Enteropathogen antibody dynamics and force of infection among children in low-resource settings

This repository includes data and computational notebooks to support the paper:

Arnold BF, Martin DL, Juma J, Mkocha H, Ochieng JB, et al. Enteropathogen antibody dynamics and force of infection among children in low-resource settings. eLife 2019; 8:e45594 doi: 10.7554/eLife.45594. https://elifesciences.org/articles/45594

The repository includes all files needed to replicate the analyses, and the repository is cross-referenced with the Open Science Framework (https://osf.io/r4av7). For questions, please write Ben Arnold at UCSF ([email protected]).

All notebooks are written in R markdown, and are located in the R subdirectory (.Rmd with corresponding, compiled .html file). You should be able to replicate all analyses by cloning this directory and creating two new subdirectories called figs and output to store results (those files excluded to save space). Notebooks reference relevant analyses from the paper in their names and titles.

The R script enterics-seroepi-run-all.R runs the notebooks in order and will re-create the entire analysis. Before running the notbooks, you will need to create directories entitled output and figs one level up, alongside the data directory, to store saved results (binary files other than datasets not pushed to GitHub).

De-identifed data from the three countries is provided in the data subdirectory. Each dataset is provided in .csv and .rds format. The files with 2.rds suffixes are datasets that include a few derived variables (e.g., seropositivity cutoffs and indicators) created by the analysis notebooks.