This repository holds the code for the species comparison between human and hamster SARS-CoV-2 neutralisation data, published by Rössler, Netzl et al. Please cite the original publication if any data or code from this repository is used.
The repository's DOI was created with Zenodo (https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content). Please cite the publication and repository when using code from this repository.
Raw data can be found in the data directory. The code for the analyses shown in the main manuscript can be found in the code directory. To obtain a titer table for antigenic map construction, execute the excel_to_titertable.R script. To construct maps execute the make_map.R script. The STAN model is stored in the model directory and executing the code/model_map_magnitude_no_bias.R script saves the sampled and optimized serum and magnitude effects shown in the main manuscript and SOM.
SOM figures can be found in the som directory.
The function directory contains utility functions.
All analyses were performed in R version 4.2.2 (2022-10-31). R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Antigenic maps were constructed using the Racmacs package, Version 1.1.35: Wilks S (2022). Racmacs: R Antigenic Cartography Macros. https://acorg.github.io/Racmacs, https://github.com/acorg/Racmacs.
The bayesian modelling was performed with cmdstanr: Gabry J, Češnovar R (2022). cmdstanr: R Interface to 'CmdStan'. https://mc-stan.org/cmdstanr/, https://discourse.mc-stan.org.