Files in mrc-ide/reestimate_covidIFR_analysis
Reestimation of IFRs using Serology Data
.Rprofile
.gitignore
DESCRIPTION
R/assertions_v5.R
R/covidcurve_helper_functions.R
R/crude_plot_summ.R
R/extra_plotting_functions.R
R/monte_carlo_cis.R
R/my_themes.R
R/process_data4.R
R/regional_time_series.R
R/remove_carehome_deaths.R
README.md
analyses/00-convalescent_seroAbs_v2.R
analyses/01-run_process_country_data_v2.R
analyses/02-descriptive_data_plots_v3.R
analyses/03-plot_methods_conceptual.R
analyses/04-analyze_overall_IFRs.R
analyses/05-analyze_age_IFRs_v2.R
analyses/06-analyze_carehome_IFRs.R
analyses/07-mod_posteriors.R
analyses/08-model_ppcs.R
analyses/09-collate_sims.R
analyses/10-plot_delay_concept.R
analyses/11-plot_seroday_concept.R
analyses/ModFits/CareHomes_drakeworker.R
analyses/ModFits/ModFits_drakeworker_v2.R
analyses/ModFits/seroRev_ModFits_drakeworker_v2.R
analyses/Rgn_Mod_Stan/README.md
analyses/Rgn_Mod_Stan/input_data/BRA1input_dat.RDS
analyses/Rgn_Mod_Stan/input_data/DNK1input_dat.RDS
analyses/Rgn_Mod_Stan/input_data/ESP1-2input_dat.RDS
analyses/Rgn_Mod_Stan/input_data/GBR3input_dat.RDS
analyses/Rgn_Mod_Stan/input_data/ITA1input_dat.RDS
analyses/Rgn_Mod_Stan/input_data/NYS1input_dat.RDS
analyses/Rgn_Mod_Stan/plot_model_fits.R
analyses/Rgn_Mod_Stan/regional_sim.R
analyses/Rgn_Mod_Stan/results/BRA1_regional_fit.jpg
analyses/Rgn_Mod_Stan/results/BRA1_sens_reg_age.csv
analyses/Rgn_Mod_Stan/results/BRA1_spec_reg_age.csv
analyses/Rgn_Mod_Stan/results/DNK1_regional_fit.jpg
analyses/Rgn_Mod_Stan/results/DNK1_sens_reg_age.csv
analyses/Rgn_Mod_Stan/results/DNK1_spec_reg_age.csv
analyses/Rgn_Mod_Stan/results/ESP1-2_regional_fit.jpg
analyses/Rgn_Mod_Stan/results/ESP1-2_regional_fit.tiff
analyses/Rgn_Mod_Stan/results/ESP1-2_sens_reg_age.csv
analyses/Rgn_Mod_Stan/results/ESP1-2_spec_reg_age.csv
analyses/Rgn_Mod_Stan/results/GBR3_regional_fit.jpg
analyses/Rgn_Mod_Stan/results/GBR3_sens_reg_age.csv
analyses/Rgn_Mod_Stan/results/GBR3_spec_reg_age.csv
analyses/Rgn_Mod_Stan/results/ITA1_regional_fit.jpg
analyses/Rgn_Mod_Stan/results/ITA1_sens_reg_age.csv
analyses/Rgn_Mod_Stan/results/ITA1_spec_reg_age.csv
analyses/Rgn_Mod_Stan/results/NYS1_regional_fit.jpg
analyses/Rgn_Mod_Stan/results/NYS1_sens_reg_age.csv
analyses/Rgn_Mod_Stan/results/NYS1_spec_reg_age.csv
analyses/Rgn_Mod_Stan/results/regional_schematic.jpg
analyses/Rgn_Mod_Stan/run_regional_model.R
analyses/Rgn_Mod_Stan/s_IFR_estimate_region_age_full_CC5.stan
analyses/Rgn_Mod_Stan/s_IFR_estimate_region_age_full_no_age_seroCC5.stan
analyses/Rgn_Mod_Stan/s_IFR_estimate_region_age_full_sep_seroCC5.stan
analyses/Rgn_Mod_Stan/s_IFR_estimate_region_onlyCC5.stan
analyses/SimWork/SeroRev_SimCurves_drakeworker_v2.R
analyses/SimWork/SimCurves_drakeworker_v2.R
analyses/SimWork/fit_conceptual_figure_delayeffects.R
analyses/SimWork/fit_seroday_concept.R
data/derived/BRA1/BRA1_agebands.RDS
data/derived/BRA1/BRA1_city.csv
data/derived/BRA1/BRA1_regions.RDS
data/derived/CHE1/CHE1_agebands.RDS
data/derived/CHE2/CHE2_agebands.RDS
data/derived/DNK1/DNK1_agebands.RDS
data/derived/DNK1/DNK1_agebands_age_sero.dat.RDS
data/derived/DNK1/DNK1_regions.RDS
data/derived/ESP1-2/ESP1-2_agebands.RDS
data/derived/ESP1-2/ESP1-2_regions.RDS
data/derived/GBR3/GBR3_agebands.RDS
data/derived/GBR3/GBR3_regions.RDS
data/derived/ITA1/ITA1_agebands.RDS
data/derived/ITA1/ITA1_regions.RDS
data/derived/KEN1/KEN1_agebands.RDS
