Analysis of COVID-19 using BEEPmbp software

COVID-19 ANALYSIS This stores the code and data for a non-spatial, age-structured analysis of COVID-19 in England using software tool BEEPmbp (Bayesian Estimation of Epidemic Parameters using Model-Based Proposals). This code is a snapshot of the BEEPmbp GitHub repository (https://github.com/ScottishCovidResponse/BEEPmbp) taken on September 14th, 2021 (hash e994dc33011a4ebcc792d2652c22b48edfeae2f5). RUNNING ANALYSIS This analysis can be executed on a Linux platform using the following commands: 1) Decompress the directory "BEEPmbp-COVID-19-analysis". 2) Compilation of the code: make 3) Load MPI module: module load mpi/openmpi-x86_64 4) Execute: mpirun -n 16 ./beepmbp inputfile="COVID 19 England/England_AS.toml" mode="abcmbp" nparticle=16 ngeneration=350 nrun=16 After completion outputs can be viewed by opening the file: "Output_COVID19_England_AS/visBEEPmbp.html" Further details of the software can be found in the manual (BEEPmbp_Manual_v1.0.pdf) and README.md. DATA AND ANALYSIS FILES: Details of data preparation are given in "Data preparation.pdf". Analysis file (which informs BEEPmbp): "COVID 19 England/England_AS.toml". The following data files are in the "COVID 19 England/Data_England_AS" directory: age_mixing_matrix.csv: Based on the BBC Pandemic study, this estimates the relative mixing of individuals within and between different age groups (see Appendix A). efoi_spline.csv: Provides an estimate for the external force of infection (see Appendix B). population.csv: Populations in different age groups (see Appendix Ci). cases_AS.csv: Daily cases for different age groups (see Appendix Cii). deaths_AS.csv: Weekly deaths in different age groups (see Appendix Cii). admissions_AS.csv: Daily hospital admissions in different age groups (see Appendix Cii). admissions.csv: Daily hospital admissions (see Appendix Cii). covid19_inf_survey_AS.csv: Fortnightly estimates for the infected population taken from the COVID-19 infection survey (see Appendix Ciii). antibody_AS.csv: Fortnightly estimates for the recovered population taken from the COVID-19 infection survey (see Appendix Ciii).

Pooley, C., Doeschl-Wilson, A., & Marion, G. (2021). Analysis of COVID-19 using BEEPmbp software. Zenodo. https://doi.org/10.5281/zenodo.5939463