# Bayesian Inference from the Conditional Genetic Stock Identification Model

## Documentation for package ‘rubias’ version 0.3.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

alewife | Microsat data from alewife herring reference populations
assess_pb_bias_correction | Test the effects of the parametric bootstrap bias correction on a reference dataset through cross-validation
assess_reference_loo | Simulate mixtures and estimate reporting group and collection proportions.
assess_reference_mc | Partition a reference dataset and estimate reporting group and collection proportions
blueback | Microsat data from blueback herring reference populations
chinook | SNP data from chinook reference populations
chinook_collection_levels | a vector that gives a desired sort order of the chinook collections
chinook_mix | SNP data from Chinook salmon taken in May/August 2015 from California fisheries
chinook_repunit_levels | a vector that gives a desired sort order of the chinook repunits
close_matching_samples | check for matching (or close to matching) genotypes in a data frame
infer_mixture | Estimate mixing proportions and origin probabilities from one or several mixtures
perfect_chinook | perfect-assignment genetic data for chinook.
perfect_chinook_mix | perfect-assignment mixture genetic data for chinook.
read_gsi_sim | read a gsi_sim formatted input file into a tibble that rubias can use
rubias | rubias: Bayesian inference from the conditional genetic stock identification model
self_assign | Do leave-one-out self-assignment of individuals in a reference baseline
sim_spec_examples | List of example ways of specifying repunit and collection quantities in simulations
small_chinook_mix | Small sample of SNP data from Chinook salmon taken in May/August 2015 from California fisheries
small_chinook_ref | SNP data from selected chinook reference populations
write_gsi_sim_mixture | Write a mixture data frame to gsi_sim format baseline and repunits file
write_gsi_sim_reference | Write a reference data frame to gsi_sim format baseline and repunits file