Folder organization

A good organization of the working directory, where we will place our files, data, and code, is a good starting point to ensure reproducibility of the data analysis. I also believe that this aspect should be reviewed from time to time during the progress of the investigation and as the number of files in the directory increases.

In the main directory, files and other directories can be organized as follows:

The description of each folder:

• data. Here we place the raw experimental data and the relevant information about them, such as the description of treatments, responses, experimental units, etc.
• data_products. This is where you store anything related to the processing of the raw data that may be needed later. This includes ANOVA tables, multiple comparisons tests, data summaries, etc.
• figures. This folder contains the figures generated by their respective R scripts.
• R. The code needed to generate tables and figures.
• tables. The tables generated by their corresponding R scripts.

For this organization I considered what is generally published in a scientific paper (mainly the folders figures and tables) and can be modified/improved depending on the researcher’s needs. In addition to the folders, three files are included in the main directory:

• main_script.R. This script allows executing the scripts in the R folder and generating the TXT file with the information of the R session at the moment of performing the whole analysis. Optionally, it also allows deleting the content of figures, tables, and data_products, which makes it possible to perform the analysis from scratch.
• directory_example.Rproj. The name of this file can be changed with something representative to the analysis. It contains information related to the project, such as the encoding of the scripts, and double-clicking it allows you to open the directory directly using RStudio.
• Session_Info.txt. Information about our R session at the time of analysis, such as our operating system and the packages we used.

This directory is available for download on GitHub at the following link: directory_example. Once downloaded, you can explore the contents of each folder. The directory contains what is needed to perform an analysis of simulated data (data_main.csv), which includes a graph and a table with means and standard deviations. For didactic purposes, sometimes it is not easy to find real data for learning and/or teaching, I also include the code to perform the simulation of the data (data_simulation.R).

Create a project with RStudio from scratch

Previously, we must install R and RStudio. When we open RStudio, we position the cursor on File and double click on New Project…

Once this is done, a new window will open. Double click on New Directory and then on New Project. Finally, select the folder where our new project will be and write a representative name:

Done, now we can create new folders and files in our new directory.

Connect RStudio with GitHub

The following steps are only necessary the first time we connect RStudio to GitHub:

1. Create a free GitHub account.
2. Installing Git on your computer.
3. Tell Git our user information. For Windows users you can simply open a window with Windows PowerShell and type the following (for Mac users, you must type the same, but opening a terminal with Terminal.app):

git config --global user.name 'Your user name’
git config --global user.email '[email protected]'
git config --global –list

4. Make sure to tell RStudio to use Git. Position the cursor on the Tools tab and click on Global Options:

5. In this new window we position ourselves in Git/SVN. At the end of the Git executable box must be indicated git.exe. Otherwise, click on Browse… and select the file. It is also highly recommended to check the Enable version control interface checkbox:

6. To connect RStudio with GitHub, we will need the usethis and gitcreds packages. Once installed, type the following in the R console, which will direct us to the GitHub page where we will be asked to log in with our account and password:

usethis::create_github_token()

7. Once this is done, we will be able to generate a token. To register it in RStudio we use the following code:

gitcreds::gitcreds_set()

It will ask us to enter the token, just copy and paste it. Press Enter and that’s it, now RStudio is connected to your GitHub account.

Create a new directory and upload it to GitHub

Okay, now let’s upload our new project to GitHub through RStudio. When creating a new project with RStudio, before clicking on Create Project we must check the box Create a git repository:

Then we follow the next steps:

1. Once we have created new subdirectories and files, in RStudio we click on the Git tab and then on Commit:

2. A new window will open. First, we must check the Stage checkboxes in the folders and files we want to upload to GitHub:

3. In the Commit message checkbox, we write something representative and click on Commit:

4. A new window will open with information about the changes and additions in our first commit, close this small window and type:

usethis::use_github()

Which will upload all the content of our first commit to GitHub:

5. Step four will only be necessary for our first commit. Subsequently, each time we make changes that we consider important in our directory, we will have to repeat the process from step one to three and then just click on push:

Which will upload the entire contents of the corresponding commit to GitHub.

All the above will allow us to have a record in our project of the different changes, updates, corrections, etc., and will make the content available to anyone who decides to explore or download it.