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

Version 4 2024-05-29, 10:28
Version 3 2023-08-11, 13:02
Version 2 2023-08-02, 13:45
Version 1 2023-08-02, 11:45
posted on 2024-05-29, 10:28 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


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


  • 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-GLMMs.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_Combined_GLMMs_Model-Figures.R - Figures for model outputs for all GLMMs
  • 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.


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


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