data/derived/LUX1/LUX1_agebands.RDS
data/derived/NLD1/NLD1_agebands.RDS
data/derived/SWE1/SWE1_agebands.RDS
data/derived/USA/LA_CA1_agebands.RDS
data/derived/USA/NYC1_agebands.RDS
data/derived/USA/NYS1_agebands.RDS
data/derived/USA/NYS1_regions.RDS
data/derived/age_summ_IFR.csv
data/derived/carehomes/CHE1_agebands_noCH.RDS
data/derived/carehomes/CHE2_agebands_noCH.RDS
data/derived/carehomes/DNK1_agebands_noCH.RDS
data/derived/carehomes/ESP1-2_agebands_noCH.RDS
data/derived/carehomes/GBR3_agebands_noCH.RDS
data/derived/carehomes/NYS1_agebands_noCH.RDS
data/derived/carehomes/SWE1_agebands_noCH.RDS
data/derived/derived_data_map.xlsx
data/derived/region_summ_IFR.csv
data/plot_aesthetics/color_studyid_map.csv
data/plot_aesthetics/study_id_order.csv
data/raw/2020-10-12_Brazil_state_age_sex_deaths.rds
data/raw/Brazil_2020_Population_Data.csv
data/raw/DNK1_age.csv
data/raw/DNK_timeseries.csv
data/raw/ESP_timeseries.csv
data/raw/ITA_timeseries.csv
data/raw/NLD_timeseries.csv
data/raw/SWE_timeseries.csv
data/raw/USA_County_Demographic_Data.csv
data/raw/bra1_city_deaths.csv
data/raw/bra1_city_pops.csv
data/raw/bra1_city_sero.csv
data/raw/care_home_deaths.csv
data/raw/cumulative_deaths.tsv
data/raw/deaths_time_series_subnat.tsv
data/raw/depreciated/BRA_state_region_key.csv
data/raw/depreciated/Brazil_seroprevalence_first_survey.csv
data/raw/depreciated/CHE1_seroprev_agg.csv
data/raw/depreciated/JHU_time_series_covid19_deaths_US_july72020.csv
data/raw/depreciated/RGN_Agg_Brazil_seroprevalence_first_survey.csv
data/raw/depreciated/SEROCoV-POP_AggData.csv
data/raw/depreciated/UK_ONS_2016_Population_Data.csv
data/raw/depreciated/covid_deaths_usafacts_july72020.csv
data/raw/depreciated/covid_deaths_usafacts_study_countys.csv
data/raw/depreciated/cumulative_deaths.csv
data/raw/depreciated/cumulative_deathsconfirmed.tsv
data/raw/depreciated/daily_deaths_ECDC20200518.csv
data/raw/depreciated/daily_deaths_ECDC20200724.csv
data/raw/depreciated/deaths copy.csv
data/raw/depreciated/deaths.csv
data/raw/depreciated/deathsTimeSeriesR.csv
data/raw/depreciated/deaths_time_series.csv
data/raw/depreciated/deathsconfirmed_time_series.tsv
data/raw/depreciated/sero_raw_data_included.xlsx
data/raw/depreciated/seroassay_validation.csv
data/raw/depreciated/seroprevalence.csv
data/raw/non_usa_non_bra_population.tsv
data/raw/seroprevalence_final_raw.tsv
data/raw/serovalidation_final_raw.tsv
data/raw/time_series_covid19_deaths_US.csv
data/raw/time_series_covid19_deaths_global.csv
data/raw/usa_study_id_county_key.csv
data/raw/wpp_un_agepopulations.xlsx
data/simdat/infxn_curve_shapes.csv
drake_clst/slurm_clustermq_LL.tmpl
reestimate_covidIFR_analysis.Rproj
reports/ModFit_report_base.Rmd
reports/Sim_report_base.Rmd
reports/bring_reports_together.sh
reports/make_ModFit_reports.R
reports/make_Sim_reports.R
results/prior_inputs/BRA1_sens_reg_age.csv
results/prior_inputs/BRA1_spec_reg_age.csv
results/prior_inputs/DNK1_sens_reg_age.csv
results/prior_inputs/DNK1_spec_reg_age.csv
results/prior_inputs/ESP1-2_sens_reg_age.csv
results/prior_inputs/ESP1-2_spec_reg_age.csv
results/prior_inputs/GBR3_sens_reg_age.csv
results/prior_inputs/GBR3_spec_reg_age.csv
results/prior_inputs/ITA1_sens_reg_age.csv
results/prior_inputs/ITA1_spec_reg_age.csv
results/prior_inputs/NYS1_sens_reg_age.csv
results/prior_inputs/NYS1_spec_reg_age.csv
results/prior_inputs/README.md
results/prior_inputs/weibull_params.RDS
run_nightly_workers.sh
