Full sibling reconstruction from SNP data

alle_freqs | counts alleles from a geno_counts matrix |

ave_err_commission_and_ommission | computes the average number of non-sibs in inferred sibships |

C_full_sibling_pair_gfreqs | compute the genotype probs of a pair of full siblings with... |

count_genos | counts up genotypes from a snp_indicators array |

find_high_logl_sib_pairs | for each individual, find the other individuals with a... |

full_sibling_pair_gfreqs | returns genotype probabilities of a pair of full siblings |

full_sib_mcmc_initialize | initilize all the variables to do a full sibling analysis... |

fullsniplings | Full-sibling inference from biallelic markers (like SNPs) |

geno_post_c | compute the posterior of Inds genotype given the genotype... |

geno_posterior | given some genotype likelihoods and a prior, compute the... |

geno_qty_array | S3 class for arrays holding probabilities and likelihoods of... |

genos_to_indicators | Take an L x N matrix of SNP genos and return a 3 x L x N... |

get_indiv_geno_lik | given genotyping error and observed genotypes, return an... |

get_snp_genos | takes a data frame of SNP alleles and converts them to a... |

gfreqs_from_afreqs | creates a vector of genotypes likelihoods from the allele... |

gibbs_update_one_indiv_in_place | does a gibbs update of the full sibling group of individual... |

gqa_natural | return a geno_qty_array in its natural representation with... |

greedy_partition | Uses the estimated posteriors for each sibgroup to come up... |

hashable_sibships | Returns a vector of strings naming the current sibships |

high_logl_pairs | return the high-sib-pair-logl indivs for each indiv |

initialize_sib_list_to_singletons | initialize the list of full siblings to a bunch of singletons |

kid_prongs_times_ind_likelihoods | Computes the posterior predictive likelihoods that an... |

lik_array_from_simple_geno_err | makes L 3x3 tables of genotype likelihoods |

make_IFS_from_FSL | create the "individuals full sibships" vector from the... |

make_KidProngs_from_FSL_and_PMMFS | create a KidProngs matrix (matrix of posterior predictives... |

make_LMMFS_from_FSL_and_LMMI | create the "Likelihood Matrix of Marriages given Full... |

make_PMMFS_from_FSL_and_LMMFS | create a "Posterior Matrix of Marriages given Full Siblings"... |

multi_kid_marriage_likelihoods | compute the marriage node likelihoods given offspring... |

NamizeSibs | adds the names of the members of the sibset if available |

ordered_fsl | Orders the Full Sibling List (FSL) by size and orders the... |

per_kid_marriage_likelihoods | Compute the likelihood of the genotypes of a marriage given... |

possible_sibgroups | return a vector of indices of sibships that include at least... |

prep_all_variables | a function to prep all the variables up through the marriage... |

print.geno_qty_array | a method for printing objects inheriting from class... |

pseudo_prior | compute the pseudo-prior for individual and individual pulled... |

run_mcmc | Run the MCMC for full sibling inference |

sib_result_plot | plot posterior bars and compare to correct or incorrect |

simulate_sib_pair_logls | simulate pairs of full sibs and pairs of unrelateds and... |

SlurpSibships | Slurps a colony inferred sibship file into a list |

sort_visited_sibgroups | sorts the visited sibgroups on the basis of posterior and... |

table_sibsizes | this function tables the sibship sizes |

trans_probs | returns a matrix of the 27 transmission probs between a pair... |

unrelated_pair_gfreqs | creates a matrix of genotype probabilities for two unrelated... |

update_marriage_likelihoods_in_place | Update one row of a marriage likelihood matrix IN PLACE! |

update_marriage_node_kid_prongs_in_place | update marriage node kid prongs IN PLACE |

update_marriage_posteriors_in_place | Calculate/update one row of a marriage Posterior matrix IN... |

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