DOCUMENT
PCI_SuppMatt.docx (8.06 MB)
DATASET
Column_Descriptions_in_repository.xlsx (20.5 kB)
ARCHIVE
Covid-19-Teesside-main.zip (45.53 MB)
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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
software
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 SmithCOVID-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-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.
