Intro to Biostatistics with R

This website collects the materials for a 4 day workshop taking place during the MIGEST Summer School in July of 2024

Quirks

Little things to keep in mind (because semi-automated) about moving form GoogleDrive (*.pptx) lecture files to R lecture files for sharing (*.pdf). Before every push to GitHub:

1. I execute a script R_resources/slides_fromDrive_2_here.R from my shell file ___render_deploy.sh
2. I execute the shell commands to convert *.pptx slides to *.pdf as soon as they are ~ready...

TO DO

• [CODE refactoring]
  • add Goggle Analytics
  • make _variable.yml
    • nome sito
• Cancell parameterize practicel slides .qmd
  • it doesn't make any sense
• turn re-usable practice slides code into tidyeval functions (plot etc) to be able to replace with different datasets

How this website was built

This is a static website built with Quarto, shared on a Github repo and served via Github Pages to be rendered at this link https://lulliter.github.io/R4biostats/, or (after buying a "custom domain"), now deployed over a custom domain registered with AWS Route 53: https://r4biostats.com/.

The main content of the website pages is contained in Quarto Markdown files (*.qmd). *.qmd files are very similar to regular Markdown (*.md) and R Markdown (*.rmd) files, except they are designed to be language agnostic.

Things needed to build the site

1. Install Quarto (an open source tool that can be used from RStudio, Jupyter, CLI, etc.)... Most R users will use RStudio
2. Install git (distributed version control software)... here some instructions
3. Create a Github account
4. Follow instructions/examples available here...
5. Font-Awsome Icons downloaded in ./images/* from Font-Awsome GH repo /svgs. To use in:

• *.md
  • ![fa-crown](images/copyright-regular.svg) (no size spec!!!)
  • <img src="images/copyright-regular.svg" width="16" height="16"> (yes size spec!!!)
• *.qmd
  • quarto wrap {{< fa brands copyright > }}
  • r inline code r fontawesome::fa("fab fa-windows", fill = "steelblue")

6. (An AWS account ...) but only for the custom domain part

Attributions

The content of this website is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except for the borrowed and mentioned with proper "Source:" statements.

Content

I acknowledge inputs received from these very valuable sources:

• An Introduction ro R software course taught by Davide Guido, an instructor of the Master in Biostatistics and Epidemiology Methods, I attended in 2018/2019
• R for Epidemiology, electronic book by the University of Texas Health Science Center School of Public Health\
• Appplied Epi Interactive R Tutorials (Licensed )
• Statology Introduction to Statistics with R Tutorials (Copyrighted )
• Autism dataset analysis
• Introductory Biostatistics with R by Dylan Z. Childs, Bethan J. Hindle and Philip H. Warren
• Biostatistics - Concepts and approaches for collecting good data and turning it into knowledge by J. Stephen Gosnell

Cool Stuff you should check out

• R package {metabolic} by Felipe Mattioni Maturana, Ph.D

Quarto specific resources

• Mine Çetinkaya-Rundel's blog A Quarto tip a day
• Cornell University's lesson Publishing reproducible documents with Quarto https://mine-cetinkaya-rundel.github.io/quarto-tip-a-day/ https://info5940.infosci.cornell.edu/slides/publishing-reproducible-documents/#/themesappearance
• Parameterized reports/slides
  • Mandy Norrbo's tutorial Generate multiple presentations with Quarto parameters
  • Jadey Ryan Talk website
  • R Medicine David Keyes workshop Presentation
  • Jumping Rivers Mandy Norrbo Presentation

Web input attributions

• Website favicon icons8.com
• Google Scholar icon from icons8.com
• Font-Awsome Icons downloaded in ./images/* from Font-Awsome svgs
• Great tutorial on "Customizing Quarto Websites" by Sam Csik: slides
• Free Adobe Express logo maker