Package index • rubias

Genetic Analysis of Mixtures

Functions for running mixed-stock analysis, also called genetic stock identification

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

Interpretation of Mixture Analyses

Functions that process the output of infer_mixture() to help interpret the estimated values, especially in regard to estimated mixture proportions that are less than 1 divided by the mixture sample size

plot_PofZ_vs_pi(): Make a plot comparing PofZs and Pi values for all collections (or repunits)

prob_at_least_one_in_sample(): Calculates the posterior probability that the sample contains at least one fish from each collection and repunit

Predicting the Accuracy Expected with a Reference Baseline

Functions simulating mixture samples and analyzing those to predict how much power you will have for distinguishing fish from different populations and reporting units and for estimating their mixture proportions

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

assess_pb_bias_correction(): Test the effects of the parametric bootstrap bias correction on a reference dataset through cross-validation

self_assign(): Do leave-one-out self-assignment of individuals in a reference baseline

Package Data Sets

Data sets and data objects that ship with the ‘rubias’ package

alewife: Microsat data from alewife herring reference populations

blueback: Microsat data from blueback herring reference populations

chinook: SNP data from chinook reference populations

chinook_mix: SNP data from Chinook salmon taken in May/August 2015 from California fisheries

chinook_collection_levels: a vector that gives a desired sort order of the chinook collections

chinook_repunit_levels: a vector that gives a desired sort order of the chinook repunits

perfect_chinook: perfect-assignment genetic data for chinook.

perfect_chinook_mix: perfect-assignment mixture genetic data for chinook.

sim_spec_examples: List of example ways of specifying repunit and collection quantities in simulations

small_chinook_ref: SNP data from selected chinook reference populations

small_chinook_mix: Small sample of SNP data from Chinook salmon taken in May/August 2015 from California fisheries

Data Input and Output

A few convenience functions to import/export data from GSI_SIM format, mostly

read_gsi_sim(): read a gsi_sim formatted input file into a tibble that rubias can use

write_gsi_sim_reference(): Write a reference data frame to gsi_sim format baseline and repunits file

write_gsi_sim_mixture(): Write a mixture data frame to gsi_sim format baseline and repunits file

General Package Information

The contents of the rubias-package file

rubias-package rubias: rubias: Bayesian inference from the conditional genetic stock identification model