SEAStats

Stats and data science learning resources for researchers in the USDA ARS Southeast Area

View the Project on GitHub
USDA-REE-ARS/SEAStats

Contents:

Contents:

This project is maintained by USDA-REE-ARS

Minimalistic — Theme by vaibhavvikas

New Orleans March 2024 Statistics Training

Pre-workshop instructions

You have two options for following along with the code in the workshop.

Option 1: I have created a project on Posit Cloud. You can run the R code on the cloud server without installing anything on your own computer. All you have to do is sign up for a Posit Cloud account (already paid for by the Area Office), join the project group, and create your own copy of the project template. Participants will receive an invitation link by email. Instructions for signing up for an account and joining the project are here.

The Posit Cloud server is only for demonstration and teaching purposes. It is not secure. NO GOVERNMENT-OWNED DATA MAY BE UPLOADED TO THIS SERVER.

Option 2: Install R, RStudio, and all necessary R packages on your own computer. For Day 2 (omics), there is an additional step to install a Python virtual environment on your computer so that you can call Python code to do certain omics analyses from within R, using this omics workshop setup script. We may not have time during the workshop to troubleshoot any installation issues that may arise. However, if you want to analyze your own data with the methods you learn in the workshop, you will eventually need to install this software locally or run it on the SciNet cluster. Instructions on how to install R, RStudio, and the needed R packages on your own computer are here.

Workshop agenda and materials

All necessary data and code worksheets are already pre-loaded on Posit Cloud. I have posted all materials here as well, in case people want to access them after the workshop when the Posit Cloud workspace is no longer available. You will need to bring your laptops to participate in hands-on sessions.

Day 1: R Boot Camp (Monday, March 4)

Day 1 Agenda

Location: SRRC

  • 11:00 AM - 12:00 noon: Quentin gives a brief introduction, followed by a 45-minute stats talk: Statistical interactions: what are they and what do they mean, anyway?, and Q&A
  • 12:00 noon - 1:30 PM: Lunch
  • 1:30 PM - 2:30 PM: Hands-on session 1
  • 2:30 PM - 2:45 PM: Break
  • 2:45 PM - 3:45 PM: Hands on session 2
  • 3:45 PM - 5:00 PM: Meetings or facility tours

Day 1 Materials

Full-text version Slides Worksheets Answers to Exercises
Day 1, session 1: R Boot Camp: the very basics Slides Worksheet Answers
Day 1, session 2: R Boot Camp: working with data frames Slides Worksheet Answers

Day 2: Multiomics Demo (Tuesday, March 5)

Day 2 Agenda

Location: SRRC

Day 2 Materials

The code notebooks are already pre-loaded on the Posit Cloud workspace in both .Rmd (source code) and .html (generated output including figures) format. All necessary data is also pre-loaded on Posit Cloud.

Day 3: Mixed Models in R (Wednesday, March 6)

Day 3 Agenda

Location: SRRC

  • 9:00 AM - 10:30 AM: Hands-on session 1
  • 10:30 AM - 11:00 AM: Break
  • 11:00 AM - 12:30 PM: Hands on session 2
  • 12:30 PM - 2:00 PM: Lunch
  • 2:00 PM - 5:00 PM: Meetings or facility tours

Day 3 Materials

The two hands-on lessons being taught on Day 3 are part of the “R for SAS Users” lesson series I developed. But it is not necessary to know any SAS to benefit from this lesson. All R code in these lessons is presented alongside equivalent SAS code so that if you’re already familiar with how to do something in SAS, you can see how to accomplish that same goal in R.

Full-text version Slides R Code Worksheet SAS Code from Lesson Answers to Exercises
Day 3, session 1: Intro to Mixed Models in R for SAS users Slides Worksheet Lesson SAS code file Answers
Day 3, session 2: My first GLMMs in R for SAS users Slides Worksheet Lesson SAS code file Answers

Day 4: Baton Rouge visit (Thursday, March 7)

Day 4 Agenda

Location: Baton Rouge

Talk slides

Here are slides for the stats talks I am giving during the location visit.

Post-workshop survey

Please help me improve future trainings by taking a quick (<5 minute) survey telling me what you thought about this workshop!

MS Forms feedback survey

Page last updated 2024-02-24