WWEIA CRP

This repository contains the scripts and data used for reproducing results and visualizations

Use and Requirements

1. Clone the repository from the terminal:
   git clone https://github.com/JulesLarke-USDA/wweia_crp
cd wweia_crp
2. Create a conda environment for running python scripts from src/wweia_crp.yml:
   cd doc
conda env create -f wweia_crp.yml

• NOTE: if running on Apple Silicon you will need to run CONDA_SUBDIR=osx-64 conda env create -f wweia_crp.yml

3. Activate the conda environment:
   conda activate wweia_crp

• NOTE: if running on Apple Silicon you will need to run
  conda env config vars set CONDA_SUBDIR=osx-64
  Then conda deactivate and conda activate wweia_crp

4. R scripts are run with a local R server within a Docker (v4.32.0) container for version control purposes
   

• Install docker and navigate to the wweia_crp directory
• Then run docker build -t wweia_crp:1.0 .
• When finished run docker run --rm -it -p 8787:8787 -e PASSWORD=yourpasswordhere -v `pwd`:/home/docker/ wweia_crp:1.0
• Open a web browser and navigate to http://localhost:8787/
• Login to the RStudio server
  • username: rstudio
  • password: yourpasswordhere
• Change directories from the R console: setwd("/home/docker")
• Navigate to the currect working directory in the Files tab: Files > More > Go To Working Directory

5. Run code seqentially starting from src/00

• NOTE: Building the NHANES dataset requires the dietary recalls wweia_all_recalls.txt which can be generated from https://github.com/JulesLarke-USDA/wweia_ingredients

Required software

• Miniconda
• R 4.1.0
• TaxaHFE
• Docker 4.32.0