oschultes/efgh_malawi_shigella_risk_factors

Analysis for the EFGH Manuscript Writing Cohort Program manuscript aiming to identify correlates of Shigella infection in Malawi # Risk factors associated with Shigella diarrhea in 6-35-month-olds: A Cross-Sectional Study, Malawi, 2022-2024 This repository contains code used in the manuscript "Risk factors associated with Shigella diarrhea in 6-35-month-olds: A Cross-Sectional Study, Malawi, 2022-2024" by Munthali et al. (doi.org). The objective of the manuscript was to characterize risk factors for Shigella among children presenting to health facilities with diarrhea. Secondary aims examined seasonal effect modification and different outcome definitions. ## Parent study and manuscript development This analysis used data from the Malawi site of the Enterics for Global Health (EFGH) study, a seven-country consortium study which enrolled children ages 6-35 months presenting to a health facility with diarrhea. The manuscript was written as part of participation in the EFGH Manuscript Writing Cohort Program, a training opportunity for junior investigators. Over 18 months participants attended didactic sessions and, with the support of mentorship teams, wrote a manuscript for publication as first author. ## Data availability EFGH data is publicly available upon request at Vivli (doi.org). ## How to use this repository - Clone this repository to your local computer - Create two new folders in the parent folder called "Raw Data" and "Last Step Datasets" - Download EFGH data from Vivli repository and save to "Raw Data" - Run 0-config.R to load necessary packages and create custom functions - Run 1-prep-data.R to clean the raw data and save to the "Last Step Datasets" folder - Run 2-analysis.R to run the analysis and export results to the "Results" folder