jadebc/washb-floors-public

Household finished flooring and soil-transmitted helminth and Giardia infections among children in rural Bangladesh and Kenya: a prospective cohort study # Household finished flooring and soil-transmitted helminth and Giardia infections among children in rural Bangladesh and Kenya: a prospective cohort study ## Overview Soil-transmitted helminth and *Giardia* infections pose a huge global health burden, and infections in young children can have especially negative and long-term consequences. A small but growing body of evidence suggests that household dirt floors may be an important exposure pathway. We conducted an observational analysis of data collected prospectively within the WASH Benefits randomized controlled trials to determine whether children living in rural homes with finished floors had lower levels of STH and *Giardia* infections compared to children living in homes with unfinished floors. ## Additional Information A pre-specified analysis plan is available on Open Science Framework. To run the scripts, the data directory for the user must be changed in **`0-config.R`**. This will allow for replication of study findings using scripts in this repository. Similar directory statement changes will be needed wherever output files are saved down (e.g., raw estimates, figures). To run all scripts required to reproduce all tables and figures in the manuscript, run the bash script **`0-run-project`**. ## Directory structure **`0-config.R` :** configuration file that sets data directories, sources base functions, and loads required libraries **`0-base-functions` :** R script containing general functions used across the analysis **`1-analysis` :** folder containing analysis scripts. To rerun all scripts in this subdirectory, run the bash script `0-run-analysis.sh`. * `1-washb-floors-mde.R` : obtain minimum detectable effects * `2a-washb-prev-mean-bd.R` : calculate prevalence, geometric mean, and confidence intervals for KK and qPCR data from Bangladesh * `2b-washb-prev-mean-ke.R` : calculate prevalence, geometric mean, and confidence intervals for KK and qPCR data from Kenya * `3-washb-floors-pfloors.R` : com …