bnpsd-package |
A package for modeling and simulating an admixed population |

admix_prop_1d_circular |
Construct admixture proportion matrix for circular 1D geography |

admix_prop_1d_linear |
Construct admixture proportion matrix for 1D geography |

admix_prop_indep_subpops |
Construct admixture proportion matrix for independent subpopulations |

bnpsd |
A package for modeling and simulating an admixed population |

coanc_admix |
Construct the coancestry matrix of an admixture model |

coanc_to_kinship |
Transform coancestry matrix to kinship matrix |

coanc_tree |
Calculate coancestry matrix corresponding to a tree |

draw_all_admix |
Simulate random allele frequencies and genotypes from the BN-PSD admixture model |

draw_genotypes_admix |
Draw genotypes from the admixture model |

draw_p_anc |
Draw random Uniform or Beta ancestral allele frequencies |

draw_p_subpops |
Draw allele frequencies for independent subpopulations |

draw_p_subpops_tree |
Draw allele frequencies for subpopulations related by a tree |

fit_tree |
Fit a tree structure to a coancestry matrix |

fixed_loci |
Identify fixed loci |

fst_admix |
Calculate FST for the admixed individuals |

make_p_ind_admix |
Construct individual-specific allele frequency matrix under the PSD admixture model |

scale_tree |
Scale a coancestry tree |

tree_additive |
Calculate additive edges for a coancestry tree, or viceversa |

tree_reindex_tips |
Reindex tree tips in order of appearance in edges |

tree_reorder |
Reorder tree tips to best match a desired order |

undiff_af |
Undifferentiate an allele distribution |