PCM for Hybridization

AdaptiveConfidenceIntervalSampling | Confidence interval under adaptive cluster sampling... |

AdjustForDet | Adjust the phylogeny. |

AICc | AICc |

AkaikeWeight | Akaike weight |

AlterMatrixUsingDE | Transforming current variance covariance matrix to a positive... |

AttachHybridsToDonor | Attach hybrids to the donor species |

AttemptDeletionFix | Delete taxa to improve matrix condition |

BMhyb | Comparative method for studying hybridization using Brownian... |

BMhybGrid | Comparative method for studying hybridization using Brownian... |

BrissetteEtAlCorrection | Transforming current variance covariance matrix to a positive... |

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... |

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 |

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