Files in mrc-ide/reactidd

Package for the temporal analysis of the REACT study

R/add_public_data_to_plot.R R/clean_death_data.R R/clean_hosp_data.R R/estimate_p_spline_average_R.R R/explore_ltla_react2.R R/exponential_estimate_R.R R/get_response_posterior.R R/load_example_data.R R/load_example_data_weighted.R R/load_example_phe_data.R R/plot_breakpoint_R.R R/plot_breakpoint_complex_R.R R/plot_exp_model.R R/plot_exp_model_phe.r R/plot_p_spline_R.R R/plot_p_spline_R_two_variants.R R/plot_p_spline_igr.R R/plot_p_spline_igr_two_variants.R R/plot_p_spline_inc.R R/plot_p_spline_minimum_density.r R/plot_p_spline_phe.R R/plot_p_spline_prev.R R/plot_p_spline_prev_two_variants.R R/plot_spline_difference.R R/r17_scripts/00_adding_urban_variable.R R/r17_scripts/01_prevalence.R R/r17_scripts/02_odds_ratios.R R/r17_scripts/03_spatial_analysis.R R/r17_scripts/04_prevalence_influenza.R R/r17_scripts/05_detailed_prevalence_influenza.R R/r17_scripts/06_ct_values_influenza.R R/r17_scripts/07_ct_by_symptoms.R R/r17_scripts/08_ct_by_symptoms_by_round.R R/r17_scripts/09_ct_by_vax_status.R R/r17_scripts/10_ct_by_vax_status_by_round.R R/r17_scripts/10b_ct_by_vax_status_by_round_omicron_only.R R/r17_scripts/11_unweighted_prevalence_symptoms.R R/r17_scripts/12_check_data.R R/r17_scripts/13_vax_linkage_comparison.R R/r17_scripts/14_prevalence_by_symptoms.R R/r17_scripts/functions/add_conf_ints.R R/r17_scripts/functions/formatting_functions.R R/r17_scripts/functions/load_packages.R R/r17_scripts/functions/make_tables.R R/r17_scripts/functions/overall_prev.R R/r17_scripts/functions/spatial_analysis_functions.R R/r17_scripts/spatial_analysis/1_data_wrangling_all_rounds.R R/r17_scripts/spatial_analysis/2_pairwise_distance_sample_all.R R/r17_scripts/spatial_analysis/3_order_sort_matrices_sample_all.R R/r17_scripts/spatial_analysis/4_nearest_neighbour_distance_sample_all.R R/reactidd-package.R R/run_time_lag_model.R R/shedding_exp_model_plot_density.R R/shedding_get_params.R R/shedding_plot_exp_models.R R/shedding_prepare_data_for_binary_model.R R/shedding_simulate_data.R R/stan_both_shedding_exp_models.R R/stan_breakpoint_model_complex_weighted.R R/stan_breakpoint_model_weighted.R R/stan_exp_model.R R/stan_exp_model_phe.R R/stan_exp_model_weighted.R R/stan_p_spline.R R/stan_p_spline_phe.R R/stan_p_spline_weighted.R R/stan_p_spline_weighted_incidence.R R/stan_p_spline_weighted_two_variants.R R/stanmodels.R R/symptom_prediction_paper_scripts/00_data_prep.R R/symptom_prediction_paper_scripts/01_EDA.R R/symptom_prediction_paper_scripts/01a_EDA_symp_prev_tables.R R/symptom_prediction_paper_scripts/02_univariate.R R/symptom_prediction_paper_scripts/03_meinhausen_buhlmann_stability.R R/symptom_prediction_paper_scripts/04_results_analysis_ROCs.R R/symptom_prediction_paper_scripts/05_xgb_prediction_sensitivity.R R/symptom_prediction_paper_scripts/06_upsets_plots.R R/symptom_prediction_paper_scripts/07_community_detection.R R/symptom_prediction_paper_scripts/README.md R/symptom_prediction_paper_scripts/functions/penalisation_functions.R R/symptom_prediction_paper_scripts/functions/univariate_models.R R/time_lag_model_getmode.R R/time_lag_model_likelihood.R R/time_lag_model_my_prior.R R/time_lag_model_param_new.R R/time_lag_model_runMCMC.R README.md SupplementaryFigure1.pdf inst/extdata/r16_data/code/00_adding_urban_variable.R inst/extdata/r16_data/code/01_prevalence.R inst/extdata/r16_data/code/01_prevalence_influenza.R inst/extdata/r16_data/code/02_odds_ratios.R inst/extdata/r16_data/code/02_odds_ratios_influenza.R inst/extdata/r16_data/code/03_spatial_analysis.R inst/extdata/r16_data/code/04_prevalence_flu.R inst/extdata/r16_data/code/05_ct_values_no_zero.R inst/extdata/r16_data/code/06_table_one_triple_infected - Copy.R inst/extdata/r16_data/code/07_prevalence_per_day_and_region.R inst/extdata/r16_data/code/08_vaccine_efficiency.R inst/extdata/r16_data/code/09_booster_vs2doses_all_adults.R inst/extdata/r16_data/code/09b_booster_vs2doses_all_adults_exclude_below6Months.R inst/extdata/r16_data/code/09c_booster_vs2doses_delta_adults.R inst/extdata/r16_data/code/09d_booster_vs2doses_omicron_adults.R