├── .gitignore ├── .projectile ├── README.md ├── a ├── estimate_hosp_capacity.do ├── impute_additional_fields.do └── predict_age_cfr.do ├── assets ├── covid_build_public.nomnoml ├── covid_build_public.svg ├── download_button.png ├── hospital-beds.html ├── hospital-beds.js ├── hospital-beds.png ├── market-volumes-livestock.html ├── market-volumes-livestock.js ├── market-volumes.html ├── market-volumes.js ├── mortality-pred.html ├── mortality-pred.js └── mortality-pred.png ├── b ├── agmark_scraper.py ├── clean_agmark.do ├── clean_ap_mort.do ├── clean_assam_mort.do ├── clean_bbmp_mort.do ├── clean_bihar_mort.do ├── clean_chennai_mort.do ├── clean_ghmc_mort.do ├── clean_haryana_mort.do ├── clean_hp_mort.do ├── clean_kmdc_mort.do ├── clean_mh_mort.do ├── clean_migration.do ├── clean_mp_mort.do ├── clean_odisha_mort.do ├── clean_rajasthan_mort.do ├── clean_state_mort.do ├── clean_up_mort.do ├── clean_wb_mort.do ├── copy_keys.do ├── create_dlhs4_pc11_district_key.do ├── create_google.do ├── ddl_nfhs_poll_hmis.do ├── gen_age_distribution.do ├── gen_lgd_pc11_demographics.do ├── gen_nss_district_key.do ├── gen_urbanization_subdist.do ├── get_case_data.do ├── get_vaccination_data.do ├── make_mortality.do ├── old │ ├── aggregate_case_data.do │ ├── gen_demographics.do │ ├── gen_pc11_states.do │ ├── get_case_data.do │ ├── get_lgd_keys.do │ ├── mse_simple.m │ └── predict_cts_uk_age_or_v2.m ├── pc11_lgd_metadata.csv ├── prep_bihar.do ├── prep_dlhs4_district.do ├── prep_ec_hosp.do ├── prep_ec_hosp_microdata.do ├── prep_hosp_pca_vd.do ├── prep_nss75.do ├── prep_pc_hosp.do ├── prep_secc.do ├── push_data.sh ├── retrieve_case_data.py ├── str │ ├── cov19india_district_fixes.txt │ ├── cov19india_vaccine_district_fixes.txt │ ├── covid_district_fixes.txt │ └── lgd_district_fixes.txt ├── update_case_cronjob.sh ├── update_case_vaccination_data.do └── vaccination_plot.py ├── como ├── a │ ├── analyze_mort_counts.do │ ├── app_age_hr_interpolation.do │ ├── app_joint_condition.do │ ├── app_table_age_bin_prev.do │ ├── app_table_nhs_vs_os.do │ ├── calc_hr_sensitivity.do │ ├── calc_prev_sensitivity.do │ ├── calc_prrs.do │ ├── covid_como_agerisks_tpl.tex │ ├── covid_como_oscompare_tpl.tex │ ├── covid_como_sumhr_tpl.tex │ ├── covid_como_sumstats_tpl.tex │ ├── examine_risk_factors_poverty.do │ ├── make_coef_plot.py │ ├── make_paper_figures.do │ ├── make_paper_tables.do │ ├── make_summary_tables.do │ ├── old │ │ └── analyze_age_mort_risk.do │ ├── prep_eng_india_prev_compare.do │ └── sumstats.do ├── b │ ├── clean_gbd_india.do │ ├── collapse_biomarkers_to_state.do │ ├── fit_cts_uk_age_hr.m │ ├── flatten_hr_data.py │ ├── old │ │ ├── prep_india_sim_prevalence.do │ │ ├── prep_populations.do │ │ ├── prep_uk_age_risks.do │ │ └── prep_uk_bmi.do │ ├── prep_age_level_data.do │ ├── prep_england_prevalence.do │ ├── prep_gbd.do │ ├── prep_health_data.do │ ├── prep_hrs.do │ ├── prep_india_comorbidities.do │ ├── prep_ny_mortality.do │ ├── prep_pop_sex.do │ └── prep_standard_errors.do ├── como_programs.do ├── csv │ ├── copd_mclean_rates.csv │ ├── england_gender_age.csv │ ├── india_condition_prevalence.csv │ ├── ny_cummings.csv │ ├── ny_hr.csv │ ├── nystate_age_comorbid_05082020.csv │ ├── nystate_or.csv │ ├── uk_condition_prevalence.csv │ ├── uk_condition_sd.csv │ ├── uk_demography.csv │ ├── uk_nhs_hazard_ratios.csv │ ├── uk_nhs_incidence.csv │ └── weighted_hrs.txt ├── e │ ├── examine_risk_factors.do │ ├── explore_gbd_vs_dlhs.do │ ├── hr_vs_or.do │ ├── summarize_india_conditions.do │ ├── test_cts_ors.do │ └── test_map.do ├── make_como.do ├── r │ └── covid_como_sumstats.csv └── tex │ ├── app_bootstrap.tex │ ├── appendix.tex │ ├── como_exhibits.tex │ ├── como_tables_figures.tex │ ├── covid-como.bib │ ├── front_matter_como.tex │ └── vancouver.bst ├── covid_progs.do ├── e ├── agmark_plot.ipynb ├── analyze_mortality.do ├── comoweb_plots.ipynb ├── compare_hosp_counts.do ├── covid_district_map.ipynb ├── create_agmark_plots.do ├── describe_migration.do ├── diff_dlsh4_doctor_definitions.do ├── dlhs.do ├── explore_agmark_by_state.do ├── explore_agmark_perishables.do ├── explore_ec_microdata.do ├── explore_idi_survey_r1.do ├── explore_idi_survey_r2.do ├── explore_migration.ipynb ├── explore_mortality.do ├── explore_pc_dlhs_doctors.do ├── explore_vacc_story.do ├── expolore_idi_survey_r2.do ├── figure_hmis.do ├── gen_map.py ├── gen_survey_map.py ├── get_vac_data.do ├── graphs_idi_r3.do ├── hmis_spatial_maps.py ├── idi_labor_ag.do ├── idi_r1_oped_graphs.do ├── idi_survey_r1_for_ppt.do ├── map_vacc_eligible.py ├── pop_estimates_21.csv ├── prep_ahs_data.do ├── prep_covid_dist_analysis.do ├── prep_dlhs_data.do ├── validate_table1.do └── validate_vacc_api.do ├── forecasting ├── README.md ├── Snakefile ├── b │ ├── create_vector_tileset.sh │ ├── data_to_geojson.py │ ├── merge_ddl_pred_data.do │ ├── old │ │ └── push_predicted_metadata.py │ ├── process_ddl_data.do │ ├── process_predicted_data.do │ ├── pull_predicted_data.sh │ ├── 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