Files in bobverity/MALECOT
Joint estimation of COI and population structure for malaria genetic data
...Rcheck/00check.log
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
MALECOT.Rproj
NAMESPACE
R/.Rapp.history
R/MALECOT.R
R/RcppExports.R
R/assertions_v3.R
R/data.R
R/main.R
R/malecot_project.R
R/misc.R
R/plot.R
README.md
R_ignore/images/documentation-click here!-blue.png
R_ignore/old code/src/Hungarian.cpp
R_ignore/old code/src/Hungarian.h
R_ignore/old code/src/MALECOT.dll
R_ignore/old code/src/MCMC_biallelic.cpp
R_ignore/old code/src/MCMC_biallelic.h
R_ignore/old code/src/MCMC_multiallelic.cpp
R_ignore/old code/src/MCMC_multiallelic.h
R_ignore/old code/src/RcppExports.cpp
R_ignore/old code/src/main.cpp
R_ignore/old code/src/misc.cpp
R_ignore/old code/src/misc.h
R_ignore/old code/src/particle_biallelic.cpp
R_ignore/old code/src/particle_biallelic.h
R_ignore/old code/src/particle_multiallelic.cpp
R_ignore/old code/src/particle_multiallelic.h
R_ignore/old code/src/probability.cpp
R_ignore/old code/src/probability.h
_pkgdown.yml
appveyor.yml
codecov.yml
docs/LICENSE-text.html
docs/articles/comparing-models.html
docs/articles/comparing-models_files/figure-html/unnamed-chunk-10-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-11-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-12-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-13-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-14-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-15-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-15-2.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-16-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-16-2.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-17-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-17-2.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-17-3.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-17-4.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-18-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-19-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-20-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-21-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-22-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-6-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-7-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-8-1.png
docs/articles/comparing-models_files/figure-html/unnamed-chunk-9-1.png
docs/articles/complex-priors.html
docs/articles/complex-priors_files/figure-html/unnamed-chunk-11-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-12-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-12-2.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-12-3.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-13-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-13-2.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-13-3.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-15-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-16-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-16-2.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-16-3.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-17-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-17-2.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-17-3.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-21-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-22-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-3-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-3-2.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-3-3.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-7-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-8-1.png
docs/articles/complex-priors_files/figure-html/unnamed-chunk-9-1.png
docs/articles/ensuring-good-mixing.html
docs/articles/ensuring-good-mixing_files/figure-html/unnamed-chunk-10-1.png
docs/articles/ensuring-good-mixing_files/figure-html/unnamed-chunk-11-1.png
docs/articles/ensuring-good-mixing_files/figure-html/unnamed-chunk-7-1.png
docs/articles/ensuring-good-mixing_files/figure-html/unnamed-chunk-8-1.png
docs/articles/faq.html
docs/articles/faq_files/figure-html/unnamed-chunk-1-1.png
docs/articles/faq_files/figure-html/unnamed-chunk-2-1.png
docs/articles/gti-mathematical-details.html
docs/articles/index.html
docs/articles/installation.html
docs/articles/known-issues.html
docs/articles/multiallelic-data.html
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-10-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-10-2.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-11-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-12-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-12-2.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-13-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-14-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-14-2.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-15-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-15-2.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-16-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-17-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-6-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-7-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-8-1.png
docs/articles/multiallelic-data_files/figure-html/unnamed-chunk-9-1.png
docs/articles/power-analysis-between-models.html
docs/articles/power-analysis-within-model.html
docs/articles/power-analysis-within-model_files/crosstalk-1.0.0/css/crosstalk.css
docs/articles/power-analysis-within-model_files/crosstalk-1.0.0/js/crosstalk.js
docs/articles/power-analysis-within-model_files/crosstalk-1.0.0/js/crosstalk.js.map
docs/articles/power-analysis-within-model_files/crosstalk-1.0.0/js/crosstalk.min.js
docs/articles/power-analysis-within-model_files/crosstalk-1.0.0/js/crosstalk.min.js.map
