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

<p dir="ltr">COVID-19_Teesside</p><p dir="ltr">Scripts and aggregated data files for the COVID-19 in Teesside research project.</p><h3>Scripts</h3><ul><li>1a_Data-Processing-IMD.R - Creates the Index of Multiple Deprivation (IMD) dataset for Teesside postcode districts.</li><li>1b_Data-Processing-Spatial.R - Creates an adjacency matrix for the spatial units for the INLA modelling, from a shapefile of the postcode districts.</li><li>1c_Data-Processing-Weather.R - Creates a data file with average weekly temperature and rainfall values from raw daily data.</li><li>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.</li><li>2_Spatial-Data-Exploration-Figure.R - Figure 1: a panel plot including a labelled map of the Teesside postcode districts and demographics.</li><li>2_Temporal-Data-Exploration-Figure.R - Figure 2: a panel plot of all the different case plots and the weather variables.</li><li>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.</li><li>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.</li><li>4b_8-Lineages-GLMMs.R - Separate lineage GLMM models, for the 8 most common lineages in Teesside during 2020.</li><li>4c_Combined_GLMMs_Model-Figures.R - Figures for model outputs for all GLMMs</li><li>SessionInfo.R - Lists the packages and versions used during analysis.</li></ul><h2>Data Files</h2><ul><li>Analysis folder - Data files used in GLMMs, disease mapping, correlation, and for creating figures.</li><li>IMD folder - Raw and processed IMD data files.</li><li>Results folder - All model output files.</li><li>Spatial folder - INLA adjacency matrix and the TS postcode polygons file (used for creating maps).</li><li>We have not included raw (unaggregated) weather or case data here as we do not have permission to share it publicy.</li></ul><p></p>