Phylogenetic Inference by Profile Parsimony

congreveLamsdellMatrices | 100 simulated data matrices |

DFact | Double factorial |

Evaluate | Evaluate tree |

ICPerStep | Information content per step |

ICSteps | Information Content Steps |

InfoAmounts | Amount of information in each character |

LDFact | Log double factorial Handles odd and even inout numbers |

LDFactorial | Log double factorial |

LogisticPoints | Logistic Points Extract points from a fitted model |

N1Spr | Number of trees on SPR step away Formula given by Given by... |

NamedConstant | Named constant |

NRooted | Number of rooted/unrooted trees These functions return the... |

PhyDat | Load phyDat object |

PrepareDataProfile | Prepare data for Profile Parsimony |

ProfileParsimony-package | Phylogenetic Inference using Profile Parsimony |

ProfileScore | Profile Parsimony Score |

referenceTree | Tree topology for matrix simulation |

WithOneExtraStep | Number of trees with one extra step |

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