Files in mrc-ide/squire.page
Functions used in global-lmic-reports-orderly and other repos

.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/booster_model.R R/booster_model_minimal.R R/data.R R/iso3cs.R R/long_covid.R R/nimue_utils.R R/odin.R R/oop_conv.R R/pipe.R R/plotting.R R/pmcmc_excess.R R/pmcmc_likelihood.R R/pmcmc_likelihood_excess.R R/pmcmc_likelihood_excess_vaccine.R R/pmcmc_likelihood_lmic.R R/pmcmc_likelihood_lmic_booster.R R/pmcmc_lmic_drjacoby.R R/projections.R R/projections_estimate_scenarios.R R/projections_extend_inputs.R R/r.R R/rt_optimise.R R/rt_optimise_internal.R R/rt_optimise_processing.R R/simulate.R R/simulate_load.R R/squire.page-package.R README.Rmd README.md
data/afg_fit.rda
data/bhu_fit.rda
inst/misc/fit_ve_curve.r inst/odin/nimue_booster.R
inst/odin/nimue_booster.json
inst/odin/nimue_booster_diff.R
inst/odin/nimue_booster_diff.json
inst/odin/nimue_booster_minimal.R
inst/odin/nimue_booster_minimal.json
inst/odin/nimue_booster_minimal_diff.R
inst/odin/nimue_booster_minimal_diff.json
inst/r_gen/create_difference_model.R man/afg_fit.Rd man/ar_plot.Rd man/beta_est.booster_min_model.Rd man/beta_est.booster_model.Rd man/beta_est.default.Rd man/bhu_fit.Rd man/block_interpolate.Rd man/calc_loglikelihood_booster.Rd man/calc_loglikelihood_variant.Rd man/cdp_plot.Rd man/compare_adjustment_plot.Rd man/country_immunity_plot.Rd man/dp_plot.Rd man/excess_log_likelihood.Rd man/excess_log_likelihood_vaccine.Rd man/extend_vaccine_inputs.Rd man/generate_draws.Rd man/generate_draws.default.Rd man/generate_draws.rt_optimised.Rd man/generate_parameters.Rd man/get_Rt.Rd man/get_WHO_region.Rd man/get_covax_iso3c.Rd man/get_data.excess_nimue_simulation.Rd man/get_data.nimue_simulation.Rd man/get_data.rt_optimised.Rd man/get_data_end_date.excess_nimue_simulation.Rd man/get_data_end_date.nimue_simulation.Rd man/get_data_end_date.rt_optimised.Rd man/get_data_end_date_inner.excess_nimue_simulation.Rd man/get_data_end_date_inner.nimue_simulation.Rd man/get_data_end_date_inner.rt_optimised.Rd man/get_data_start_date.excess_nimue_simulation.Rd man/get_data_start_date.nimue_simulation.Rd man/get_data_start_date.rt_optimised.Rd man/get_dates.excess_nimue_simulation.Rd man/get_dates.nimue_simulation.Rd man/get_dates.rt_optimised.Rd man/get_dates_greater.excess_nimue_simulation.Rd man/get_dates_greater.nimue_simulation.Rd man/get_dates_greater.rt_optimised.Rd man/get_future_Rt.Rd man/get_gavi_iso3c.Rd man/get_global_fund_iso3c.Rd man/get_immunity_ratios.Rd man/get_immunity_ratios.default.Rd man/get_immunity_ratios.rt_optimised.Rd man/get_income_group.Rd man/get_parameters.default.Rd man/get_parameters.rt_optimised.Rd man/loadCounterfactualData.Rd man/nimue_booster_min_model.Rd man/nimue_booster_model.Rd man/nimue_format.Rd man/pipe.Rd man/plot.excess_nimue_simulation.Rd man/plot.rt_optimised.Rd man/plot.rt_optimised_trimmed.Rd man/pmcmc_drjacoby.Rd man/pmcmc_excess.Rd man/projections.Rd man/rt_optimise.Rd man/rt_plot_immunity.Rd man/run_booster.Rd man/sero_plot.Rd man/setup_parameters.booster_min_model.Rd man/setup_parameters.default.Rd man/setup_parameters.nimue_model.Rd man/squire.page-package.Rd man/trim_rt_optimise.Rd man/update_Rt.Rd
squire.page.Rproj
src/odin.c
src/odin.o
src/registration.c
src/registration.o
src/squire.page.so
tests/testthat.R tests/testthat/test-booster_model.R tests/testthat/test-get_fits.R tests/testthat/test-iso3cs.R tests/testthat/test-nimue_format.R tests/testthat/test-particle_fit.R
vignettes/.gitignore
vignettes/GBR.Rds
vignettes/Nimue_Booster_Diagram.png
vignettes/booster_pathway.Rmd vignettes/difference_model.Rmd vignettes/fitted_value_plot.pdf
vignettes/fitted_value_plot.png
vignettes/rt_optimise.Rmd
vignettes/rt_optimise_example_annotated.png
mrc-ide/squire.page documentation built on May 27, 2023, 11:20 a.m.