Nonparametric method for identifying discordant phylogenetic trees

adjustClassifierParameter | Adjust Classification Tuning Parameter for fitted kdetrees... |

apicomplexa | Apicomplexa gene trees sample data set. |

as.data.frame.kdetrees | Convert kdetrees object to data.frame |

as.matrix.multiPhylo | dissimilarity map tree vectorization |

bhv.consts | Find BHV constant lower bound |

bhv.orthant.lb | Lower orthant bound for tree t with bw h. |

bw.nn | nearest-neighbor adaptive bandwidth selection |

cutoff | Find cutoff value based on IQR |

dG.expPoly | Pfaffian matrix for Exponential-polynomial distribution |

dist.diss | Compute pairwise tree distances |

estimate | estimate densities from kernel matrix |

Gpartial | Evaluate |

hgm.expPoly | Normalizing constant for Exponential-Polynomial distribution |

hist.kdetrees | Create a histogram of tree density estimates |

internal.blens | Extract vector of internal branch lengths |

kdetrees | Identify discordant trees in a sample |

kdetrees.complete | Complete kdetrees analysis convenience function |

kdetrees-package | kdetrees |

load.trees | Read Newick trees from a set of files. |

make.theta | Create a theta vector from a phylo object |

normkern | Generalized Gaussian kernel |

Northant | Count semi-labeled rooted trees on n taxa |

plot.kdetrees | Plot the unnormalized density estimates for each tree. |

print.kdetrees | Summarize a kdetrees object in human-readable form. |

sort.kdetrees | Reorder objects in a kdetrees object based on current density... |

which.outliers | Find outlier indices based on Tukey's IQR method. |

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