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Stat 414 - Mixed and Multilevel Models

Lecture schedule with readings and assignments for each class day
  Monday Wednesday Friday

To Do for Monday

  • Initial survey in Canvas
  • Video introduction in Canvas
  • Pre-course assessment in Canvas
  • Syllabus
  • Install R/RStudio
Optional: "Ecological correlations and the behavior of individuals" (Robinson, 2009)

Day 1: What is Multilevel Data?

  • Overview/history(ppt)
  • Review: Models (qmd) (anno)
    • applet demo
    • BCStyleGuide.docx (updated 9/27)

Submit (in Canvas):

  • CP 1 (7am Wednesday)
  • Quiz 1 (7am Wednesday)

Day 2: How do I estimate my model?

  • Least Squares vs. Maximum Likelihood (ppt)
  • Fitting and comparing models in R (qmd) (anno)
    • applet demo

Submit (in Canvas):

  • CP 2 (noon Friday)
  • Quiz 2 (noon Friday)
 HW 1 (due Sunday night)
  • A few updates 9/24:
    • see red in (c), (d), (e)
Optional: "The illusion of predictability: How regression statistics mislead experts" (Soyer & Hogarth)

Optional: "Another cautionary note about R2: Its use in weighted least-squares analysis" (Willet & Singer) 		Day 3: Inference for regression models
  • Recap (ppt)
  • F-tests and Likeihood ratio tests (qmd) (anno)
    • applet demo
Submit (in Canvas)
  • CP 3 (7am Wednesday)
  • Quiz 3 (7am Wednesday)
 Day 4: Violating Equal Variance Assumption
  • Overview (ppt)
  • BP-test, weighted least squares, HC standard errors (qmd) (anno)
Submit (in Canvas)
  • CP 4
  • Quiz 4 (noon Friday)

 HW 2 (due Sunday night)
  • A few updates 9/30 3:45pm
  • Also complete Week 2 survey and we will talk more about projects on Monday
Optional: "Regressions are commonly misinterpreted," Hoaglin (2016)

Optional:"A reassessment of ANOVA reporting practices: A Review of Three APA Journals" (Zhou & Skidmore, 2017)
 Day 5: Categorical predictors/ANOVA
  • Recap (ppt)
  • Handout (pdf) (anno)
  • Categorical predictors (qmd) (anno)
    • qmd file shouldn't have "answer()" entries?
    • 4.5.1 version of R gives a warning when loading the iscam functions but you should be able to ignore it
Submit (in Canvas)
  • CP 5 (7am Wednesday)
  • Quiz 5 (7am Wednesday)
 Day 6: Adjusted associations
  • Recap (ppt)
  • Adding categorical variables (qmd) (anno)
  • Handout (pdf) (anno)
Submit (in Canvas)
  • CP 6 (noon Friday)
  • Quiz 6 (noon Friday)
 HW 3 (due Monday 8am)
Optional: "Repeated Measures ANOVA, R.I.P.?" (McCulloch) Day 7: Modelling covariance
  • Recap (ppt)
  • Examples (qmd) (anno)
  • Output (pdf) (anno)
Submit (in Canvas)
  • CP 7 (two parts) (7am Wednesday)
  • Quiz 7 (7am Wednesday)
 Day 8: Fixed vs. Random effects
  • Slides (ppt)
  • Examples (qmd) (anno)
To do
  • CP 8 (due 7am Monday)
  • Quiz 8 (noon Friday)
 HW 4 (due Monday 8am)
Optional: cross validation example of fixed vs. random effects models
Optional: More details on R-sq, ICC with mixed models
 Day 9: Random intercepts models
  • Slides
  • Examples (qmd) (anno)
  • Handout
To do
  • Review handout
  • Review problems
    • solutions
  • Optional:
    • Discussion board Q&A
    • Tuesday night office hour (I will try to be on zoom at least 8-9 pm)
      • Regular Tues OH 9-10, 1-2
 Exam 1
 Project part 2 (due midnight Monday)
To see some applications of multilevel models, read this article and/or this article. Day 10: Adding Level 2 variables
  • Slides
  • Examples (qmd) (anno)
To do
  • Submit Project Part 2 (midnight Monday)
  • CP 10 (7 am Wednesday)
  • Quiz 10 (7 am Wednesday)
  • Start HW 5
  • Office hours this week
    • Tues 9-10, 1-2pm
    • Wed (email)
    • Thur 12-1 (zoom)
 Day 11: Interactions
  • Slides
  • Examples (qmd) (anno) (output)
To do
  • CP 11 (noon Friday)
  • Quiz 11 (noon Friday)
  • Finish HW 5
 HW 5 (due Monday 8am)
Optional: "Impact of Exercise Intensity and Sex on Endogenous Ghrelin Levels and Appetite in Healthy Humans" (Nov 2024) Day 12: Random slopes (4.6, 5.2)
  • Slides
  • Examples (qmd) (anno) (output) 
To do
  • Start HW 6
  • CP 12 (due 7am Wednesday)
  • Quiz 12 (due 7am Wednesday)
 Day 13: Random slopes/Introduction to Logistic Regression
  • Slides
  • Examples (qmd) (anno) 
    • Typo was 203 vs. 230
To do
  • Start HW 6
  • CP 12 (due 7am Wednesday)
  • Quiz 12 (due 7am Wednesday)
  • Thursday office hour 11-12pm


