Bayesian Inference from the Conditional Genetic Stock Identification Model

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Documentation for package ‘rubias’ version 0.3.4

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

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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