlid dataset
SimulateTips

Simulate trait data
summary.BMhybResult

Summarize BMhyb result
nicotiana

Nicotiana dataset
plot.BMhybExhaustiveResult

Plot BMhybExhaustive result
summary.BMhybExhaustiveResult

Summarize BMhybExhaustive result
ComputeLikelihood

Compute the likelihood for a set of parameters
print.BMhybResult

Print BMhyb result
print.BMhybExhaustiveResult

Print BMhybExhaustive result
MergeExhaustiveForPlotting

Function to merge adaptive sampling sims for plotting
BMhyb

Optimize model
AddHybridization

Add hybrid events to a phy.graph
CreateHybridlessEvonet

Convert phylo object to evonet
GetConvexHull

Get convex hull at a given threshold
SimulateNetwork

Simulate a phylogenetic network
BMhybExhaustive

Exhaustively evaluate models
ComputeVCV

Compute the variance-covariance matrix
ConvertEvonetToIgraphWithNodeNumbers

Convert an evonet object into igraph