BMhyd: PCM for Hybridization
Version 1.2-8

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.

Browse man pages Browse package API and functions Browse package files

AuthorDwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu> and Brian O'Meara <omeara.brian@gmail.com>
Date of publication2015-08-06 07:15:38
MaintainerDwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu>
LicenseGPL (>= 2)
Version1.2-8
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BMhyd")

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

Functions

AICc Man page Source code
AdaptiveConfidenceIntervalSampling Man page Source code
AdjustForDet Man page Source code
AkaikeWeight Man page Source code
AttachHybridsToDonor Man page Source code
BMhyd Man page Source code
CalculateLikelihood Man page Source code
ContourFromAdaptiveSampling Man page Source code
DetPass Man page Source code
GenerateValues Man page Source code
GetAncestor Man page Source code
GetClade Man page Source code
GetMeansModified Man page Source code
GetVModified Man page Source code
LumpIntoClades Man page Source code
PlotNetwork Man page Source code
Plot_ConvexHull Man page Source code
SimulateNetwork Man page Source code
SimulateTipData Man page Source code
cichlid Man page
nicotiana Man page

Files

NAMESPACE
data
data/cichlid.RData
data/nicotiana.RData
R
R/bmhyd.r
MD5
DESCRIPTION
man
man/Plot_ConvexHull.Rd
man/cichlid.Rd
man/GetMeansModified.Rd
man/AttachHybridsToDonor.Rd
man/ContourFromAdaptiveSampling.Rd
man/AdaptiveConfidenceIntervalSampling.Rd
man/LumpIntoClades.Rd
man/AdjustForDet.Rd
man/AkaikeWeight.Rd
man/bmhyd.Rd
man/AICc.Rd
man/SimulateTipData.Rd
man/GetVModified.Rd
man/CalculateLikelihood.Rd
man/GetAncestor.Rd
man/nicotiana.Rd
man/PlotNetwork.Rd
man/DetPass.Rd
man/GetClade.Rd
man/GenerateValues.Rd
man/SimulateNetwork.Rd
BMhyd documentation built on May 19, 2017, 8:52 p.m.