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⚠️There's a newer version (2.1.5) of this package.Take me there.

This is a package for doing comparative methods on networks. It's been in peer review twice but not accepted, and the current version has a fatal flaw. So don't use it.

To install it (but see caveat above):

install.packages("BMhyb")
devtools::install_github("bomeara/BMhyb")

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Version

Install

install.packages('BMhyb')

Monthly Downloads

23

Version

1.5.2

License

GPL (>= 2)

Maintainer

DwuengChwuan Jhwueng

Last Published

October 8th, 2017

Functions in BMhyb (1.5.2)

AdjustForDet

Adjust the phylogeny.
AkaikeWeight

Akaike weight
AttemptDeletionFix

Delete taxa to improve matrix condition
BMhyb

Comparative method for studying hybridization using Brownian motion for trait evolution
AlterMatrixUsingDE

Transforming current variance covariance matrix to a positive definite matrix
AttachHybridsToDonor

Attach hybrids to the donor species
BMhybGrid

Comparative method for studying hybridization using Brownian motion for trait evolution
BrissetteEtAlCorrection

Transforming current variance covariance matrix to a positive definite matrix
AICc

AICc
AdaptiveConfidenceIntervalSampling

Confidence interval under adaptive cluster sampling technique.
ConvertVectorToMatrix

Convert a vector into a matrix
DetPass

determinant of the matrix
GetClade

Get clade from the tree
GetMeansModified

The species means for the network model
CalculateLikelihood

Calculate the likelihood value for the model
ContourFromAdaptiveSampling

Contour maps
GetVModified

Variance covariance matrix for the network model
IsPositiveDefinite

Check to make sure a variance covariance network (from a tree or network) is positive definite
SimulateTipData

Simulate data on a network
GenerateValues

Generate parameter values
GetAncestor

Identify the ancestor
PositiveDefiniteOptimizationFn

Distance function for optimization
SimulateNetwork

Simulate phylogenetic network
GenerateRandomPositiveDefiniteMatrix

Generate positive definite matrix
GenerateRandomValues

Generate random values
PlotConvexHull

Convex hull
nicotiana

nicotiana data
PlotNetwork

Phylogenetic Network Plot
cichlid

Cichlid data from Kobmuller et al. 2007
ConvertExpm1

Exponentials
ConvertLog1P

Logarithms
LumpIntoClades

Lump into clades
PlotAICRegion

Plot the region from which points were estimated