Reproductive effects on viral detection in bats

This repository contains code, data, figures, and tables that support the manuscript:

Eskew, E.A., K.J. Olival, J.A.K. Mazet, and P. Daszak. 2025. A global-scale dataset of bat viral detection suggests that pregnancy reduces viral shedding. Proceedings of the Royal Society B 292: 20242381.

The paper's analyses broadly address reproductive effects on bat viral detection and leverage data from the USAID-funded PREDICT project. Data were accessed from the Emering Infectious Disease Information Technology Hub (EIDITH) database using the eidith R package.

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Repository Contents

The contents of the repository subdirectories are as follows:

• R contains internal functions used in the repository code

• data contains various lookup tables used during data cleaning as well as the cleaned viral detection data used for model-fitting

• outputs contains all figures and tables associated with the analyses

• scripts contains the core analysis scripts:

  • 01_data_prep.R accesses, cleans, and filters EIDITH data for downstream analysis
  • 02_stan_model_fitting.R fits Bayesian models to the cleaned datasets using cmdstanr
  • 03_plotting.R generates all figures

• stan contains cleaned data in Stan-friendly formats and the Stan models used in the analysis

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Reproducing the Analyses

To facilitate reproducibility for those without EIDITH access, cleaned data analyzed here are contained in both the data/cleaned_data subdirectory (full analysis set in CSV format) and the stan/cleaned_data subdirectory (full analysis set and data subsets as Stan-friendly objects). Users cloning the repository will therefore be able to proceed with the recreation of the analyses starting with 02_stan_model_fitting.R, which will fit the Stan models, saving them to stan/saved_models. Subsequently, 03_plotting.R will recreate all figures using the saved models.