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/demographic_data_intersect.csv
data/flight_data_intersect.csv
data/latitudes_intersect.csv
data/regions_clean.csv
data/risk_group_data.csv
inst/doc/usage.R inst/doc/usage.Rmd
inst/doc/usage.html
man/add.Rd man/calc_approx_final_size_distribution.Rd man/calc_country_attack.Rd man/calc_country_time_series.Rd man/calc_incidence_time_series.Rd man/calc_incidence_vaccinated_peak_times_attack_rates.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/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_incidence_vaccinated_peak_times_attack_rates.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/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
raw_data/JH_cleaning/CLEAN/adjuted_atrisk.csv
raw_data/JH_cleaning/CLEAN/latitudes_clean.csv
raw_data/JH_cleaning/CLEAN/regions_clean.csv
raw_data/JH_cleaning/Huang2013/AirportInfo.csv
raw_data/JH_cleaning/Huang2013/Huang_2013_PLoSONE.pdf
raw_data/JH_cleaning/Huang2013/airports_extended_huang2013.csv
raw_data/JH_cleaning/Huang2013/huang2013_extraction.R
raw_data/JH_cleaning/Huang2013/huang2013_heatmap.png
raw_data/JH_cleaning/Huang2013/huang2013_melted.csv
raw_data/JH_cleaning/Huang2013/huang2013_numbers
raw_data/JH_cleaning/Huang2013/huang2013_travel_mat.csv
raw_data/JH_cleaning/Huang2013/prediction_huang2013.csv
raw_data/JH_cleaning/LocationData/centroids.png
raw_data/JH_cleaning/LocationData/latitudes.csv
raw_data/JH_cleaning/LocationData/regions.csv
raw_data/JH_cleaning/LocationData/source.txt
raw_data/JH_cleaning/OAG/airline_extraction_oag.R
raw_data/JH_cleaning/OAG/countries.txt
raw_data/JH_cleaning/OAG/f2008_05.txt
raw_data/JH_cleaning/OAG/f2008_06.txt
raw_data/JH_cleaning/OAG/f2008_07.txt
raw_data/JH_cleaning/OAG/f2008_07_heatmap.png
raw_data/JH_cleaning/OAG/f2008_07_melted.csv
raw_data/JH_cleaning/OAG/f2008_07_numbers.png
raw_data/JH_cleaning/OAG/f2008_08.txt
raw_data/JH_cleaning/OAG/f2008_09.txt
raw_data/JH_cleaning/OAG/f2008_10.txt
raw_data/JH_cleaning/OAG/f2008_11.txt
raw_data/JH_cleaning/OAG/f2008_12.txt
raw_data/JH_cleaning/OAG/f2009_01.txt
raw_data/JH_cleaning/OAG/f2009_02.txt
raw_data/JH_cleaning/OAG/f2009_03.txt
raw_data/JH_cleaning/OAG/f2009_04.txt
raw_data/JH_cleaning/OAG_countries.csv
raw_data/JH_cleaning/WTO/flight_ids_WTO.csv
raw_data/JH_cleaning/WTO/no_arrivals_locations.csv
raw_data/JH_cleaning/WTO/nonresident_travel_extraction.R
raw_data/JH_cleaning/WTO/raw_flights_WTO.csv
raw_data/JH_cleaning/WTO/wto_heatmap.png
raw_data/JH_cleaning/WTO/wto_melted.csv
raw_data/JH_cleaning/WTO/wto_numbers.png
raw_data/JH_cleaning/WTO_countries.csv
raw_data/JH_cleaning/all_countries_FINAL.csv
raw_data/JH_cleaning/atRisk/Baguelin2013.PDF
raw_data/JH_cleaning/atRisk/adjuted_atrisk.csv
raw_data/JH_cleaning/atRisk/at_risk_propns_baguelin2013.csv
raw_data/JH_cleaning/at_risk_propns_baguelin2013.csv
raw_data/JH_cleaning/combine_all_countries.R
raw_data/JH_cleaning/combined_countries.csv
raw_data/JH_cleaning/contact_countries.csv
raw_data/JH_cleaning/contact_data_clean.csv
raw_data/JH_cleaning/correct_countries.csv
raw_data/JH_cleaning/coverage_countries.csv
raw_data/JH_cleaning/demography_countries.csv
raw_data/JH_cleaning/demography_data_clean.csv
raw_data/JH_cleaning/extract_countries_other.R raw_data/JH_cleaning/generate_correct_country_list.R
raw_data/JH_cleaning/huang2013_countries.csv
raw_data/JH_cleaning/original_ids.csv
raw_data/JH_cleaning/test_add.csv
raw_data/JH_cleaning/travel_plotting_funcs.R
raw_data/MUestimates_all_locations_1.xlsx
raw_data/MUestimates_all_locations_2.xlsx
raw_data/age_structured_contacts.csv
raw_data/airline_extraction_oag.R
raw_data/at_risk_propns_baguelin2013.ods
raw_data/contact_data_clean.csv
raw_data/demographic_data_clean.csv
raw_data/demography_data_processing.R
raw_data/demography_data_world_population_prospects.csv
raw_data/example_args_list.rds
raw_data/example_travel.png
raw_data/flight_ids.csv
raw_data/locations.xlsx
raw_data/population_risk_groups.csv
raw_data/population_stats.csv
raw_data/raw_flights.csv
raw_data/seasonal_coverage/Palache2015.pdf raw_data/seasonal_coverage/extract_seasonal_coverage.R
raw_data/seasonal_coverage/high_coverage.xlsx
raw_data/seasonal_coverage/low_coverage.xlsx
raw_data/seasonal_coverage/seasonal_coverage_clean.csv
raw_data/travel_data.csv
raw_data/two_countries/contact_data.csv
raw_data/two_countries/demographic_data.csv
scripts/example.R scripts/example_load_params.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 July 29, 2018, 12:43 p.m.