R Training Workshops for HJF Global Infectious Diseases - Given in Aug and Sept 2023

{:.no_toc}

R Training Workshops for HJF Global Infectious Diseases - Given in Aug and Sept 2023

---

Workshop Instructor:

• Melinda Higgins, PhD
  • Director Biostatistics and Data Core
  • Office of Nursing Research
  • School of Nursing - Emory University
  • [email protected]

---

Table of Contents

• TOC 1 {:toc}

Preparation

• Download and install R
• Download and install RStudio Desktop
• optional read - Ch1 Getting Started with R/RStudio in "ModernDive" Book
• Instructions for installing R packages - we will cover package installation during the workshop.

R Packages

• R Packages for Workshops 1 & 2

  • arsenal
  • broom
  • ggthemes (optional)
  • ggthemr (optional)
    • This package is NOT on CRAN and is installed from Github. You will need the devtools package to run the devtools::install_github('Mikata-Project/ggthemr') command.
  • gmodels
  • gtsummary
  • Hmisc
  • knitr
  • patchwork
  • palmerpenguins
  • plyr
  • psych
  • rmarkdown
  • tidyverse [includes dplyr, ggplot2, tidyr, readr, and more...]
  • tinytex & run the installation - see instructions at https://yihui.org/tinytex/
  • usmap

• R Packages for Workshop 3

  • TBA

• R Packages for Workshop 4

  • TBA

Workshop 1 - August 24, 2023: Data Visualization

(plus Intros to R and RStudio and Rmarkdown)

Times	Materials Covered
08:30-09:45	Part 1 - Intro to R and RStudio
	- module01_Rscript.R - right click "save as"
	Part 2 - Working with R Packages
09:45-10:00	Break
10:00-11:15	Part 3 - Intro to Visualizations with ggplot2
	- ggplot_Rscript_01.R
	- ggplot_Rscript_02.R
	Part 4 - Intro to Rmarkdown [if time - see materials below]
11:15-11:30	Q&A

• [If Time] Part 4: The Utility of Rmarkdown - Report and Slides all from 1 file!
  • Learn more about the Abalone dataset - freely available from the "UC Irvine Machine Learning Repository", see https://archive.ics.uci.edu/ml/datasets/abalone
  • Files:
    • Rmarkdown file with codes
    • abalone dataset - CSV format
    • Abalone Report - HTML
    • Abalone Report - DOCX - DOWNLOAD File
    • Abalone Report - PDF
    • Abalone Report - HTML Slides, ioslides
    • Abalone Report - HTML Slides, slidy
    • Abalone Report - PDF Slides, beamer
    • Abalone Report - PPT Slides - DOWNLOAD File

Workshop 2 - August 25, 2023: Data Wrangling and Summary

Times	Materials Covered
08:30-09:45	Part 5 - Data Wrangling with dplyr
	- UPDATED dplyr_Rscript.R
	- UPDATED dplyr_Rscript_wAnswers.R
	Part 6 - Clean and Explore Abalones - R Script
	- Part 6 R Script Answers
	- abalone_clean.RData
	- abalone_table.Rmd
	- abalone_table.html
09:45-10:00	Break
10:00-11:15	Part 7 - Merging Data
	- module07_Rscript.R
	- data1.csv
	- data2.csv
	- data3.csv
	Part 8 - Data Restructuring
	- module08_Rscript.R
	- long1.csv
	- wide1.csv
	Part 9 - If Time Simple Maps - R script
	- Dataset hospital_ops.csv
	- Map Report Simple RMD HTML
	- Map Report w/Parameters RMD HTML
	- Map Report w/choice RMD HTML
11:15-11:30	Q&A

Question on importing datafiles with text blocks

A question was asked about what happens if a data file has text blocks with commas or carriage returns that might cause a problem reading in a delimited file format.

Here is a quick example to illustrate that it does work.

Example Data in CSV and EXCEL formats:

• textwrap.csv
• textwrap.xlsx

Example R Code to read these files:

• textwrap.R

See this document illustrating this textwrap example.

Workshop 3 - September 7, 2023: Regression Methods/Modeling

Additional R packages to be used today:

• purrr
• stargazer
• apaTables
• easystats
• parameters
• see
• sjPlot
• sjstats
• pROC

Times	Materials Covered
08:30-09:45	review workshops 1, 2 and textwrap question
	Quick Overview of R Objects
	R Program - Clean Abalone Data
	R Program - Performing Statistical Tests
09:45-10:00	Break
10:00-11:15	Working with Rmarkdown
	Regression - linear and logistic
	AbaloneReport_Sept2023.Rmd
	AbaloneReport_Sept2023.html
	AbaloneReport_Sept2023.pdf
11:15-11:30	Q&A

Workshop 4 - September 8, 2023: Missing Data

Additional packages for today:

• VIM
• naniar
• mice

Times	Materials Covered
08:30-09:45	missingData.R R Script
09:45-10:00	Break
10:00-11:15	More with Rmarkdown
	Part 9 - If Time Simple Maps - R script
	- Dataset hospital_ops.csv
	- Map Report Simple RMD HTML
	- Map Report w/Parameters RMD HTML
	- Map Report w/choice RMD HTML
11:15-11:30	Open Discussion and Q&A

Useful reference on missing data:

• CH.20 in the Epidimiologist R Handbook

---

Learn more about Rmarkdown at:

• Rmarkdown by RStudio
• R Markdown: The Definitive Guide
• R Markdown Cookbook
• Yihui Xie's knitr site
• Example Blog http://jenrichmond.rbind.io/post/2021-08-31-parameterised-penguins/
• Example Document https://rpubs.com/jenrichmond/adelie

---

More R Resources - get help and inspiration

• RStudio Education
• Quick-R
• BOOK: R in Action, 3rd ed.
• Datacamp
  • R for SAS Users - My Datacamp Course
• Coursera
  • Reproducible Templates for Analysis and Dissemination - My Coursera Course
• My Emory Courses:
  • Emory N741
  • Emory N736
• BOOK: Statistical Inference via Data Science
• BOOK: The Epidemiologist R Handbook
• BOOK: R Graphics Cookbook, 2nd edition by Winston Chang
• R Graphics Cookbook website also by Winston Chang
• The R Graph Gallery