Bayesian Inference from the Conditional Genetic Stock Identification Model

a_freq_list | Convert data frame of allele frequencies to nested lists |

alewife | Microsat data from alewife herring reference populations |

allelic_list | Create genotype lists for each locus |

assess_pb_bias_correction | Test the effects of the parametric bootstrap bias correction... |

assess_reference_loo | Simulate mixtures and estimate reporting group and collection... |

assess_reference_mc | Partition a reference dataset and estimate reporting group... |

avg_coll2correctRU | Get the average within-RU assignment rate for each collection |

blueback | Microsat data from blueback herring reference populations |

bootstrap_rho | Perform a parametric bootstrapping correction on an estimated... |

check_known_collections | check a baseline and mixture file together to ensure the... |

check_refmix | A helper function to check that the input data frame is OK |

chinook | SNP data from chinook reference populations |

chinook_collection_levels | a vector that gives a desired sort order of the chinook... |

chinook_mix | SNP data from Chinook salmon taken in May/August 2015 from... |

chinook_repunit_levels | a vector that gives a desired sort order of the chinook... |

close_matching_samples | check for matching (or close to matching) genotypes in a data... |

count_missing_data | for each individual count the number or loci missing and... |

custom_pi_prior | Create a vector of pi Dirichlet priors with specified values... |

dirch_from_allocations | Given a vector of different categories in 1...n and a prior,... |

dirch_from_counts | Given a vector of counts for different categories in 1...n... |

geno_logL | Calculate a matrix of genotype log-likelihoods for a genetic... |

geno_logL_ssq | Calculate a matrix of sum-of-squares of genotype... |

get_ploidy_from_frame | infer the ploidy from the pattern of NAs in the columns of... |

gprob_sim_gc | Simulate genotype log-likelihoods from a population by gene... |

gprob_sim_gc_missing | Simulate genotypes by gene copy, with missing data from... |

gprob_sim_ind | Simulate genotype log-likelihoods from a population by... |

gsi_em_1 | EM algorithm from the simplest GSI model for pi and the... |

gsi_mcmc_1 | MCMC from the simplest GSI model for pi and the individual... |

gsi_mcmc_fb | MCMC from the fully Bayesian GSI model for pi and the... |

Hasselman_sim_colls | Generate a random population structure and mixture sample, as... |

infer_mixture | Estimate mixing proportions and origin probabilities from one... |

list_diploid_params | Collect essential data values before mixture proportion... |

mixture_draw | Separate a chosen proportion of a reference dataset into a... |

modify_scaled_likelihoods_for_known_mixture_fish | for individuals of known origin in the mixture, put all their... |

perfect_chinook | perfect-assignment genetic data for chinook. |

perfect_chinook_mix | perfect-assignment mixture genetic data for chinook. |

per_locus_means_and_vars | Compute the mean and variance of the single-locus genotype... |

pipe | Pipe operator |

rcpp_close_matchers | Find all pairs that have close matches |

rcpp_indiv_specific_logl_means_and_vars | From the pattern of missing data at each individual, compute... |

rcpp_per_locus_logls | Return a matrix of locus-specific self-assignment logls |

read_gsi_sim | read a gsi_sim formatted input file into a tibble that rubias... |

ref_and_mix_pipeline | Estimate mixing proportions from reference and mixture... |

reference_allele_counts | Tabulate occurrences of all observed alleles in reference... |

round2 | Round a given number, with 5 always rounded up |

rubias | rubias: Bayesian inference from the conditional genetic stock... |

samp_from_mat | Sample 1 observation from cell probabilities that are columns... |

self_assign | Do leave-one-out self-assignment of individuals in a... |

sim_spec_examples | List of example ways of specifying repunit and collection... |

simulate_random_samples | Generate a samples for a mixture. |

small_chinook_mix | Small sample of SNP data from Chinook salmon taken in... |

small_chinook_ref | SNP data from selected chinook reference populations |

tcf2long | Convert Two-Column Genetic Data to Long Format |

tcf2param_list | Generate MCMC parameter list from two-column genetic data &... |

tidy_mcmc_coll_rep_stuff | A helper function to tidy up the output from the gsi_mcmc... |

tidy_mcmc_pofz | A helper function to tidy up the PofZ-like output from the... |

tidy_pi_traces | a helper function to tidy up the pi-traces that come out of... |

write_gsi_sim_mixture | Write a mixture data frame to gsi_sim format baseline and... |

write_gsi_sim_reference | Write a reference data frame to gsi_sim format baseline and... |

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