Files in benmoran11/rubias
Bayesian Inference from the Conditional Genetic Stock Identification Model
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R-main/README.Rmd
R-main/README.md
R-main/cjfas_graphs.R
R-main/coalescent_sim.R
R-main/cross-validation.R
R-main/proportion_sig_test.R
R-presentation/oral_presentation_graphs.R
R/RcppExports.R
R/assess_pb_bias_correction.R
R/assess_reference_loo.R
R/assess_reference_mc.R
R/check_known_collections.R
R/close_matching_samples.R
R/count_missing_data.R
R/custom_pi_prior.R
R/data.R
R/data_conversion.R
R/eca-internal-funcs.R
R/import.R
R/infer_mixture.R
R/modify-scaled-likelihoods-for-known-mixture-fish.R
R/per_locus_means_and_vars.R
R/read_gsi_sim.R
R/rubias.R
R/self_assign.R
R/simulate_random_samples.R
R/simulation_pipelines.R
R/utilities.R
R/write_gsi_sim_mixture.R
R/write_gsi_sim_reference.R
README-data-structures.Rmd
README.Rmd
README.md
TODO.md
cran-comments.md
data/alewife.rda
data/blueback.rda
data/chinook.rda
data/chinook_collection_levels.rda
data/chinook_mix.rda
data/chinook_repunit_levels.rda
data/perfect_chinook.rda
data/perfect_chinook_mix.rda
data/sim_spec_examples.rda
data/small_chinook_mix.rda
data/small_chinook_ref.rda
development/.gitignore
development/R-main/baseline-resamp-timings-nmfs.R
development/R-main/explore-adding-knowns-in-mixture.R
development/R-main/fix-bug-for-rachael.R
development/R-main/playing-with-simulating-refs.R
development/R-main/show-for-dan.R
development/Rmd/.gitignore
development/Rmd/a-perfect-assignment-chinook-data-set.Rmd
development/Rmd/brendan-labrador-sims.Rmd
development/Rmd/dev-repuclust.Rmd
development/Rmd/explore-known-collections-DFO-data.Rmd
development/Rmd/helping-kerry-with-rubias.Rmd
development/Rmd/investigate-alewife-snp-baseline.Rmd
development/Rmd/investigate_dfo_data.Rmd
development/Rmd/investigate_dfo_data.nb.html
development/Rmd/kyle-shed-haploid-markers.Rmd
development/Rmd/rubias-demo-for-colin-and-terry.Rmd
development/Rmd/test-haploid-marker-calcs.Rmd
development/Rmd/testing-assess-reference-mc.Rmd
development/Rmd/testing-simulate-random-samples.Rmd
development/data/.gitignore
development/data/5000_locus_mixture.rds
development/data/5000_locus_reference.rds
development/data/Ots-19-grps.txt
development/data/Ots-baseline-numerical.csv
development/data/Ots-lat-long.txt
development/data/bco_baseline.rds
development/mclapply_testing/.gitignore
development/mclapply_testing/test_mclapply_speed_on_choppy_matrix.Rmd
development/mclapply_testing/test_mclapply_speed_on_choppy_matrix.nb.html
inst/CITATION
inst/scripts/clean-up-gsisim-repunits.awk
inst/scripts/clean-up-gsisim.awk
man/Hasselman_sim_colls.Rd
man/a_freq_list.Rd
man/alewife.Rd
man/allelic_list.Rd
man/assess_pb_bias_correction.Rd
man/assess_reference_loo.Rd
man/assess_reference_mc.Rd
man/avg_coll2correctRU.Rd
man/blueback.Rd
man/bootstrap_rho.Rd
man/check_known_collections.Rd
man/check_refmix.Rd
man/chinook.Rd
man/chinook_collection_levels.Rd
man/chinook_mix.Rd
man/chinook_repunit_levels.Rd
man/close_matching_samples.Rd
man/count_missing_data.Rd
man/custom_pi_prior.Rd
man/dirch_from_allocations.Rd
man/dirch_from_counts.Rd
man/geno_logL.Rd
man/geno_logL_ssq.Rd
man/get_ploidy_from_frame.Rd
man/gprob_sim_gc.Rd
man/gprob_sim_gc_missing.Rd
man/gprob_sim_ind.Rd
man/gsi_em_1.Rd
man/gsi_mcmc_1.Rd
man/gsi_mcmc_fb.Rd
man/infer_mixture.Rd
man/list_diploid_params.Rd
man/mixture_draw.Rd
man/modify_scaled_likelihoods_for_known_mixture_fish.Rd
man/per_locus_means_and_vars.Rd
man/perfect_chinook.Rd
man/perfect_chinook_mix.Rd
man/pipe.Rd
man/rcpp_close_matchers.Rd
man/rcpp_indiv_specific_logl_means_and_vars.Rd
man/rcpp_per_locus_logls.Rd
man/read_gsi_sim.Rd
man/ref_and_mix_pipeline.Rd
man/reference_allele_counts.Rd
man/round2.Rd
man/rubias.Rd
man/samp_from_mat.Rd
man/self_assign.Rd
man/sim_spec_examples.Rd
man/simulate_random_samples.Rd
man/small_chinook_mix.Rd
man/small_chinook_ref.Rd
man/tcf2long.Rd
man/tcf2param_list.Rd
man/tidy_mcmc_coll_rep_stuff.Rd
man/tidy_mcmc_pofz.Rd
man/tidy_pi_traces.Rd
man/write_gsi_sim_mixture.Rd
man/write_gsi_sim_reference.Rd
rubias.Rproj
rubias_bib.bibtex
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/macros.h
src/rcpp_close_matchers.cpp
src/rcpp_fullBayes_mcmc.cpp
src/rcpp_gprobs.cpp
src/rcpp_indiv_specific_logl_means_and_vars.cpp
src/rcpp_per_locus_logls.cpp
src/rcpp_sampling.cpp
src/rcpp_sampling.h
src/rcpp_simulation.cpp
src/simple_pi_em.cpp
src/simple_pi_mcmc.cpp
src/utilities.cpp
src/utilities.h
tools/boxplot-pofz-gc-sim-1.png
tools/boxplot-pofz-indiv-sim-1.png
tools/plot-6-1.png
tools/plot-top6-1.png
tools/plot-top6-n-1.png
tools/unnamed-chunk-4-1.png
tools/unnamed-chunk-6-1.png
tools/z-score-density-1.png
vignettes/rubias-fully-bayesian.Rmd
vignettes/rubias-overview.Rmd
vignettes/rubias-underlying-data-structures.Rmd
