Repository for the PLGA research project

This is the repository where you can find the R code, data and results about the paper entitled: Microbial plankton uptake enhances the degradation of a biodegradable microplastic (PLGA)

Repository structure

The file structure of this repository is as follows:

PLGA
|
|--- data          (To store input datasets; NEVER overwrite/modify these original files)
|     |--- raw     (Copies of the raw data, if that is ready to use, and the data sheets generated by any processing of the raw data)
|     |--- processed
|
|--- notebooks_R    (Notebooks. To clean the raw data, visualize processed data, and fit the models.)
|
|--- output       (Processing outputs)
|     |          
|     |--- figures
|     |--- models
|--- renv         (System library necesssary for `renv` to work. DON'T TOUCH)

Use the folders as indicated to store the different files and generate the outputs of the analysis by the notebooks.

License

This template is licensed under the Creative Commons Attribution 4.0 International license. Please see the license file.

Attributions

Rstudio project template

This project makes use of the rproj-template Github template created by Daniel Morillo and licensed under the Creative Commons Attribution 4.0 International license.

Project installation

Software components

Start by installing the following software components:

• R version 4.4.1: In Windows, using the binary installer is recommended.

• Rstudio Desktop: Although not strictly necessary, it is recommended to install the Rstudio IDE; for strict reproducibility, use build 2024.09.0+375 for Windows 10/11.

• Quarto publishing system: An additional component used by Rstudio to generate and publish literate computing outputs. For strict reproducibility please use build 1.5.57; On Windows, use the 64-bit installer.

• Git client: Install the Git client in order to be able to clone locally the project repository. On Windows, use the 64-bit Windows installer.

Installing the project locally

This project is hosted as a GitHub repository. It can be cloned as a local Git repository following these instructions (steps 2 through 7). Note that this will create a local copy of (‘clone’) the GitHub repository as an Rstudio project in the folder specified. The URL that must be entered into the Repository URL text box is:

https://github.com/leomarameo7/PLGA

IMPORTANT: It is totally unrecommended to clone a git repository inside a cloud storage folder (e.g., Dropbox, OneDrive). Please note that GitHub serves the purpose of backing up the repository, so no cloud storage is necessary. Similarly, cloning the repository in a network folder may cause problems with the renv environment (see below); do it at your own risk!

After cloning the repository, the Rstudio project will open automatically in the Rstudio IDE. If it doesn’t, or you want to return later to the project in Rstudio, you can do so by double clicking on the file rstudio_project.Rproj that has been created in the project folder when cloning the repository.

NOTE: It is common practice to avoid using and versioning .Rprofile files. However, this project uses package renv to create a reproducible environment, which needs the .Rprofile file that lives in the root directory of the project. Please DO NOT delete or edit this file; it will install and activate the renv package and make it ready for restoring the environment.

Restoring the environment

The reproducible environment created by renv must be restored to install all the packages this project needs to be built properly. If renv does not initialize automatically (check the console for messages about this), you will need to manually install the package first:

install.packages("renv")

Once it is successfully installed, use the “renv” -> “Restore library…” button in Rstudio’s “Packages” tab to restore the environment. Alternatively, you can type in the console:

renv::restore(prompt = FALSE)