docs/articles/power-analysis-within-model_files/figure-html/unnamed-chunk-2-1.png
docs/articles/power-analysis-within-model_files/figure-html/unnamed-chunk-3-1.png
docs/articles/power-analysis-within-model_files/figure-html/unnamed-chunk-3-2.png
docs/articles/power-analysis-within-model_files/figure-html/unnamed-chunk-4-1.png
docs/articles/power-analysis-within-model_files/figure-html/unnamed-chunk-5-1.png
docs/articles/power-analysis-within-model_files/figure-html/unnamed-chunk-6-1.png
docs/articles/power-analysis-within-model_files/figure-html/unnamed-chunk-7-1.png
docs/articles/power-analysis-within-model_files/htmlwidgets-1.0/htmlwidgets.js
docs/articles/power-analysis-within-model_files/htmlwidgets-1.3/htmlwidgets.js
docs/articles/power-analysis-within-model_files/jquery-1.11.3/jquery-AUTHORS.txt
docs/articles/power-analysis-within-model_files/jquery-1.11.3/jquery.js
docs/articles/power-analysis-within-model_files/jquery-1.11.3/jquery.min.js
docs/articles/power-analysis-within-model_files/jquery-1.11.3/jquery.min.map
docs/articles/power-analysis-within-model_files/plotly-binding-4.7.1/plotly.js
docs/articles/power-analysis-within-model_files/plotly-binding-4.8.0.9000/plotly.js
docs/articles/power-analysis-within-model_files/plotly-htmlwidgets-css-1.42.5/plotly-htmlwidgets.css
docs/articles/power-analysis-within-model_files/plotly-main-1.42.5/plotly-latest.min.js
docs/articles/power-analysis-within-model_files/plotlyjs-1.29.2/LICENSE
docs/articles/power-analysis-within-model_files/plotlyjs-1.29.2/plotly-htmlwidgets.css
docs/articles/power-analysis-within-model_files/plotlyjs-1.29.2/plotly-latest.min.js
docs/articles/power-analysis-within-model_files/typedarray-0.1/typedarray.min.js
docs/articles/running-in-parallel.html
docs/articles/tutorial-biallelic.html
docs/articles/tutorial-biallelic_files/figure-html/unnamed-chunk-12-1.png
docs/articles/tutorial-biallelic_files/figure-html/unnamed-chunk-14-1.png
docs/articles/tutorial-biallelic_files/figure-html/unnamed-chunk-15-1.png
docs/articles/tutorial-biallelic_files/figure-html/unnamed-chunk-17-1.png
docs/articles/tutorial-biallelic_files/figure-html/unnamed-chunk-17-2.png
docs/articles/tutorial-biallelic_files/figure-html/unnamed-chunk-17-3.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/MALECOT.html
docs/reference/active_set.html
docs/reference/bind_data_biallelic.html
docs/reference/bind_data_multiallelic.html
docs/reference/check_MALECOT_loaded.html
docs/reference/delete_set.html
docs/reference/fix_labels.html
docs/reference/get_ESS.html
docs/reference/get_group_order.html
docs/reference/index.html
docs/reference/is.malecot_project.html
docs/reference/malecot_file.html
docs/reference/malecot_project.html
docs/reference/more_colours.html
docs/reference/new_set.html
docs/reference/plot_COI.html
docs/reference/plot_COI_mean.html
docs/reference/plot_COI_mean_quantiles.html
docs/reference/plot_GTI_path.html
docs/reference/plot_acf.html
docs/reference/plot_coupling.html
docs/reference/plot_density.html
docs/reference/plot_e.html
docs/reference/plot_e_quantiles.html
docs/reference/plot_logevidence_K.html
docs/reference/plot_logevidence_model.html
docs/reference/plot_loglike.html
docs/reference/plot_loglike_dignostic.html
docs/reference/plot_loglike_quantiles.html
docs/reference/plot_m_quantiles.html
docs/reference/plot_p.html
docs/reference/plot_p_quantiles.html
docs/reference/plot_pca.html
docs/reference/plot_posterior_K.html
docs/reference/plot_posterior_model.html
docs/reference/plot_prior_COI.html
docs/reference/plot_prior_p.html
docs/reference/plot_qmatrix.html
docs/reference/plot_structure.html
docs/reference/plot_trace.html
docs/reference/print.malecot_project.html
docs/reference/print_full.html
docs/reference/recalculate_evidence.html
docs/reference/run_mcmc.html
docs/reference/sim_data.html
docs/reference/sim_data_safe.html
docs/reference/summary.malecot_project.html
index.md
inst/extdata/power_within_results_mean.rds
inst/extdata/tutorial1_myproj.rds
inst/extdata/tutorial1_mysim.rds
man/MALECOT.Rd
man/active_set.Rd
man/bind_data_biallelic.Rd
man/bind_data_multiallelic.Rd
man/check_MALECOT_loaded.Rd
man/delete_set.Rd
man/get_ESS.Rd
man/get_group_order.Rd
man/is.malecot_project.Rd
man/malecot_file.Rd
man/malecot_project.Rd
man/more_colours.Rd
man/new_set.Rd
man/plot_COI.Rd
man/plot_COI_mean.Rd
man/plot_GTI_path.Rd
man/plot_acf.Rd
man/plot_coupling.Rd
man/plot_density.Rd
man/plot_e.Rd
man/plot_logevidence_K.Rd
man/plot_logevidence_model.Rd
man/plot_loglike.Rd
man/plot_loglike_dignostic.Rd
man/plot_p.Rd
man/plot_posterior_K.Rd
man/plot_posterior_model.Rd
man/plot_prior_COI.Rd
man/plot_prior_p.Rd
man/plot_structure.Rd
man/plot_trace.Rd
man/print.malecot_project.Rd
man/print_full.Rd
man/recalculate_evidence.Rd
man/run_mcmc.Rd
man/sim_data.Rd
man/sim_data_safe.Rd
man/summary.malecot_project.Rd
src/.gitignore
src/Data.cpp
src/Data.h
src/Data_counts.cpp
src/Data_counts.h
src/Lookup.cpp
src/Lookup.h
src/MCMC_biallelic.cpp
src/MCMC_biallelic.h
src/MCMC_multiallelic.cpp
src/MCMC_multiallelic.h
src/Parameters.cpp
src/Parameters.h
src/Particle_biallelic.cpp
src/Particle_biallelic.h
src/Particle_multiallelic.cpp
src/Particle_multiallelic.h
src/RcppExports.cpp
src/hungarian.cpp
src/hungarian.h
src/main.cpp
src/main.h
src/misc_v1.cpp
src/misc_v1.h
src/probability.cpp
src/probability.h
tests/testthat.R
tests/testthat/test-assertions_v3.R
tests/testthat/test-misc.R
vignettes/.gitignore
vignettes/comparing-models.Rmd
vignettes/complex-priors.Rmd
vignettes/ensuring-good-mixing.Rmd
vignettes/ensuring-good-mixing.bib
vignettes/faq.Rmd
vignettes/gti-mathematical-details.Rmd
vignettes/gti-mathematical-details.bib
vignettes/installation.Rmd
vignettes/known-issues.Rmd
vignettes/multiallelic-data.Rmd
vignettes/power-analysis-between-models.Rmd
vignettes/power-analysis-within-model.Rmd
vignettes/running-in-parallel.Rmd
vignettes/tutorial-biallelic.Rmd
