This repository contains the data and code used for the analysis of paired mumps serology samples, as described in "Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology", by Michiel van Boven, Jantien A. Backer, Irene Veldhuijzen, Justin Gomme, Rob van Binnendijk, and Patricia Kaaijk, consisting of:
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script: code for analysis and figures -
data: data of 746 persons with paired serology samples
All code has been written in the programming language R; see Requirements for detailed specification.
The data comprises:
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ID: identification number of person
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Pre: pre-outbreak IgG antibody concentration (log2-transformed)
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Post: post-outbreak IgG antibody concentration (log2-transformed)
The raw data is not publicly available due to GDPR constraints.
script contains the code for analysis and figures, consisting of several numbered R files that reproduce the results when executed in order. Note that intermediate results and figures are not part of this repository, but can be reproduced.
The code has been developed and runs under the RIVM R-Studio servers.
R version 4.3.1 (2023-06-16) Beagle Scouts
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Cloud Infrastructure
Next to the R base packages, the following packages(_versions) were used
loo_2.6.0
rstan_2.21.8
StanHeaders_2.21.0-7
ggExtra_0.10.1
cowplot_1.1.1
lubridate_1.9.2
forcats_1.0.0
stringr_1.5.0
dplyr_1.1.2
purrr_1.0.2
readr_2.1.4
tidyr_1.3.0
tibble_3.2.1
ggplot2_3.4.3
ggbeeswarm_0.7.2
tidyverse_2.0.0
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/.
If you encounter a clear bug, please file an issue with a minimal reproducible example on GitHub.