Files in jameshay218/vaxedemic
Optimal allocation of vaccination during a pandemic

.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/analyses.R R/calc_summaries_funcs.R R/cluster_tools.R
R/data_management.R
R/funcs_for_tests.R R/helpers.R R/plots.R R/postprocessing_funcs.R R/run_funcs.R R/setup.R R/simulation.R
R/simulation.R~
R/tmpFuncs.R
R/tmpFuncs.R~
R/vax_alloc_funcs.R R/vax_production_funcs.R
R/zzz.R~
README.md VaxademicSCM.R
data/contact_data_intersect.csv
data/countries_intersect.csv
data/coverage_data_intersect.csv
data/coverage_tables_by_popn/coverage_data_1.csv
data/coverage_tables_by_popn/coverage_data_10.csv
data/coverage_tables_by_popn/coverage_data_100.csv
data/coverage_tables_by_popn/coverage_data_110.csv
data/coverage_tables_by_popn/coverage_data_120.csv
data/coverage_tables_by_popn/coverage_data_127.csv
data/coverage_tables_by_popn/coverage_data_2.csv
data/coverage_tables_by_popn/coverage_data_20.csv
data/coverage_tables_by_popn/coverage_data_3.csv
data/coverage_tables_by_popn/coverage_data_30.csv
data/coverage_tables_by_popn/coverage_data_4.csv
data/coverage_tables_by_popn/coverage_data_40.csv
data/coverage_tables_by_popn/coverage_data_5.csv
data/coverage_tables_by_popn/coverage_data_50.csv
data/coverage_tables_by_popn/coverage_data_60.csv
data/coverage_tables_by_popn/coverage_data_70.csv
data/coverage_tables_by_popn/coverage_data_80.csv
data/coverage_tables_by_popn/coverage_data_90.csv
data/coverage_tables_fn_pop_size/coverage_data_0.csv
data/coverage_tables_fn_pop_size/coverage_data_0point1.csv
data/coverage_tables_fn_pop_size/coverage_data_0point2.csv
data/coverage_tables_fn_pop_size/coverage_data_0point3.csv
data/coverage_tables_fn_pop_size/coverage_data_0point4.csv
data/coverage_tables_fn_pop_size/coverage_data_0point5.csv
data/coverage_tables_fn_pop_size/coverage_data_0point6.csv
data/coverage_tables_fn_pop_size/coverage_data_0point7.csv
data/coverage_tables_fn_pop_size/coverage_data_0point8.csv
data/coverage_tables_fn_pop_size/coverage_data_0point9.csv
data/coverage_tables_fn_pop_size/coverage_data_1.csv
data/coverage_tables_fn_pop_size/coverage_data_1point5.csv
data/coverage_tables_fn_pop_size/coverage_data_2.csv
data/coverage_tables_fn_pop_size/coverage_data_2point5.csv
data/coverage_tables_fn_pop_size/coverage_data_3.csv
data/coverage_tables_fn_pop_size/coverage_data_3point5.csv
data/coverage_tables_fn_pop_size/coverage_data_4.csv
data/coverage_tables_fn_pop_size/coverage_data_4point5.csv
data/coverage_tables_fn_pop_size/coverage_data_5.csv
data/demographic_data_intersect.csv
data/flight_data_intersect.csv
data/latitudes_intersect.csv
data/random_coverage_tables/random_coverage_data_1.csv
data/random_coverage_tables/random_coverage_data_10.csv
data/random_coverage_tables/random_coverage_data_100.csv
data/random_coverage_tables/random_coverage_data_11.csv
data/random_coverage_tables/random_coverage_data_12.csv
data/random_coverage_tables/random_coverage_data_13.csv
data/random_coverage_tables/random_coverage_data_14.csv
data/random_coverage_tables/random_coverage_data_15.csv
data/random_coverage_tables/random_coverage_data_16.csv
data/random_coverage_tables/random_coverage_data_17.csv
data/random_coverage_tables/random_coverage_data_18.csv
data/random_coverage_tables/random_coverage_data_19.csv
data/random_coverage_tables/random_coverage_data_2.csv
data/random_coverage_tables/random_coverage_data_20.csv
data/random_coverage_tables/random_coverage_data_21.csv
data/random_coverage_tables/random_coverage_data_22.csv
data/random_coverage_tables/random_coverage_data_23.csv
data/random_coverage_tables/random_coverage_data_24.csv
data/random_coverage_tables/random_coverage_data_25.csv
data/random_coverage_tables/random_coverage_data_26.csv
data/random_coverage_tables/random_coverage_data_27.csv
data/random_coverage_tables/random_coverage_data_28.csv
data/random_coverage_tables/random_coverage_data_29.csv
