AICc                    AICc
AdaptiveConfidenceIntervalSampling
                        Confidence interval under adaptive cluster
                        sampling technique.
AdjustForDet            Adjust the phylogeny.
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
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
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
cichlid                 Cichlid data from Kobmuller et al. 2007
nicotiana               nicotiana data
