Files in eriqande/SNPcontam
Detecting contaminated samples from SNP genotypes
.Rbuildignore
.gitignore
Compile.R
DESCRIPTION
NAMESPACE
R/.gitignore
R/ROC.R
R/RcppExports.R
R/SNPcontam.R
R/analyze_MCMC.R
R/analyzed_mixed_MCMC.R
R/contam_MCMC.R
R/data.R
R/hetero.R
R/likelihood.R
R/lratio.R
R/mixed_MCMC.R
R/multi_pop_MCMC.R
R/prepare_base_and_mix_for_mixed_MCMC.R
R/random_gene.R
R/single_pop_MCMC.R
R/threshold.R
README.md
SNPcontam.Rproj
TERMS.md
data/cdfg_port_samples.rda
data/swfsc_chinook_baseline.rda
man/.gitignore
man/P_likelihood.Rd
man/Pcontam.Rd
man/SNPcontam.Rd
man/analyze_MCMC.Rd
man/cdfg_port_samples.Rd
man/likelihood.Rd
man/mixed_MCMC.Rd
man/prepare_base_and_mix_for_mixed_MCMC.Rd
man/swfsc_chinook_baseline.Rd
not-package/checking_calculations/.gitignore
not-package/checking_calculations/compare_to_gsi_sim.Rmd
not-package/compile-analyses-and-documents.R
not-package/data/ca_fishery_props.rda
not-package/data/contaminated_coho.rda
not-package/data/kl_genotypes.rda
not-package/data/noyo_genotypes.rda
not-package/extras/Knitr.engine
not-package/extras/patchKnitrSynctex.R
not-package/inkscape/DAG_1.svg
not-package/inkscape/DAG_2.svg
not-package/manuscript/.gitignore
not-package/manuscript/abstract.Rnw
not-package/manuscript/appendices.Rnw
not-package/manuscript/author-title-etc.tex
not-package/manuscript/brownhonorsthesis.cls
not-package/manuscript/ev-honors-thesis.tex
not-package/manuscript/images/DAG_1.pdf
not-package/manuscript/images/DAG_2.pdf
not-package/manuscript/images/README.md
not-package/manuscript/images/banner.pdf
not-package/manuscript/images/mixed_rho.pdf
not-package/manuscript/images/rho_and_allele.pdf
not-package/manuscript/main-body-text.Rnw
not-package/manuscript/men.bst
not-package/manuscript/snp-contam-main.Rnw
not-package/manuscript/snp-contam.bib
not-package/manuscript/tables/.gitignore
not-package/manuscript/tables/afreq_ci_coverage.tex
not-package/manuscript/tables/mixed_z_table.tex
not-package/manuscript/tables/z_table_p_one_half.tex
not-package/notes/.gitignore
not-package/notes/README.md
not-package/notes/convert-to-gsi-sim.R
not-package/notes/elena-work-log.md
not-package/notes/population_compare.R
not-package/notes/sim_mixture.R
not-package/notes/test_data.R
not-package/notes/work-plan.md
not-package/presentation/.gitignore
not-package/presentation/abstract.tex
not-package/presentation/images/.gitignore
not-package/presentation/images/DAG_1.pdf
not-package/presentation/images/DAG_2.pdf
not-package/presentation/images/NOAA_Logo.pdf
not-package/presentation/images/bad_lab.pdf
not-package/presentation/images/bad_lab2.pdf
not-package/presentation/images/chinooksalmon.pdf
not-package/presentation/images/conclusion_salmon.pdf
not-package/presentation/images/conclusion_salmon2.pdf
not-package/presentation/images/heap_fish.pdf
not-package/presentation/images/hetero_figure.svg
not-package/presentation/images/hetero_figure2.pdf
not-package/presentation/images/mixed_rho.pdf
not-package/presentation/images/official_NOAA_logo.pdf
not-package/presentation/images/pipette.pdf
not-package/presentation/images/rho_and_allele.pdf
not-package/presentation/images/salmon_individual.pdf
not-package/presentation/images/snp_diagram.pdf
not-package/presentation/images/snp_diagram2.pdf
not-package/presentation/presentation_slides.tex
not-package/presentation/tables/.gitignore
not-package/presentation/tables/afreq_ci_coverage.tex
not-package/presentation/tables/mixed_z_table.tex
not-package/presentation/tables/z_table_p_one_half.tex
not-package/readings-etc/.gitignore
not-package/readings-etc/ASHG2013-SNPtrace-Panel-Quality.pdf
not-package/readings-etc/articles-to-read-and-cite.md
not-package/simulations/01_simulation_1.R
not-package/simulations/02_makecharts_1.R
not-package/simulations/03_maketables_1.R
not-package/simulations/04_simulation_2.R
not-package/simulations/05_makecharts_tables_2.R
not-package/simulations/06_testing_baseline.R
not-package/simulations/07_testing_cdfg_port_samples.R
not-package/simulations/mixed_simulation_functions.R
not-package/simulations/out_list_01.rda
not-package/simulations/out_list_02.rda
not-package/simulations/run_all_simulations.R
not-package/simulations/simulation_functions.R
not-package/supplements/images/.gitignore
not-package/supplements/images/README.md
src/.gitignore
src/P_likelihood.cpp
src/Pcontam.cpp
src/RcppExports.cpp
vignettes/.gitignore
vignettes/MCMC_functionflow.Rmd
vignettes/lh_functionflow.Rmd
