Newcastle University
Browse
1/1
3 files

Scripts and aggregated data files for the COVID-19 in Teesside research project

Download all (1.2 MB)
Version 3 2023-08-11, 13:02
Version 2 2023-08-02, 13:45
Version 1 2023-08-02, 11:45
software
posted on 2023-08-11, 13:02 authored by Ellen MossEllen Moss, Stephen Rushton, P Baker, Matthew BashtonMatthew Bashton, Rui Dos Santos, Sarah O'Brien, Roy SandersonRoy Sanderson, Wen Chyin YewWen Chyin Yew, Gregory Young, Clare McCann, Darren SmithDarren Smith
COVID-19_Teesside

Scripts and aggregated data files for the COVID-19 in Teesside research project.

Scripts

  • 1a_Data-Processing-IMD.R - Creates the Index of Multiple Deprivation (IMD) dataset for Teesside postcode districts.
  • 1b_Data-Processing-Spatial.R - Creates an adjacency matrix for the spatial units for the INLA modelling, from a shapefile of the postcode districts.
  • 1c_Data-Processing-Weather.R - Creates a data file with average weekly temperature and rainfall values from raw daily data.
  • 1d_Data-Processing-Cases.R - Creates several data files aggregating positive cases of COVID-19 by space (postcode), time (week), virus lineage, and testing regime.
  • 2_Spatial-Data-Exploration-Figure.R - Figure 1: a panel plot including a labelled map of the Teesside postcode districts and demographics.
  • 2_Temporal-Data-Exploration-Figure.R - Figure 2: a panel plot of all the different case plots and the weather variables.
  • 3_Disease-Mapping_Relative-Risk-Figures.R - INLA models and maps (Figure 3, S1, and S2) showing the relative risk of disease in each postcode.
  • 4a_All-Cases-GLMM_and_Model-Figures.R - All-cases GLMM model and figures showing the model output. Also includes the correlation of positive tests for the two pillars, and the GLMM modelling total cases from the 6 second wave lineages.
  • 4b_8-Lineages-GLMMs.R - Separate lineage GLMM models, for the 8 most common lineages in Teesside during 2020.
  • 4c_8-Lineages-GLMMs_Model-Figures.R - Figure 4: model outputs from the all-cases and separate lineage GLMM models.
  • SessionInfo.R - Lists the packages and versions used during analysis.

Data Files

  • Analysis folder - Data files used in GLMMs, disease mapping, correlation, and for creating figures.
  • IMD folder - Raw and processed IMD data files.
  • Results folder - All model output files.
  • Spatial folder - INLA adjacency matrix and the TS postcode polygons file (used for creating maps).
  • We have not included raw (unaggregated) weather or case data here as we do not have permission to share it publicy.

Funding

MRC, National Institute of Health Research (NIHR) [grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute

History

Usage metrics

    Newcastle University

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC