Analysis of COVID-19 using BEEPmbp software
Authors/Creators
- 1. Biomathematics and Statistics Scotland, James Clerk Maxwell Building, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
- 2. The Roslin Institute, The University of Edinburgh, Midlothian, EH25 9RG, UK
Description
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).