Files in mrc-ide/gonovax
Deterministic Compartmental Model of Gonorrhoea with Vaccination
.Rbuildignore
.covrignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
.lintr
DESCRIPTION
LICENSE
Makefile
NAMESPACE
NEWS.md
R/data.R
R/mcmc-parameters.R
R/mcmc-tools.R
R/mcmc.R
R/model.R
R/novax.R
R/odin.R
R/onevax_xpvwrh.R
R/onevax_xpvwrh_trackvt.R
R/onevax_xvw.R
R/onevax_xvw_trial.R
R/onevax_xvwr.R
R/onevax_xvwrh.R
R/onevax_xvwv.R
R/parameters.R
R/parameters_trial.R
R/run_grid.R
R/run_trial.R
R/stratum_indexes.R
R/support.R
R/uptake_maps.R
R/utils.R
R/utils_assert.R
R/zzz.R
README.md
_pkgdown.yml
codecov.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/getting_started.html
docs/articles/getting_started_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/getting_started_files/figure-html/unnamed-chunk-3-1.png
docs/articles/getting_started_files/figure-html/unnamed-chunk-4-1.png
docs/articles/getting_started_files/figure-html/unnamed-chunk-5-1.png
docs/articles/getting_started_files/figure-html/unnamed-chunk-6-1.png
docs/articles/getting_started_files/figure-html/unnamed-chunk-7-1.png
docs/articles/getting_started_files/figure-html/unnamed-chunk-8-1.png
docs/articles/getting_started_files/figure-html/unnamed-chunk-9-1.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/aggregate.html
docs/reference/compare.html
docs/reference/compare_basic.html
docs/reference/create_vax_map.html
docs/reference/create_waning_map.html
docs/reference/dbetabinom.html
docs/reference/extract_flows.html
docs/reference/figures/vax_diagram.png
docs/reference/gono_params.html
docs/reference/gonovax_data.html
docs/reference/gonovax_year.html
docs/reference/gonovax_year_as_year.html
docs/reference/index.html
docs/reference/initial_params.html
docs/reference/mcmc.html
docs/reference/mcmc_combine.html
docs/reference/mcmc_thin.html
docs/reference/model.html
docs/reference/model_params.html
docs/reference/restart_params.html
docs/reference/run.html
docs/reference/run_grid.html
docs/reference/run_onevax_xvwr.html
docs/reference/run_onevax_xvwv.html
docs/reference/transform.html
docs/reference/transform_fixed.html
docs/reference/vax_params0.html
docs/reference/vax_params_xvwr.html
docs/reference/vax_params_xvwv.html
gonovax.Rproj
inst/extdata/README.md
inst/extdata/gono_params.csv
inst/extdata/gono_params_t.csv
inst/extdata/gono_params_trial.csv
inst/extdata/gono_params_updated.csv
inst/extdata/novax_baseline.rds
inst/extdata/novax_equilib.rds
inst/extdata/observed_data.csv
inst/odin/model.R
inst/odin/model.json
inst/odin/model_trial.R
inst/odin/model_trial.json
inst/odin/model_trial_stochastic.R
inst/odin/model_trial_stochastic.json
inst/odin/model_withPN.json
inst/odin/model_withoutPN.R
inst/odin/model_withoutPN.json
inst/odin/model_withouthistory.R
inst/odin/model_withouthistory.json
man/adjust_baseline.Rd
man/aggregate.Rd
man/compare.Rd
man/compare_baseline.Rd
man/compare_baseline_xpvwrh.Rd
man/compare_basic.Rd
man/create_diagnosis_waning_map.Rd
man/create_uptake_map.Rd
man/create_uptake_map_xpvwrh.Rd
man/create_uptake_map_xpvwrh_trackvt.Rd
man/create_uptake_map_xvw.Rd
man/create_uptake_map_xvwr.Rd
man/create_uptake_map_xvwv.Rd
man/create_vax_map.Rd
man/create_vax_map_branching.Rd
man/create_waning_map.Rd
man/create_waning_map_branching.Rd
man/create_waning_map_trial.Rd
man/dbetabinom.Rd
man/extract_flows.Rd
man/extract_flows_trial.Rd
man/extract_flows_xpvwrh.Rd
man/figures/vax_diagram.png
man/gen_erlang_labels.Rd
man/gen_erlang_labels_trackvt.Rd
man/gen_labels.Rd
man/gen_trial_labels.Rd
man/gono_params.Rd
man/gono_params_trial.Rd
man/gonovax_data.Rd
man/gonovax_year.Rd
man/gonovax_year_as_year.Rd
man/initial_params.Rd
man/initial_params_trial.Rd
man/initial_params_xpvwrh.Rd
man/initial_params_xpvwrh_trackvt.Rd
man/initial_params_xvw_trial.Rd
man/initial_params_xvwrh.Rd
man/mcmc.Rd
man/mcmc_combine.Rd
man/mcmc_thin.Rd
man/model.Rd
man/model_params.Rd
man/model_params_trial.Rd
man/model_params_xpvwrh.Rd
man/model_params_xpvwrh_trackvt.Rd
man/restart_hes.Rd
man/restart_params.Rd
man/run.Rd
man/run_grid.Rd
man/run_onevax_xpvwrh.Rd
man/run_onevax_xpvwrh_trackvt.Rd
man/run_onevax_xvw.Rd
man/run_onevax_xvw_trial.Rd
man/run_onevax_xvwr.Rd
man/run_onevax_xvwrh.Rd
man/run_onevax_xvwv.Rd
man/run_trial.Rd
man/run_xpvwrh.Rd
man/run_xpvwrh_trackvt.Rd
man/set_protection.Rd
man/set_protection_trackvt.Rd
man/set_strategy.Rd
man/stratum_index_xpvwrh.Rd
man/stratum_index_xpvwrh_trackvt.Rd
man/stratum_index_xvw.Rd
man/stratum_index_xvw_trial.Rd
man/stratum_index_xvwr.Rd
man/stratum_index_xvwrh.Rd
man/stratum_index_xvwv.Rd
man/transform.Rd
man/transform_fixed.Rd
man/vax_params0.Rd
man/vax_params_xpvwrh.Rd
man/vax_params_xpvwrh_trackvt.Rd
man/vax_params_xvw.Rd
man/vax_params_xvw_trial.Rd
man/vax_params_xvwr.Rd
man/vax_params_xvwrh.Rd
man/vax_params_xvwv.Rd
scripts/generate_novax_baseline.R
scripts/generate_novax_equilib.R
scripts/generate_odin
scripts/update_web.sh
src/odin.c
src/registration.c
tests/testthat.R
tests/testthat/helper-gonovax.R
tests/testthat/test-data.R
tests/testthat/test-mcmc-tools.R
tests/testthat/test-mcmc.R
tests/testthat/test-model.R
tests/testthat/test-model_trial.R
tests/testthat/test-model_trial_stochastic.R
tests/testthat/test-model_withdiagnosishistory.R
tests/testthat/test-onevax_xpvwrh.R
tests/testthat/test-onevax_xpvwrh_trackvt.R
tests/testthat/test-onevax_xpvwrh_withdiagnosishistory.R
tests/testthat/test-onevax_xpvwrh_withdiagnosishistory_trackvt.R
tests/testthat/test-onevax_xvw.R
tests/testthat/test-onevax_xvwr.R
tests/testthat/test-onevax_xvwrh.R
tests/testthat/test-onevax_xvwv.R
tests/testthat/test-parameters.R
tests/testthat/test-run_grid.R
tests/testthat/test-support.R
tests/testthat/test-utils-assert.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/getting_started.Rmd