data/random_coverage_tables/random_coverage_data_3.csv
data/random_coverage_tables/random_coverage_data_30.csv
data/random_coverage_tables/random_coverage_data_31.csv
data/random_coverage_tables/random_coverage_data_32.csv
data/random_coverage_tables/random_coverage_data_33.csv
data/random_coverage_tables/random_coverage_data_34.csv
data/random_coverage_tables/random_coverage_data_35.csv
data/random_coverage_tables/random_coverage_data_36.csv
data/random_coverage_tables/random_coverage_data_37.csv
data/random_coverage_tables/random_coverage_data_38.csv
data/random_coverage_tables/random_coverage_data_39.csv
data/random_coverage_tables/random_coverage_data_4.csv
data/random_coverage_tables/random_coverage_data_40.csv
data/random_coverage_tables/random_coverage_data_41.csv
data/random_coverage_tables/random_coverage_data_42.csv
data/random_coverage_tables/random_coverage_data_43.csv
data/random_coverage_tables/random_coverage_data_44.csv
data/random_coverage_tables/random_coverage_data_45.csv
data/random_coverage_tables/random_coverage_data_46.csv
data/random_coverage_tables/random_coverage_data_47.csv
data/random_coverage_tables/random_coverage_data_48.csv
data/random_coverage_tables/random_coverage_data_49.csv
data/random_coverage_tables/random_coverage_data_5.csv
data/random_coverage_tables/random_coverage_data_50.csv
data/random_coverage_tables/random_coverage_data_51.csv
data/random_coverage_tables/random_coverage_data_52.csv
data/random_coverage_tables/random_coverage_data_53.csv
data/random_coverage_tables/random_coverage_data_54.csv
data/random_coverage_tables/random_coverage_data_55.csv
data/random_coverage_tables/random_coverage_data_56.csv
data/random_coverage_tables/random_coverage_data_57.csv
data/random_coverage_tables/random_coverage_data_58.csv
data/random_coverage_tables/random_coverage_data_59.csv
data/random_coverage_tables/random_coverage_data_6.csv
data/random_coverage_tables/random_coverage_data_60.csv
data/random_coverage_tables/random_coverage_data_61.csv
data/random_coverage_tables/random_coverage_data_62.csv
data/random_coverage_tables/random_coverage_data_63.csv
data/random_coverage_tables/random_coverage_data_64.csv
data/random_coverage_tables/random_coverage_data_65.csv
data/random_coverage_tables/random_coverage_data_66.csv
data/random_coverage_tables/random_coverage_data_67.csv
data/random_coverage_tables/random_coverage_data_68.csv
data/random_coverage_tables/random_coverage_data_69.csv
data/random_coverage_tables/random_coverage_data_7.csv
data/random_coverage_tables/random_coverage_data_70.csv
data/random_coverage_tables/random_coverage_data_71.csv
data/random_coverage_tables/random_coverage_data_72.csv
data/random_coverage_tables/random_coverage_data_73.csv
data/random_coverage_tables/random_coverage_data_74.csv
data/random_coverage_tables/random_coverage_data_75.csv
data/random_coverage_tables/random_coverage_data_76.csv
data/random_coverage_tables/random_coverage_data_77.csv
data/random_coverage_tables/random_coverage_data_78.csv
data/random_coverage_tables/random_coverage_data_79.csv
data/random_coverage_tables/random_coverage_data_8.csv
data/random_coverage_tables/random_coverage_data_80.csv
data/random_coverage_tables/random_coverage_data_81.csv
data/random_coverage_tables/random_coverage_data_82.csv
data/random_coverage_tables/random_coverage_data_83.csv
data/random_coverage_tables/random_coverage_data_84.csv
data/random_coverage_tables/random_coverage_data_85.csv
data/random_coverage_tables/random_coverage_data_86.csv
data/random_coverage_tables/random_coverage_data_87.csv
data/random_coverage_tables/random_coverage_data_88.csv
data/random_coverage_tables/random_coverage_data_89.csv
data/random_coverage_tables/random_coverage_data_9.csv
data/random_coverage_tables/random_coverage_data_90.csv
data/random_coverage_tables/random_coverage_data_91.csv
data/random_coverage_tables/random_coverage_data_92.csv
