epitemplate-repo

Template project structure for collaborative work 🚀

Getting started

This template requires the path to your OneDrive Sharepoint folder. Set it up in your .Renviron file located in your HOME or project directory.

Setting the environment variables in your HOME directory will make it available to all your R projects. On the other hand project level .Renviron make the environment variables only available to your specific project.

• In the .Renviron file, add:

  SHAREPOINT_PATH="ADD YOUR SHAREPOINT PATH HERE"

• Restart your R session so that the updated .Renviron is loaded

• The set_paths() function allows you to quickly access your sharepoint path as well as all of the synced sub-folders in the sharepoint folder. This function requires to have {janitor}, {stringr} and {fs} packages installed.

Ignored folders

In every project, the following directories are gitignored by default, you can add them to the project depending on your needs:

• data for local data storage.
• local for local output (ex. pdfs, html, png, excels files).
• temp for temporary/sensitive files.
• renv files and folders if you configured renv for your project.

Rmd template

You can create rmarkdown template using the epitemplates R package.

• Install the epitemplates R package

# install.packages("remotes")
remotes::install_github("epicentre-msf/epitemplates")

• To create a new Rmd file in the project, run in the console

epitemplates::epi_rmd(path = "Rmd/[newfile].Rmd")

where [newfile] is the new file to add. Start editing the .Rmd file.

Alternatively if you are using RStudio you can create a new Rmd file by using the addins Addins > Epitemplates > Rmd document. You will be prompted to pick a file path.

Quarto template

You can create quarto template using the epitemplates R package.

• Install the epitemplates quarto package

# install.packages("remotes")
remotes::install_github("epicentre-msf/epitemplates")

• To create a new Rmd file in the project, run in the R console

epitemplates::epi_qmd(path = "Qmd/[newfile].qmd")

where [newfile] is the new file to add. Start editing the .qmd file.

Alternatively if you are using RStudio you can create a new Rmd file by using the addins Addins > Epitemplates > Quarto document. You will be prompted to pick a file path.

Rendering documents

We usually render documents to a local folder called local. quartodoes not allow to render a file to an output directory other than the one of the quarto document, unless you have a project structure. epitemplates has a wrapper function for rendering documents to your local folder.

# render qmd to your local folder
epitemplates::epi_render(
    input = "Qmd/[yourfile].qmd",
    output_format = "all",
    output_folder = "local"
)

# render Rmd to your local folder
epitemplates::epi_render(
    input = "Rmd/[yourfile].Rmd",
    output_format = "all",
    output_folder = "local"
)

Depending on the setup of your local folder you may want to render to a specific sub-folders of your local folder. For example, render all Rmd/Qmd files to a report sub-folder, or one specific Rmd/Qmd file to a specific sub-folder. You can configure these options in the YAML _outputs.yml in each Rmd/Qmd folder. There is a default one in the current project structure you can start with.