# Description
This repository includes data and R code to run all of the analysis for the paper:
Torres Ayala et al. **Multiplex PCR detection of enteric pathogens in a community-based birth cohort in Ecuador: comparison of xTAG-GPP and TaqMan array card assays**. _Open Forum Infectious Diseases_ (2025). (in press)
This work was funded by the National Institute of Allery and Infectious Diseases (R01-AI162867, R01-A137679).
If you have any questions about the files in this repository, please contact Ben Arnold at UCSF (ben.arnold@ucsf.edu).
## Linked Repositories and Additional Resources
### GitHub
The `scripts` component in this repository mirrors the GitHub repository:
https://github.com/proctor-ucsf/ecomid-gpp-tac
## Additional Information
### System Requirements
All analyses were run using R software version 4.4.1 on Mac OSX Sequoia using the RStudio IDE (https://www.rstudio.com).
`> sessionInfo()`
`R version 4.4.1 (2024-06-14)`
`Platform: aarch64-apple-darwin20`
`Running under: macOS 15.1.1`
In this repository we have used the `renv` package to archive the package versions so that you and reproduce the exact compute environment, should you wish to do so.
### Installation Guide and Instructions for Use (Desktop)
You can download and install R from CRAN: https://cran.r-project.org
You can download and install RStudio from their website: https://www.rstudio.com
All R packages required to run the analyses are sourced in the file `0-config.R`.
The installation time should be < 2 minutes total on a typical desktop computer.
To reproduce all analyses in the paper, we recommend that you:
1. Clone the GitHub repository to your computer
For example, in the location on your computer where you would like to clone the repository, you could type into the Terminal command:
`git clone https://github.com/proctor-ucsf/ecomid-gpp-tac.git`
2. Recreate the exact package environment using the `renv` package.
You can do this by opening the R project file ([gpp-tac-comp.Rproj](https://github.com/proctor-ucsf/ecomid-gpp-tac/blob/main/gpp-tac-comp.Rproj)) in RStudio, loading the `renv` package, and typing `renv::restore()` to restore the package environment from the projects [renv.lock](https://github.com/proctor-ucsf/ecomid-gpp-tac/blob/main/renv.lock) file.
3. Download the public data from the OSF repository by running the script [`0-gpp-tac-comp-download-public-data.R`](https://github.com/proctor-ucsf/ecomid-gpp-tac/blob/main/R/0-gpp-tac-comp-download-public-data.R).
4. All of the analysis scripts should run smoothly (scripts `1-xx.Rmd` to `4-xx.Rmd`).
### Additional details
The data analyses on the above Mac desktop configuration required <2 minutes to run.
### License
This project is covered by the CC0 1.0 Universal license.
