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BMhyd (version 1.2-8)

PCM for Hybridization

Description

The BMhyd package analyzes the phenotypic evolution of species of hybrid origin on a phylogenetic network. This package can detect the hybrid vigor effect, a burst of variation at formation, and the relative portion of heritability from its parents. Parameters are estimated by maximum likelihood. Users need to enter a comparative data set, a phylogeny, and information on gene flow leading to hybrids.

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Version

Install

install.packages('BMhyd')

Monthly Downloads

10

Version

1.2-8

License

GPL (>= 2)

Maintainer

DwuengChwuan Jhwueng

Last Published

August 6th, 2015

Functions in BMhyd (1.2-8)

AkaikeWeight

Akaike weight
ContourFromAdaptiveSampling

Contour maps
GenerateValues

Generate parameter values
GetClade

Get clade from the tree
GetMeansModified

The species means for the network model
PlotNetwork

Phylogenetic Network Plot
BMhyd

Comparative method for studying hyridization using Brownian motion for trait evolution
GetVModified

Variance covariance matrix for the network model
Plot_ConvexHull

Convex hull
AdjustForDet

Adjust the phylogeny
SimulateTipData

Simulate data on a network
nicotiana

nicotiana data
AttachHybridsToDonor

Attach hybrids to the donor species
cichlid

Cichlid data from Kobmuller et al. 2007
AdaptiveConfidenceIntervalSampling

Confidence interval under adaptive cluster sampling technique
LumpIntoClades

Lump into clades
CalculateLikelihood

Calculate the likelihood value for the model
SimulateNetwork

Simulate phylogenetic network
AICc

AICc
DetPass

determinant of the matrix
GetAncestor

Identify the ancestor