BMhyd: PCM for Hybridization

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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.

Author
Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu> and Brian O'Meara <omeara.brian@gmail.com>
Date of publication
2015-08-06 07:15:38
Maintainer
Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu>
License
GPL (>= 2)
Version
1.2-8

View on CRAN

Man pages

AdaptiveConfidenceIntervalSampling
Confidence interval under adaptive cluster sampling technique
AdjustForDet
Adjust the phylogeny
AICc
AICc
AkaikeWeight
Akaike weight
AttachHybridsToDonor
Attach hybrids to the donor species
bmhyd
Comparative method for studying hyridization using Brownian...
CalculateLikelihood
Calculate the likelihood value for the model
cichlid
Cichlid data from Kobmuller et al. 2007
ContourFromAdaptiveSampling
Contour maps
DetPass
determinant of the matrix
GenerateValues
Generate parameter values
GetAncestor
Identify the ancestor
GetClade
Get clade from the tree
GetMeansModified
The species means for the network model
GetVModified
Variance covariance matrix for the network model
LumpIntoClades
Lump into clades
nicotiana
nicotiana data
Plot_ConvexHull
Convex hull
PlotNetwork
Phylogenetic Network Plot
SimulateNetwork
Simulate phylogenetic network
SimulateTipData
Simulate data on a network

Files in this package

BMhyd
BMhyd/NAMESPACE
BMhyd/data
BMhyd/data/cichlid.RData
BMhyd/data/nicotiana.RData
BMhyd/R
BMhyd/R/bmhyd.r
BMhyd/MD5
BMhyd/DESCRIPTION
BMhyd/man
BMhyd/man/Plot_ConvexHull.Rd
BMhyd/man/cichlid.Rd
BMhyd/man/GetMeansModified.Rd
BMhyd/man/AttachHybridsToDonor.Rd
BMhyd/man/ContourFromAdaptiveSampling.Rd
BMhyd/man/AdaptiveConfidenceIntervalSampling.Rd
BMhyd/man/LumpIntoClades.Rd
BMhyd/man/AdjustForDet.Rd
BMhyd/man/AkaikeWeight.Rd
BMhyd/man/bmhyd.Rd
BMhyd/man/AICc.Rd
BMhyd/man/SimulateTipData.Rd
BMhyd/man/GetVModified.Rd
BMhyd/man/CalculateLikelihood.Rd
BMhyd/man/GetAncestor.Rd
BMhyd/man/nicotiana.Rd
BMhyd/man/PlotNetwork.Rd
BMhyd/man/DetPass.Rd
BMhyd/man/GetClade.Rd
BMhyd/man/GenerateValues.Rd
BMhyd/man/SimulateNetwork.Rd