Files in mrc-ide/squire
SEIR transmission model of COVID-19
.Rbuildignore
.covrignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/make-release.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/align.R
R/assertions.R
R/beta.R
R/calibration.R
R/check.R
R/contact_matrices.R
R/data.R
R/drjacoby_utils.R
R/estimation.R
R/format_output.R
R/models.R
R/object.R
R/odin.R
R/parameters.R
R/particle.R
R/pmcmc.R
R/pmcmc_object.R
R/pmcmc_utils.R
R/population.R
R/projections.R
R/run.R
R/triggering.R
R/util.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data-raw/Hospital_Bed_Capacity_Predictions.Rds
data-raw/Income_Strata_Predicted_Hospital_and_ICU_Beds.Rds
data-raw/WPP_demog_matrix.csv
data-raw/contact_matrices.rds
data-raw/hospital_bed_capacity.csv
data-raw/prepare_raw_data.R
data/contact_matrices.rda
data/country_specific_healthcare_capacity.rda
data/elderly_pop.rda
data/income_group.rda
data/income_strata_healthcare_capacity.rda
data/population.rda
images/Explicit_Healthcare_Mechanical_Ventilation_Decision_Tree.JPG
images/Explicit_Healthcare_Model_Structure.JPG
images/Explicit_Healthcare_Oxygen_Decision_Tree.JPG
inst/extdata/example.csv
inst/extdata/example_DZA.csv
inst/extdata/example_DZA_intervention.csv
inst/extdata/example_GIN.csv
inst/extdata/example_guinea.csv
inst/extdata/example_intervention.csv
inst/odin/.gitignore
inst/odin/SEIR.json
inst/odin/explicit_SEIR.R
inst/odin/explicit_SEIR.json
inst/odin/explicit_SEIR_deterministic.R
inst/odin/explicit_SEIR_deterministic.json
inst/odin/less_basic_model_for_js.R
inst/odin/less_basic_model_for_js.json
inst/odin/simple_SEIR.R
inst/odin/simple_SEIR.json
inst/other/det_basic_SEIR.R
inst/other/run_det_basic_SEIR.R
inst/other/test_out
inst/other/test_out.zip
man/adjusted_eigen.Rd
man/align.Rd
man/beta_est.Rd
man/beta_est_explicit.Rd
man/beta_est_simple.Rd
man/calibrate.Rd
man/check_squire.Rd
man/check_time_change.Rd
man/compare_output.Rd
man/conduct_replicate.Rd
man/contact_matrices.Rd
man/country_specific_healthcare_capacity.Rd
man/create_master_chain.Rd
man/default_durations.Rd
man/default_probs.Rd
man/deterministic_model.Rd
man/div_pop.Rd
man/drjacoby_mcmc.Rd
man/elderly_pop.Rd
man/explicit_model.Rd
man/extract_ICU_occ.Rd
man/extract_deaths.Rd
man/extract_hospital_occ.Rd
man/extract_infection_incidence.Rd
man/figures/README-base plot-1.png
man/figures/README-calibration-1.png
man/figures/README-cases over time-1.png
man/figures/README-change healthcare capacity-1.png
man/figures/README-deaths over time-1.png
man/figures/README-healthcare forecast over time-1.png
man/figures/README-healthcare over time-1.png
man/figures/README-orderly style-1.png
man/figures/README-particle fit ints-1.png
man/figures/README-particle fit no ints-1.png
man/figures/README-particle gin alt proj-1.png
man/figures/README-particle gin alt-1.png
man/figures/README-particle gin forecast-1.png
man/figures/README-particle gin plots-1.png
man/figures/README-plot gcu-1.png
man/figures/README-plot particle deaths-1.png
man/figures/README-pressure-1.png
man/figures/README-projection plotting absolute-1.png
man/figures/README-projection plotting-1.png
man/figures/README-projection relative beds-1.png
man/figures/README-set R0 decrease-1.png
man/figures/README-set contact matrix decrease and relax-1.png
man/figures/README-set contact matrix decrease-1.png
man/figures/README-set params-1.png
man/figures/README-show grid fits probs-1.png
man/figures/README-show grid fits-1.png
man/figures/README-subset variables plot-1.png
man/figures/README-subset variables plot2-1.png
man/figures/README-total deaths projection-1.png
man/figures/README-untransformed-1.png
man/format_deterministic_output.Rd
man/format_output.Rd
man/format_output_simple_model.Rd
man/get_elderly_population.Rd
man/get_healthcare_capacity.Rd
man/get_lmic_countries.Rd
man/get_mixing_matrix.Rd
man/get_population.Rd
man/income_group.Rd
man/income_strata_healthcare_capacity.Rd
man/init_check.Rd
man/init_check_explicit.Rd
man/intervention_dates_for_odin.Rd
man/jc_prop_update.Rd
man/matrix_check.Rd
man/matrix_set.Rd
man/parameters_explicit_SEEIR.Rd
man/parameters_simple_SEEIR.Rd
man/parse_country_severity.Rd
man/particle_filter.Rd
man/particle_filter_data.Rd
man/plot.squire_scan.Rd
man/plot.squire_simulation.Rd
man/pmcmc.Rd
man/population.Rd
man/pos_num.Rd
man/print.squire_simulation.Rd
man/process_contact_matrix.Rd
man/process_contact_matrix_scaled_age.Rd
man/projection_plotting.Rd
man/projections.Rd
man/run_deterministic_SEIR_model.Rd
man/run_deterministic_comparison.Rd
man/run_explicit_SEEIR_model.Rd
man/run_particle_filter.Rd
man/run_simple_SEEIR_model.Rd
man/sample_3d_grid_scan.Rd
man/sample_drjacoby.Rd
man/sample_grid_scan.Rd
man/sample_pmcmc.Rd
man/scan_R0_date.Rd
man/scan_R0_date_Meff.Rd
man/simple_model.Rd
man/summary.squire_simulation.Rd
man/trigger_projections.Rd
squire.Rproj
src/odin.c
src/registration.c
tests/testthat.R
tests/testthat/test-align.R
tests/testthat/test-assertions.R
tests/testthat/test-beta.R
tests/testthat/test-calibration.R
tests/testthat/test-checks.R
tests/testthat/test-data.R
tests/testthat/test-drjacoby.R
tests/testthat/test-estimation.R
tests/testthat/test-js.R
tests/testthat/test-matrix.R
tests/testthat/test-object.R
tests/testthat/test-output.R
tests/testthat/test-particle.R
tests/testthat/test-pmcmc.R
tests/testthat/test-population.R
tests/testthat/test-projections.R
tests/testthat/test-run.R
tests/testthat/test-triggers.R
tests/testthat/test-util.R
tests/testthat/test-waning.R
vignettes/.gitignore
vignettes/parameters.Rmd
