Hybrid Trait Evolution under Brownian Motion

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Documentation for package ‘BMhyb’ version 1.5.2

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AdaptiveConfidenceIntervalSampling Confidence interval under adaptive cluster sampling technique.
AdjustForDet Adjust the phylogeny.
AICc AICc
AkaikeWeight Akaike weight
AlterMatrixUsingDE Transforming current variance covariance matrix to a positive definite matrix
AttachHybridsToDonor Attach hybrids to the donor species
AttemptDeletionFix Delete taxa to improve matrix condition
BMhyb Comparative method for studying hybridization using Brownian motion for trait evolution
BMhybGrid Comparative method for studying hybridization using Brownian motion for trait evolution
BrissetteEtAlCorrection Transforming current variance covariance matrix to a positive definite matrix
CalculateLikelihood Calculate the likelihood value for the model
cichlid Cichlid data from Kobmuller et al. 2007
ContourFromAdaptiveSampling Contour maps
ConvertExpm1 Exponentials
ConvertLog1P Logarithms
ConvertVectorToMatrix Convert a vector into a matrix
DetPass determinant of the matrix
GenerateRandomPositiveDefiniteMatrix Generate positive definite matrix
GenerateRandomValues Generate random values
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
IsPositiveDefinite Check to make sure a variance covariance network (from a tree or network) is positive definite
LumpIntoClades Lump into clades
nicotiana nicotiana data
PlotAICRegion Plot the region from which points were estimated
PlotConvexHull Convex hull
PlotNetwork Phylogenetic Network Plot
PositiveDefiniteOptimizationFn Distance function for optimization
SimulateNetwork Simulate phylogenetic network
SimulateTipData Simulate data on a network