Appendix B — Tools used to make this book

To set up the environment for replicating the code used in this book the R language is needed as well as R and Rstudio IDE environments. The following sections contain the directions for installing R and RStudio, how to set up a book with quarto and how to use GitHub as a version saver source.

B.1 RStudio installation

Download and install R and RStudio IDE

B.2 Info on how to setup this project in quarto

quarto is the new version of Rmarkdown, it can be used for making notes, presentations, websites, books and more.

In this project the book has been made in quarto and version saved on github.

Quarto publishing

B.2.1 GitHub useful commands

You can do the same using the command line. In RStudio create a new project on a new directory, add git, and select quarto book project

The automated process will create a _quarto.yml file, the top of the file will look like this one:

project:
  type: book

On terminal type: quarto preview

It creates a folder _book

B.2.1.1 Add Github later:

existing-github-last to connect with github create a github repo with the same name of your project then type

usethis::use_git()

It asks you to commit all files in the RStudio project. This pushes all files in R to a remote folder designed to head to the github repo.

In terminal connect with the github repo:

git init 
git remote add origin

https://github.com/Fgazzelloni/infectious.git

git branch -M main 
git push -u origin main 

B.2.2 Publish your book on github pages

change the quarto.yml file into:

project: 
  type: book 
  output-dir: docs 

add a .nojekyll file, type in terminal:

touch .nojekyll 

then type

quarto render 

some issues might arise if more than one calculation is made inside a single chunks split the chunks!

quarto render creates a folder docs

---

B.3 Add a package

devtools::create("yourpkg")

Now that you have your book done, you might need to add some customized data to use within your analysis.

In order to do that, you’ll need to just add data in the way that is usually done when inside a package.

B.3.1 Building blocks of the package inside the quarto book

B.3.1.1 ADD DATA TO PACKAGE

set the data from the original source and tidy appropriately

usethis::use_data_raw()

it creates a .R script where to put the steps for get the data ready

once data are ready

usethis::use_data(yourdata)

It creates the R folder where the .R scripts of data documentation is located

usethis::use_r("yourdataset")

read how to document your work

vignette("rd-other") # for datasets
vignette("rd")

devtools::document()
devtools::load_all(".")

B.3.1.2 ADD PACKAGE INFO

so the ? (NAMESPACE) works

usethis::use_package_doc()
devtools::document()

B.3.1.3 ADD DATA PACKAGE INFO

usethis::use_r("yourdataset")
devtools::document()

when filling the data .R script for explaining what’s inside the dataset a specific structure needs to be used (see examples)

when new data are added

Build tab and —> More —> clean and install (this is not there anymore whae you start with devtools::create("yourpkg")) to add the new data to NAMESPACE