Respository respond-wp2-ecs

Data integration tasks of the Edad con Salud cohort data for Respond-WP2

Project installation

Software components

• Install R version 4.2.1: 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 2022.07.1+554 for Windows 10/11.

• 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/CCOMS-UAM/respond-wp2-ecs.git

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 mapping-initiatives.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. Hoever, 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. Use the "renv" => "Restore library..." button in Rstudio's "Packages" tab to restore the environment. Alternatively, you can type in the console:

renv::restore()

Repository structure

The file structure of this repository is as follows:

respond-wp2-ecs
|
|--- dat       (To store input datasets; must NEVER be checked-in to Github)
|
|--- notebooks (Notebooks to explore data and test processes live here)
|
|--- output    (Processing outputs; files must be individually "checked-in" if necessary)
|
|--- R         (R functions created for this project live here)
|
|--- renv      (System library necesssary for `renv` to work. DON'T TOUCH)
|
|--- src       (Source scripts that implement the main processes)
|
|--- www       (Project assets, e.g., images, bibliography files, etc.)

Use the folders as indicated to store the different files and generate the outputs of the processes.