This repository contains the code developed and used for the analysis of the SCONE study in the Netherlands, as described in "Contact patterns of frail and non-frail elderly persons in the Netherlands during the COVID-19 pandemic", by Jantien A Backer, Jan van de Kassteele, Fatima El Fakiri, Niel Hens, and Jacco Wallinga, consisting of:
-
scripts: code for two scripts (data cleaning and analysis) and helper functions -
data: additional data files that are needed for analysis -
article: Rmd and helper files of submitted version(s) of the manuscript and supplementary material -
results: intermediate results produced by analysis script, used in Rmd files -
figures: figures produced by analysis script, used in Rmd files
All code has been written in the programming language R; see Requirements for detailed specification.
The cleaned data is publicly available on Zenodo in the socialcontactdata.org format. You can either:
-
Download the data files from the repository and place them in the
datafolder, or -
Run the analysis script which will download the data files from the repository without storing them
The raw data is not publicly available due to GDPR constraints.
scripts contains the scripts for data cleaning and analysis, and some helper functions. Each script consists of several numbered R files that reproduce the results when executed in order. Note that the data cleaning script can't be run for lack of raw data.
The code has been developed and runs under the RIVM R-Studio servers.
R version 4.2.3 (2023-03-15) Shortstop Beagle
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Cloud Infrastructure
Next to the R base packages, the following packages need to be installed
readxl
tidyverse
lubridate
mgcv
mgcv.helper
emmeans
ggsignif
viridis
cowplot
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
The SCONE study has been financed by the Netherlands Organisation for Health Research and Development (ZonMw; grant number 10150511910020).
If you encounter a clear bug, please file an issue with a minimal reproducible example on GitHub.