inst/extdata/r16_data/code/10a_children_vaccine_effectiveness_strict.R inst/extdata/r16_data/code/10b_children_vaccine_effectiveness_nonStrict.R inst/extdata/r16_data/code/11_omicron_linked_vacc_props_chisq_test.R inst/extdata/r16_data/code/12_variant_characteristics.R inst/extdata/r16_data/code/13_variant_3vs2doses_adult.R inst/extdata/r16_data/code/14_prevalence_by_variant.R inst/extdata/r16_data/code/15_extract_flu_info.R inst/extdata/r16_data/code/16_ct_values_extracted_GT.R inst/extdata/r16_data/code/17_omicron_and_delta.R inst/extdata/react1_round_19/01_prevalence.R inst/extdata/react1_round_19/01_prevalence_covida_restrictions.R inst/extdata/react1_round_19/02_odds_ratios.R inst/extdata/react1_round_19/02_odds_ratios_with_covida.R inst/extdata/react1_round_19/03_spatial_analysis.R inst/extdata/react1_round_19/04_prevalence_influenza.R inst/extdata/react1_round_19/05_detailed_prevalence_influenza.R inst/extdata/react1_round_19/06_ct_values_influenza.R inst/extdata/react1_round_19/08_ct_values_lineage.R inst/extdata/react1_round_19/09_medianCTvals.R inst/extdata/react1_round_19/10_odds_ratios_addition.R inst/extdata/react1_round_19/readme.md inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/0_data_wrangling_round19.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/1_linked_vacc_prop.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/1_linked_vacc_prop_linked.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/1_temporal_exp_weighted.r inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/1_vacc_prop_by_age.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/1_wt_prev_round19.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/2_prev_plot_round19.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/2_temporal_pspline_weighted.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/2_temporal_pspline_weighted_subsets.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/3_temporal_pspline_weighted_subsets_plots.r inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Ct_values_byLineage_classicSym_2022-03-04.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Ct_values_byLineage_classicSym_2022-03-06.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Ct_values_byLineage_classicSym_AnySym_2022-03-05.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_all.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_all_above_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_all_below_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_no.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_no_above_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_no_below_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_unknown.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_unknown_above_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_unknown_below_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_yes.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_yes_above_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/Venn_diagram_vacc_yes_below_18.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/km_nn_ltla_map_other_r19.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Figures/weightedRatiovsweightedVaccKids.pdf inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/01_prevalence.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/01_prevalence_covida_restrictions.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/01_prevalence_covida_restrictions_smoking.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/02_odds_ratios.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/02_odds_ratios_with_covida.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/02_odds_ratios_with_smoking.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/03_spatial_analysis.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/04_prevalence_influenza.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/05_detailed_prevalence_influenza.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/06_ct_values_influenza.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/08_ct_values_lineage.