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 |