Files in rplzzz/CovMitigation
COVID-19 infection model for Virginia
.Rbuildignore
.gitignore
.gitmodules
CovMitigation.Rproj
DESCRIPTION
NAMESPACE
R/CovMitigation.R
R/bayes-filter.R
R/census-model.R
R/data.R
R/diagplots.R
R/ensemble-eval.R
R/eval-model.R
R/filter-fit-locality.R
R/likelihood.R
R/llanalysis.R
R/obs.R
R/parms.R
R/policy.R
R/prior.R
R/refresh-ensemble.R
R/run-mc.R
R/scenarios.R
R/sim.R
R/util.R
R/vdh.R
analysis/.gitignore
analysis/bayesian-filter-tests/.gitignore
analysis/bayesian-filter-tests/bayesian-filter-testrun.R
analysis/bayesian-filter-tests/filter-fit-simdata.R
analysis/bayesian-filter-tests/simulated-obs.R
analysis/college-reopenings.Rmd
analysis/data-difference.Rmd
analysis/diagnostic-plots.Rmd
analysis/fraction-estimates.csv
analysis/gr-diagnostic.R
analysis/mcmc-analysis.Rmd
analysis/mcmc.R
analysis/model-results-report.Rmd
analysis/opt-parm.R
analysis/parameter-sensitivity.Rmd
analysis/parm-dist-mc.Rmd
analysis/parm-dist-mc.pdf
analysis/parm-dist-mc_files/figure-html/makeplots-1.png
analysis/parm-dist-mc_files/figure-html/makeplots-2.png
analysis/parm-dist-mc_files/figure-html/makeplots-3.png
analysis/parm-dist-mc_files/figure-html/makeplots2-1.png
analysis/parm-dist-mc_files/figure-html/makeplots2-2.png
analysis/parm-dist-mc_files/figure-html/makeplots2-3.png
analysis/parm-dist-mc_files/figure-latex/makeplots-1.pdf
analysis/parm-dist-mc_files/figure-latex/makeplots-2.pdf
analysis/parm-dist-mc_files/figure-latex/makeplots-3.pdf
analysis/parm-dist-mc_files/figure-latex/makeplots2-1.pdf
analysis/parm-dist-mc_files/figure-latex/makeplots2-2.pdf
analysis/parm-dist-mc_files/figure-latex/makeplots2-3.pdf
analysis/projection-scenarios.R
analysis/reopening.Rmd
analysis/run-scenarios.R
analysis/scenario-outputs/infect-scenario-MAP.csv
analysis/scenario-outputs/infect-scenarios.csv
analysis/test-targeting.Rmd
analysis/warmup-analysis.Rmd
data-raw/COVID_counts_uva.csv
data-raw/Census_2018_AgeSexEstimates_forVA_2019-08.csv
data-raw/DATASET.R
data-raw/VA_county_FIPScodes.csv
data-raw/VA_health_districts.csv
data-raw/county-growth-categories.R
data-raw/day-zero.R
data-raw/install-mobility-data.R
data-raw/marketShareAllDRG_UVA_VCU.csv
data-raw/marketShareRespDRG_UVA_VCU.csv
data-raw/testing-by-district.csv
data-raw/uva_covid_count.R
data-raw/uvahs-hospitalizations.R
data-raw/va-college-population.csv
data-raw/va-college-reopening.R
data-raw/va-college-reopening.csv
data-raw/va-health-districts.csv
data/.gitignore
data/hi_counties.rda
data/hospitalizations.rda
data/lo_counties.rda
data/marketFractionFinal.rda
data/sampleCounties.rda
data/uhi_counties.rda
data/ulo_counties.rda
data/uva_covid_count.rda
data/vaMyAgeBands.rda
data/va_college_reopening.rda
data/va_county_first_case.rda
data/vdh_covid19.rda
inst/scripts/filter-ensemble.zsh
inst/scripts/filter-fits.zsh
inst/scripts/gen-filter-ensemble.R
inst/scripts/mcmc-continue.zsh
inst/scripts/mcmc-init.R
inst/scripts/mcmc-init.zsh
inst/scripts/mcmc-main.zsh
inst/scripts/mcmc-warmup.zsh
inst/scripts/merge-ensembles.R
inst/scripts/run-bi-fcst.zsh
inst/scripts/run-cal-fcst.zsh
inst/scripts/run-filter-fit-loc.R
inst/scripts/run-mcmc.R
inst/scripts/update-filter-fits.zsh
man/CovMitigation.Rd
man/Scenario.Rd
man/bayesian_filter.Rd
man/calc_nhosp.Rd
man/census_model_output.Rd
man/coefs.Rd
man/complete_params.Rd
man/cutdate.Rd
man/ensemble_deviance.Rd
man/ensemble_eval.Rd
man/extend_filter_model.Rd
man/fetch_vdh_cov19.Rd
man/filter_fit_locality.Rd
man/filter_model_comparison_plot.Rd
man/filter_model_diagnositc_plots.Rd
man/filter_model_ensemble_plot.Rd
man/fit_filter.Rd
man/fsympto.Rd
man/gen_likelihood.Rd
man/gen_parm_vec.Rd
man/gen_post.Rd
man/gen_prior.Rd
man/gen_simobs_likelihood.Rd
man/gen_simobs_posterior.Rd
man/get_obsdata.Rd
man/getparam.Rd
man/growth_categories.Rd
man/hospitalizations.Rd
man/initialize_parmset.Rd
man/is.Scenario.Rd
man/llanalysis.Rd
man/local_mobility.Rd
man/localbeta.Rd
man/locality_startdate.Rd
man/localize_scenario.Rd
man/losig.Rd
man/marketFractionFinal.Rd
man/mask_indicator.Rd
man/mobility_adjust.Rd
man/namebackup.Rd
man/newsympto.Rd
man/nhosp_likelihood.Rd
man/padjust.Rd
man/parameters.Rd
man/pdist.Rd
man/plt_modobs.Rd
man/plt_projections.Rd
man/project_filter_model.Rd
man/qprior.Rd
man/refresh_ensemble.Rd
man/run_mc.Rd
man/run_parms.Rd
man/run_parmset.Rd
man/run_scenario.Rd
man/run_single_county.Rd
man/sampleCounties.Rd
man/scenario_change_times.Rd
man/scenario_parm_value.Rd
man/seir_equations.Rd
man/simobs.Rd
man/update_filter_models.Rd
man/uva_covid_count.Rd
man/vaMyAgeBands.Rd
man/va_county_first_case.Rd
man/validate_params.Rd
man/vintage_plot.Rd
man/wkagg.Rd
tests/testthat.R
tests/testthat/test-policy.R
tests/testthat/test-scenarios.R
tests/testthat/test-util.R
vignettes/.gitignore
vignettes/apr-growth-rates.Rmd
vignettes/obs-growth.Rmd
