index.qmd

---
title: "Course Materials for PHC 6099: 'R Computing for Health Sciences'"
author:
  - name: Gabriel Odom
    affiliations:
      - Florida International University
      - Robert Stempel College of Public Health and Social Work
toc: true
number-sections: true
format: html
embed-resources: false
---


## Source Code for PHC6099 Course Notes

This material is for the course "R Computing for Health Sciences". The course notes are published here: <https://gabrielodom.github.io/PHC6099_rBiostat/>


### Topics  
The chapters are:

1. Exploring Data  
    - `ggplot2::` mosaic plots, histograms, and violin plots
    - `ggplot2::` scatterplots and facets
    <!-- - `rayshader::` -->
    - `skimr::`
    - `table1::`
    - `gtsummary::`
2. One-Sample Tests  
    - $Z$-test
    - Paired $t$-test
    - Paired Wilcoxon test
    - Transformations to Normality
    - McNemar's Test 
    - Fisher's Exact Test
    - Chi-Square Goodness of Fit
    - Bootstrapped Confidence Intervals
3. Two-Sample Tests  
    - $t$-test
    - Welch's $t$-test
    - Mann-Whitney $U$ test
    - Cochran's $Q$ test
    - $\chi^2$ Test for Independence
4. ANOVA and Linear Regression  
    - One-Way ANOVA
    - Two-way ANOVA
    - Welch's ANOVA
    - Kruskal-Wallace Test
    - Tukey HSD Post-Hoc Test
    - Repeated Measures ANOVA
    - Random Intercept Models
    - Correlation Matrices and Covariances
    - Multiple Regression (linear)
    - Polynomial regression
5. Generalized Linear Models  
    - Generalized Linear Models: Binary
    - Generalized Linear Models: Ordered
    - Generalized Linear Models: Count (Poisson)
    - Generalized Linear Models: Count (Negative Binomial)
6. Special Topics  
    - Linear Mixed Effects Models
    - Structural Equation Models
    - Cox Proportional Hazards Regression
    - (TBD) Multivariate Methods for Genetics/Genomics
    - Ridge, LASSO, and Elastic Net Regression
7. Power Calculations (in progress)


### Lesson Outline
This is a shell of a lesson that can be copied and pasted for new lessons (or to edit and clean up existing lessons). If you copy this shell, then change all the headings from level 4 to 2. Replace \<the method\> with the name of your method, or its abbreviation. The file `lessons/00_lesson_template.qmd` has a `.qmd` template with these sections.

#### Introduction to \<the method\>
#### Mathematical definition of \<the method\>
#### Data source and description
#### Cleaning the data to create a model data frame
#### Assumptions of \<the method\>
#### Checking the assumptions with plots
#### Code to run \<the method\>
#### Code output
#### Brief interpretation of the output