Impacts of black rat invasion on the primary rodent host of Lassa virus, Mastomys natalensis

This repository contains code, data, and figures that support:

Eskew, E.A., B.H. Bird, B.M. Ghersi, J. Bangura, A.J. Basinski, E. Amara, M.A. Bah, M.C. Kanu, O.T. Kanu, E.G. Lavalie, V. Lungay, W. Robert, M.A. Vandi, E. Fichet-Calvet, and S.L. Nuismer. 2024. Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk. Nature Communications 15: 3589.

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Repository Structure

• /R contains code for custom functions that are sourced in the analysis scripts

• /data contains data files necessary for the analysis, including:

  • A clean data subdirectory (/clean) with:

    • Cleaned site- and visit-level rodent trapping data for Sierra Leone and Guinea (/combined)

    • Cleaned house-level rodent trapping data for Sierra Leone (/house)

    • Cleaned rodent trapping data for occupancy modeling of house-level data from Sierra Leone (/occupancy)

  • Data used for data cleaning (/cleaning_tables)

  • A raw data subdirectory (/raw) with:

    • Data on Mastomys natalensis catch per trap from prior studies that were used to formulate an informative prior for Bayesian modeling (/catch_per_trap)

    • Data manually extracted from the McCormick et al. 1987 manuscript (/McCormick)

    • GenBank accession codes for Lassa virus sequence data from Mastomys natalensis collected in both Sierra Leone and Guinea (/sequencing_tables)

  • Source data that can be used to recreate the main text figures (/source_data)

• /outputs contains all main text figures (and a handful of others) output from the analysis scripts

  • The /supplementary subdirectory contains figures that appear in the manuscript's Supplementary Information file

• /scripts contains all analysis scripts, ordered sequentially by number

• /stan_models contains the Stan code sourced in the analysis scripts, including:

  • A visit-level model of Mastomys natalensis count with a site-level rodent presence predictor (visit_model.stan)

  • A house-level model of Mastomys natalensis count with a site-level rodent presence predictor (house_model_site_predictor.stan)

  • An alternative house-level model of Mastomys natalensis count with a house-level rodent presence predictor (house_model_house_predictor.stan)

  • A visit-level zoonotic spillover risk model of Lassa-positive Mastomys natalensis count with a site-level rodent presence predictor (spillover_risk_visit_level.stan)

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Notes on Reproducibility

Site-, visit-, and house-level data analyses and statistical modeling for this project (using the respective analysis scripts) are reproducible given the cleaned data in the data/clean subdirectory. Large raster data files necessary to reproduce the supplementary environmental analyses (07_environmental_analyses.R script) have not been uploaded to GitHub because of file sizes but are available on the project's Zenodo repository.