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/09_medianCTvals.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/10_odds_ratios_addition.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/11_weightedPrev_weightedVacc_kids.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/12a_spatial_analysis_by_lineage.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/12b_spatial_analysis_by_lineage.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/12c_spatial_analysis_by_lineage.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/13_draft_check_cases_in_lineage.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/14_maps_12_to_19.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/15_maps_with_sub_lineages.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/16_maps_with_sub_lineages_jitterBA1_BA2.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/Marc_04_prevalence_influenza.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/functions/add_conf_ints.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/functions/formatting_functions.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/functions/load_packages.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/functions/make_tables.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/functions/overall_prev.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/functions/spatial_analysis_functions.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/spatial_analysis/1_data_wrangling_all_rounds.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/spatial_analysis/1_data_wrangling_all_rounds_safecopy.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/spatial_analysis/2_pairwise_distance_sample_all.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/spatial_analysis/3_order_sort_matrices_sample_all.R inst/extdata/react1_round_19/round19_twin_peaks_scripts_and_tabs/Scripts/spatial_analysis/4_nearest_neighbour_distance_sample_all.R inst/extdata/round_14_sup_date_figs/Figure1.pdf inst/extdata/round_14_sup_date_figs/Figure2.pdf inst/extdata/round_14_sup_date_figs/Figure3.pdf inst/extdata/round_14_sup_date_figs/Figure4.pdf inst/extdata/round_14_sup_date_figs/Figure5.pdf inst/extdata/round_14_sup_date_figs/FigureS1.pdf inst/extdata/variant_symptom_profiling_paper/code/00_bits_and_pieces.R inst/extdata/variant_symptom_profiling_paper/code/00_data_prep.R inst/extdata/variant_symptom_profiling_paper/code/01_stability_selection.R inst/extdata/variant_symptom_profiling_paper/code/02_univariate_variant_compare.R inst/extdata/variant_symptom_profiling_paper/code/03_CT_value_analysis.R inst/extdata/variant_symptom_profiling_paper/code/04_BA1_vs_BA2.R inst/extdata/variant_symptom_profiling_paper/code/05_variant_transitions.R inst/extdata/variant_symptom_profiling_paper/code/06_matched_analysis.R inst/extdata/variant_symptom_profiling_paper/code/07_BA1_BA2_waning.R inst/extdata/variant_symptom_profiling_paper/code/08_eda.R inst/extdata/variant_symptom_profiling_paper/code/09_correlation_structure.R inst/spatial/01_data-cleaning.R inst/spatial/02_model-fitting.R inst/spatial/03_predictions.R inst/spatial/04_mapping.R inst/spatial/05_tables.R inst/spatial/R/functions.R man/exponential_estimate_R.Rd man/load_example_data.Rd man/load_example_phe_data.Rd man/plot_exp_model.Rd man/plot_exp_model_phe.Rd man/plot_p_spline_minimum_density.Rd man/plot_p_spline_phe.Rd man/plot_p_spline_prev.Rd man/reacttemporal2-package.Rd man/stan_exp_model.Rd man/stan_exp_model_phe.Rd man/stan_p_spline.Rd man/stan_p_spline_phe.Rd vignettes/IFR_IHR_paper/TemporalAnalysisIFR_IHR_CaseAscertainment.rmd vignettes/PCR_Positivity_Paper/EstimatingDurationOfSwabPositivity.rmd vignettes/PCR_Positivity_Paper/SupplementaryFigure1.pdf vignettes/RestrictionsPaper/REACT_rounds_8_13_restrictions_paper.rmd vignettes/TemporalAnalysisPHE.rmd vignettes/TemporalAnalysisREACT.rmd vignettes/TemporalAnalysisREACT_rounds12and13.rmd vignettes/TemporalMethodsPaper/PHE_rounds1-7_analysis.rmd vignettes/TemporalMethodsPaper/REACT_rounds1-7_analysis.rmd vignettes/TemporalOmicronPaper/REACT_rounds14-18_omicron_analysis.rmd