usda-ree-ars.github.io/SEAStats
This page hosts learning materials for USDA ARS SEA statistics and data science trainings created by SEA area statistician Quentin Read. Please contact me if you have issues with accessibility of any of the content on these pages, or if you would like the source code of any of these materials.
For scientists interested in contacting me for a consultation, please check out the frequently asked questions page!
For USDA personnel only: to access video recordings of previous training sessions, please visit the SEA Statistics Training page on USDA Axon intranet.
For participants in the June 2023 Stoneville stats training: June 2023 Stoneville stats syllabus
R Installation instructions
Instructions for installing R, RStudio, and R packages
Follow these instructions before starting any of the lessons if you do not have R and RStudio installed on your laptop.
R Boot Camp
Two one-hour lessons on basic R programming for complete beginners (Lessons 1 and 2 in a six-lesson series).
Taught in hybrid format in Raleigh, NC, December 8-9, 2022, and in person in Fayetteville, AR, January 9, 2023, and Booneville, AR, January 12, 2023.
| Full-text version | Slides | Worksheets | Answers to Exercises |
|---|---|---|---|
| Lesson 1: R Boot Camp: the very basics | Slides | Worksheet | Answers |
| Lesson 2: R Boot Camp: working with data frames | Slides | Worksheet | Answers |
- Zip file including all worksheets for lessons 1-6
- GitHub repository with source code of course materials (USDA internal)
A practical toolkit for mixed models in R
Four one-hour lessons on fitting simple linear mixed models in R (Lessons 3-6 in a six-lesson series).
Taught in hybrid format in Raleigh, NC, December 8-9, 2022.
| Full-text version | Slides | Worksheets | Answers to Exercises |
|---|---|---|---|
| Lesson 3: From linear model to linear mixed model | Slides | Worksheet | Answers |
| Lesson 4: Going further with mixed models | Slides | Worksheet | Answers |
| Lesson 5: Generalized linear mixed models | Slides | Worksheet | Answers |
| Lesson 6: Estimating and comparing treatment means | Slides | Worksheet | Answers |
- Zip file including all worksheets for lessons 1-6
- GitHub repository with source code of course materials (USDA internal)
Data visualization basics with R and ggplot2
90-minute session introducing students to visualizing data with R and ggplot2.
Taught in Fayetteville, AR, January 10, 2023; Athens, GA, February 8, 2023
- Text version of lesson
- Slides version of lesson
- Worksheet (.R script)
- GitHub repository with source code of course materials
A crash course in Bayesian mixed models with brms
Two-hour session introducing students to Bayesian inference, and showing how to fit some simple Bayesian mixed models with brms.
Taught in Fayetteville, AR, January 10, 2023 (older version); Athens, GA, February 9, 2023 (updated version)
- Instructions for installing and configuring brms (do this before starting the course)
- Text version of lesson
- Slides version of lesson
- Worksheet (.R script)
- GitHub repository with source code of course materials and older versions (USDA internal)
R for SAS Users
Two 90-minute lessons showing basic data processing and model fitting procedures in R and SAS side-by-side.
Lesson 1 taught in Athens, GA, February 7, 2023.
| Full-text version | Slides | R Code Worksheet | SAS Code from Lesson | Answers to Exercises |
|---|---|---|---|---|
| Lesson 1: Basic R for SAS users | Slides | Worksheet | Lesson SAS code file | Answers |
| Lesson 2: Intro to Mixed Models in R for SAS users | Slides | Worksheet | Lesson SAS code file | Coming soon! |
Other learning resources
I compiled a list of my favorite learning resources, including materials on R programming and mixed models, for a recent stats workshop. I expect to add more material to this list in the future; please check back soon for updates!
Archived course and workshop pages
- Course homepage from two-day workshop including “R Boot Camp” and “A Practical Toolkit for Mixed Models in R” including links to text version of lesson, slides, worksheets, and example datasets
This page last updated by QDR on 2023-05-28. This page’s contents were created by the author and do not reflect official USDA policy.