data/random_coverage_tables/random_coverage_data_93.csv
data/random_coverage_tables/random_coverage_data_94.csv
data/random_coverage_tables/random_coverage_data_95.csv
data/random_coverage_tables/random_coverage_data_96.csv
data/random_coverage_tables/random_coverage_data_97.csv
data/random_coverage_tables/random_coverage_data_98.csv
data/random_coverage_tables/random_coverage_data_99.csv
data/regions_clean.csv
data/risk_group_data.csv
inst/doc/usage.R inst/doc/usage.Rmd
inst/doc/usage.html
man/Map_vapply.Rd man/add.Rd man/apply_named_args.Rd man/calc_approx_final_size_distribution.Rd man/calc_country_attack.Rd man/calc_country_time_series.Rd man/calc_cumulative_deaths_time_series.Rd man/calc_incidence_peak_times_attack_rates_deaths.Rd man/calc_incidence_time_series.Rd man/calc_incidence_vaccinated_peak_times_attack_rates.Rd man/calc_incidence_vaccinated_peak_times_attack_rates_deaths.Rd man/calc_median_ci_by_country.Rd man/calc_peak_times.Rd man/calc_peak_times_and_attack_rates.Rd man/calc_vaccinated_time_series.Rd man/calibrating_amp_and_travel.Rd man/cum_vax_pool_func_closure.Rd man/density_country_attack_rates.Rd man/density_country_peak_times.Rd man/distribute_vax_among_age_risk_closure.Rd man/gen_int_sum_int.Rd man/generate_age_matrix.Rd man/generate_age_matrix_uniform.Rd man/generate_age_mixing.Rd man/generate_contact_matrix.Rd man/get_final_sizes_with_R_eff.Rd man/get_func_names.Rd man/get_user_options.Rd man/get_vars_from_list_with_check.Rd man/get_vaxedemic_func_options.Rd man/initial_test.Rd man/is_integer_like.Rd man/list2here.Rd man/list_vars_from_environment.Rd man/main_simulation.Rd man/make_arg_list.Rd man/make_y_label.Rd man/model_plot_simple.Rd man/model_plots.Rd man/neaten_raw_output_by_country.Rd man/normalise.Rd man/num2str.Rd man/plot_country_attack_rates.Rd man/plot_country_incidence.Rd man/plot_country_time_series.Rd man/plot_country_vaccinated.Rd man/plot_peak_times.Rd man/postprocessing_country_attack.Rd man/postprocessing_deaths.Rd man/postprocessing_incidence_peak_times_attack_rates_deaths.Rd man/postprocessing_incidence_vaccinated_peak_times_attack_rates.Rd man/postprocessing_incidence_vaccinated_peak_times_attack_rates_deaths.Rd man/postprocessing_peak_times.Rd man/postprocessing_peak_times_and_attack_rates.Rd man/postprocessing_save_country_incidence.Rd man/postprocessing_save_country_vaccinated.Rd man/postprocessing_simple_save.Rd man/produce_vax_linear_with_delay.Rd man/read_contact_data.Rd man/read_coverage_data.Rd man/read_latitude_data.Rd man/return_all_res.Rd man/round_preserve_sum.Rd man/run_and_get_deaths_recovered.Rd man/run_fixed_params.Rd man/run_fixed_params_and_postprocess.Rd man/run_simulation.Rd man/scientific_10x.Rd man/setup_cluster.Rd man/setup_inputs.Rd man/setup_populations.Rd man/setup_populations_real_data.Rd man/setup_travel_real_data.Rd man/shorten_runs.Rd man/sum_age_risk_closure.Rd man/sum_list.Rd man/thin_time_series.Rd man/vaccinate_by_current_seasonal_alloc.Rd man/vaccinate_by_incidence.Rd man/vaccine_allocation_closure.Rd man/vcapply.Rd man/viapply.Rd man/vlapply.Rd man/vnapply.Rd scripts/allocate_by_pop_size_ada.R scripts/ar_cor_plots.R scripts/batch_random_allocations.R scripts/compare_alloc_runs.R scripts/compare_global_attack_rate_all_ada.R scripts/example.R scripts/example_load_params.R scripts/global_attack_rate_plot.R scripts/make_world_map.R scripts/manuscript_figures.R scripts/plot_attack_rate_by_continent.R scripts/run_no_vax_no_seasonality_ada.R scripts/run_no_vax_seed_ada.R scripts/run_strategy_ada.R scripts/run_strategy_no_seasonality_ada.R scripts/summary_plots_allocate_by_pop_size_ada.R scripts/summary_plots_sim1000.R tests/testthat.R
tests/testthat.R~
tests/testthat/test.R
tests/testthat/test.R~
tests/testthat/test_deaths.R tests/testthat/test_helpers.R vignettes/usage.Rmd
jameshay218/vaxedemic documentation built on Jan. 30, 2020, 2:58 a.m.