The structure of this research compendium loosely follows the framework of an R-package for reproducing our analysis (for more information on research compendiums, see ROpenSci Team).
An overview of the compendium is below:
├── R # "Helper" R functions specific to this research project
├── README.md
├── analyses/ # Scripts for data wrangling, fitting, figures, and tables
│ ├── ModFits/
│ │ ├── CareHomes_drakeworker.R
│ │ ├── ModFits_drakeworker_v2.R
│ │ ├── seroRev_ModFits_drakeworker_v2.R
│ ├── Rgn_Mod_Stan/
│ │ ├── run_regional_model.R
│ ├── SimWork/
│ │ ├── SeroRev_SimCurves_drakeworker_v2.R
│ │ ├── SimCurves_drakeworker_v2.R
│ │ ├── fit_conceptual_figure_delayeffects.R
│ │ ├── fit_seroday_concept.R
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│ ├── 00-convalescent_seroAbs_v2.R
│ ├── 01-run_process_country_data_v2.R
│ ├── 02-descriptive_data_plots_v3.R
│ ├── 03-plot_methods_conceptual.R
│ ├── 04-analyze_overall_IFRs.R
│ ├── 05-analyze_age_IFRs_v2.R
│ ├── 06-analyze_carehome_IFRs.R
│ ├── 07-mod_posteriors.R
│ ├── 08-model_ppcs.R
│ ├── 09-collate_sims.R
│ ├── 10-plot_delay_concept.R
│ ├── 11-plot_seroday_concept.R
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├── data/ # DO NOT EDIT ANY FILES IN THIS DIRECTORY BY HAND
│ ├── raw/
│ ├── derived/
│ ├── simdat/
│ ├── plot_aesthetics/
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├── drake_clst/ # Instructions for a slurm scheduler for resource allocation
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├── reports/ # Reports for simulations and study-specific runs
├── reestimate_covidIFR_analysis.Rproj # R-proj
├── run_nightly_workers.sh # Workers for generating MCMCMC fits
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Users will first need to perform model fitting for each of the included studies and/or the simulation runs with code provided in the analyses/ModFits/ and analyse/SimWork/ directories, respectively. These age-based models depend on the COVIDCurve R-Package. Individual "worker" scripts for models without and with seroconversion are available (you can send these out on a slurm cluster with the run_nightly_workers.sh script). From experience on a Linux-based cluster, fits take approximately 8-32 hours to complete.
After you have produced the model fits, you can run the rest of the analyses in sequential order 01-11 (script 00-convalescent_seroAbs_v2.R relies on data that is available upon request. The needed parameter results are provided in the results/prior_inputs directory).