Additional file 1 of Predicting subnational incidence of COVID-19 cases and deaths in EU countries
Creators: name: Robert, Alexis
name: Chapman, Lloyd A. C.
name: Grah, Rok
name: Niehus, Rene
name: Sandmann, Frank
name: Prasse, Bastian
name: Funk, Sebastian
name: Kucharski, Adam J.
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Supplementary Figure 1. Lag distribution used in the epidemic component in the model. Supplementary Table 1. Definitions and sources of covariates included in the model.  Supplementary Table 2. Median and 95% interval of ranked probability score (RPS), Dawid-Sebastiani score (DSS) and squared error score (SES) of one-, two-, three- and four-week-ahead local age-stratified case forecasts for Czechia and France and non-age-stratified forecasts for Italy for the baseline Endemic-Epidemic model (without transmission between regions, covariates or seasonality) and full Endemic-Epidemic model (with covariates and seasonality) across all time points in the prediction period from 29th October 2022 to 22nd April 2023. Supplementary Figure 2. PIT histograms showing the calibration of the daily case forecasts from the model for Czechia for 0-19 year-olds, 20-59 year-olds, 60-79 year-olds and 80+ year-olds (rows, top to bottom) for one-, two-, three- and four-week-ahead forecast horizons (columns, left to right) for 29th October 2022 to 22nd April 2023. Supplementary Figure 3. PIT histograms showing the calibration of the daily case forecasts for France for 0-19 year-olds, 20-59 year-olds, 60-79 year-olds and 80+ year-olds (rows, top to bottom) for one-, two-, three- and four-week-ahead forecast horizons (columns, left to right) for 29th October 2022 to 22nd April 2023. Supplementary Figure 4. PIT histograms showing the calibration of the weekly death forecasts from the model for Czechia for 0-19 year-olds, 20-59 year-olds, 60-79 year-olds and 80+ year-olds (rows, top to bottom) for one-, two-, three- and four-week-ahead forecast horizons (columns, left to right) for 29th October 2022 to 22nd April 2023. Supplementary Figure 5. PIT histograms showing the calibration of the weekly death forecasts from the model for France for 0-19 year-olds, 20-59 year-olds, 60-79 year-olds and 80+ year-olds (rows, top to bottom) for one-, two-, three- and four-week-ahead forecast horizons (columns, left to right) for 29th October 2022 to 22nd April 2023. Supplementary Figure 6. Comparison of one-, two-, three- and four-week-ahead national-level case forecasts (rows, top to bottom) for Italy, Czechia and France (columns, left to right) from non-age-stratified version of our model (Endemic-Epidemic (EE) model) with ensemble forecasts from the European COVID-19 Forecast Hub (ensemble) and observed cases (data) for 29th October 2022 to 22nd April 2023. Supplementary Figure 7. PIT histograms showing the calibration of the daily case forecasts from the non-age-stratified version of the model for Italy, Czechia and France (columns, left to right) for one-, two-, three- and four-week-ahead forecast horizons (rows, top to bottom) for 29th October 2022 to 22nd April 2023. Supplementary Figure 8. Comparison of one-, two-, three- and four-week-ahead national-level death forecasts (rows, top to bottom) for Italy, Czechia and France (columns, left to right) from non-age-stratified version of our model (Endemic-Epidemic (EE) model) with ensemble forecasts from the European COVID-19 Forecast Hub (ensemble) and observed cases (data) for 29th October 2022 to 22nd April 2023. Dashed lines show median forecasts, shaded regions the 95% prediction interval for the forecasts. Supplementary Figure 9. PIT histograms showing the calibration of the weekly death forecasts from the non-age-stratified version of the model for Italy, Czechia and France (columns, left to right) for one-, two-, three- and four-week-ahead forecast horizons (rows, top to bottom) for 29th October 2022 to 22nd April 2023.