sabrenet-rousettus-dynamics

This repository contains data and R code which are supplements to:

Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony – considerations for spillover, by Marike Geldenhuys , Noam Ross , Muriel Dietrich , John L. de Vries , Marinda Mortlock , Jonathan H. Epstein , Jacqueline Weyer , Janusz T. Pawęska, and Wanda Markotter . Scientific Reports 13, 15829 (2023). https://doi.org/10.1038/s41598-023-42938-w

If referring to the study or methods, please cite the publication. If you re-use these data and/or code in a publication please be sure to cite the Zenodo reference, as well (https://doi.org/10.5281/zenodo.7709716).

Repository Structure and Reproducibility

• data/ contains data from the study and a data dictionary describing all variables.
• R/ contains functions used in this analysis.
• reports/ contains literate code for R Markdown reports generated in the analysis
• outputs/ contains compiled reports and figures.
• This project uses the {targets} framework to organize build steps for analysis pipeline. The steps are defined in the _targets.R file and the workflow can be executed by running run.R via source("run.R") in your R terminal or Rscript run.R in your system shell. The schematic figure below summarizes the steps. (The figure is generated using mermaid.js syntax and should display as a graph on GitHub. It can also be viewed by pasting the code into https://mermaid.live.)

graph LR
subgraph Project Workflow
    direction LR
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  end
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• This project requires R version 4.3.1 (2023-06-16). This project uses the {renv} framework to record R package dependencies and versions. Packages and versions used are recorded in renv.lock and code used to manage dependencies is in renv/ and other files in the root project directory. On starting an R session in the working directory, run renv::restore() to install R package dependencies.
• The package also requires cmdstan to be installed. (Version 2.32.0 was used). If not already installed, run cmdstanr::install_cmdstan(version = "2.32.0") after renv::restore()