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, check out the frequently asked questions page!
To see a list of my favorite stats and R learning resources, check out the learning resources page.
For USDA personnel only: to access video recordings of previous training sessions, visit the SEA Statistics Training page on USDA Axon+ intranet.
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 90-minute 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; Booneville, AR, January 12, 2023; Stoneville, MS, June 14, 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 |
A practical toolkit for mixed models in R
Four 90-minute 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 |
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
Three-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; and Stoneville, MS, June 16, 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. Lessons 1 and 2 taught in Stoneville, MS, June 14-15, 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 | Answers |
| Lesson 3: My first GLMMs in R for SAS users | Slides | Worksheet | Lesson SAS code file | Answers |
Other stats and data science talks
I have given talks on a wide range of topics in stats and data science to different scientific audiences. I’ve provided the lecture slides as PDF or HTML files here. Video recordings of some of these talks are available on the Axon+ page (USDA personnel only).
| Talk (PDF slides) | Date | Venue |
|---|---|---|
| (Un)ethical practices in biostatistics | February 28, 2023 | NCSU Biotechnology guest lecture, Raleigh, NC |
| Power analysis: bureaucratic busywork or critical part of the scientific method? | July 25, 2023 | IACUC workshop, Athens, GA (virtual) |
| Structural equation modeling in food science | August 1, 2023 | FSMQHRU unit meeting, Raleigh, NC |
| Statistical interactions: what are they and what do they mean, anyway? (DRAFT SLIDES) | Upcoming (TBD) | MMRU & Arkansas Children’s Nutrition Center, Little Rock, AR |
| Everything you ever wanted to know about means comparisons but were afraid to ask (DRAFT SLIDES) | Upcoming (TBD) | TBD |
| Troubleshooting common errors and warnings in (G)L(M)Ms (DRAFT SLIDES) | Upcoming (TBD) | TBD |
| A smorgasbord of options for multiomics data analysis (SLIDES WILL BE POSTED SOON) | Upcoming (TBD) | TBD |
Archived course and workshop pages
These are the homepages for multi-day training workshops I have held in the past in case anyone needs to refer to them. They include the syllabi for the workshops, with links to the text and slides versions of the lessons I taught, as well as the worksheets and example datasets.
This page last updated by QDR on 2023-11-28. This page’s contents were created by the author and do not reflect official USDA policy.