Structure

R code for paper Armbruster and Reinert, 2024, "Network-based time series modeling for COVID-19 incidence in the Republic of Ireland"

For citation:

@article{armbruster2024network,
title={Network-based time series modeling for COVID-19 incidence in the Republic of Ireland},
author={Armbruster, Stephanie and Reinert, Gesine},
journal={Springer Nature},
year={2024}
}

Data

Folder Data includes the following datasets:

COVID-19_HPSC_County_Statistics_Historic_Data.csv: data set with daily cumulative COVID-19 incidence from Ordnance Survey Ireland, 2023
ireland_covid_weekly.csv: data set after pre-processing
ireland_covid_weekly_2.csv: data with lag-2 COVID-19 incidences after pre-processing
ireland_shapefile.shp: shapefile for plotting network maps, generated by saving data downloaded from the GADM database
county_towns_ireland.csv: data set with coordinates for Irish counties from the Ireland Cities Database on simplemaps
Folder RObjects: contains networks (as GNAR and igraph objects) as well as subsetted data according to COVID-19 regulations

Functions

The file functions_paper.R includes all functions written to pre-process data, fit GNAR models, analyse and plot residuals etc.
The files GNARdesign.R, GNARfit.R and NofNeighbours.R in the folder GNAR contain adapted GNAR functions.

Application

The file Data_processing.R performs some initial data exploration, the data aggregation to a weekly level and the necessary smoothing for extreme peaks in COVID-19 incidence.
The file Data_processing_restrictions.R processes the data according to COVID-19 restrictions and summarises the datasets belonging to restricted and unrestricted pandemic phases.
The COVID-19 networks are constructed in the file Network_construction.R.
The GNAR models are fit to the restricted and unrestricted datasets, MASE values plotted and residuals testes in the file Model_fitting.R.
The folder Figures contains all generated figures for the paper.

Supplementary Material