 		HW 6 (due Monday 8am)
Optional: "nflWAR: A Reproducible Method for Offensive Player Evaluation in Football" (Canvas) Day 14: Multilevel Logistic Regression (Ch. 17)
  • Guest Speaker
  • Slides (qmd) (anno)
To do
  • CP 14 (due 7am Wednesday)
  • See Ch. 13: Cross-classified/imperfect hierarchies
  • Quiz 14 (due noon Friday)
  • Start HW 7
  • Project Report 3 (see ppt for some presentation advice)
 Day 15: Longitudinal Models (Ch. 15)
  • Recap multilevel logistic regression (Ch. 17)
  • Recap crossed classified effects (Ch. 13)
  • Longitudinal models:Slides (qmd) (anno)
    • The issue with performance::r2 was needs to be by_level and doesn't work with random slopes
To do
  • Quiz 14 (due noon Friday)
  • CP 15 (due noon Friday)
  • See Ch. 13: Cross-classified/imperfect hierarchies
  • Optional Quiz 15 (due noon Friday) (can replace earlier quiz)
  • Continue HW 7


 HW 7 (due Monday 8am)

Day 16: Longintudinal data cont.
  • Guest speaker
  • Slides (qmd) (handout) (anno)
To Do:
  • Day 16 Quiz (due 7am Wednesday)
    • On 3-level models, read discussion first
  • Optional Day 16 Quiz (due Dec. 1)
  • Start HW 8

 Day 17: Three-level models
  • Recap three-level models (slides) (qmd) (anno)
    • Check out the new graphs in the annotated version - why the random effects correlations changed sign!
  • Projects
To do:
  • Optional Day 17 quiz (due Dec. 1)
  • Finish HW 8

 HW 8 (due midnight Monday Dec 1)
Optional: "Fixed and random effects models: Making an informed choice" (2019) (pdf)

Optional: "Revisiting fixed- and random-effects models: Some considerations for policy-relevant education research" (2013) (Canvas)		 Day 18: Wrap-up
  • Case Study (anno) (ppt)
  • Guest speaker
  • HW 8
  • Projects
BC 		Day 19:
  • Project presentations
  • Final review (ppt)
    • handout
    • Review problems sols

To Do
  • Course evaluations!  
    • Cal Poly (due Friday midnight)
    • BC form

Final Exam - 7:10-10am

© 2025 Stat 414 course materials. Last updated Sep 29, 2025.