## Description This repository includes data and replication files to reproduce the analyses in the manuscript: Arnold, B. F., Kanyi, H., Njenga, S. M., Rawago, F. O., Priest, J. W., Secor, W. E., Lammie, P. J., Won, K. Y. & Odiere, M. R. Fine-scale heterogeneity in _Schistosoma mansoni_ force of infection measured through antibody response. _Proceedings of the National Academy of Sciences, U.S.A_ (2020). https://www.pnas.org/cgi/doi/10.1073/pnas.2008951117 The materials in this repo are dynamically linked to GitHub: https://github.com/ben-arnold/mbita-schisto and are cross-linked with the Dryad repository: https://doi.org/10.7272/Q6DZ06J3 Additionally, the GitHub repo includes a Binder virtual machine that you can use to run the scripts interactively in RStudio cloud. The `data` subdirectory includes the datasets for the analysis. The `R` subdirectory includes all computational notebooks, organized by display item. To re-run the analyses, clone the GitHub directory (above), and create a new `output` subdirectory alongside `data` and `R` to store the output files (which are not pushed to GitHub to save space). Each dataset includes a codebook. We have not included lon/lat village coordinates under guidance from our IRB, so the notebook that creates Figure 1, Figure S2 and Figure S3 cannot be run on the publicly available data (i.e., you will not be able to run files `1-mbita-schisto-format-data.Rmd` and `3-mbita-schisto-map.Rmd`. Those rely on identifiable data but are provided for completeness). If you have any questions about these files, please contact Ben Arnold at UCSF (ben.arnold@ucsf.edu).