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# Mixed Effects Models - Level-2 Variables

Lecture 8 from my mixed-effects modeling course: Level-2 variables

Lecture 8 from my mixed-effects modeling course: Level-2 variables

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### Mixed Effects Models - Level-2 Variables

1. 1. Week 5.1: Level-2 Variables ! Notation ! Multiple Random Effects ! Combining Datasets in R ! Modeling ! Level-2 Variables ! Including Level-2 Variables in R ! Modeling Consequences ! Cross-Level Interactions ! Lab
2. 2. Recap • Last week, we created a model of middle schoolers’ math performance that included a random intercept for Classroom • model1 <- lmer(FinalMathScore ~ 1 + TOI + (1|Classroom), data=math) Fixed effect of naive theory of intelligence Average intercept (averaged all classrooms) Variance in that intercept from one class to the next Residual (unexplained) variance at the child level
3. 3. Notation • What is this model doing mathematically? • Let’s go back to our model of individual students (now slightly different): Student Error Ei(j) = End-of-year math exam score + + Baseline Yi(j) B0j Fixed mindset γ10x1i(j)
4. 4. Notation • What is this model doing mathematically? • Let’s go back to our model of individual students (now slightly different): Student Error Ei(j) = End-of-year math exam score + + Baseline Yi(j) B0j Fixed mindset γ10x1i(j) What now determines the baseline that we should expect for students with fixed mindset=0?
5. 5. Notation • What is this model doing mathematically? • Baseline (intercept) for a student in classroom j now depends on two things: • Let’s go back to our model of individual students (now slightly different): Student Error Ei(j) = End-of-year math exam score + + Baseline Yi(j) B0j Fixed mindset γ10x1i(j) U0j = Intercept + Overall intercept across everyone B0j γ00 Teacher effect for this classroom (Error)
6. 6. Notation • Essentially, we have two regression models • Hierarchical linear model • Model of classroom j: • Model of student i: Student Error Ei(j) = End-of-year math exam score + + Baseline Yi(j) B0j Fixed mindset γ10x1i(j) U0j = Intercept + B0j γ00 Teacher effect for this classroom (Error) LEVEL-1 MODEL (Student) LEVEL-2 MODEL (Classroom) Overall intercept across everyone
7. 7. Hierarchical Linear Model Student 1 Student 2 Student 3 Student 4 Level-1 model: Sampled STUDENTS Mr. Wagner’s Class Ms. Fulton’s Class Ms. Green’s Class Ms. Cornell’s Class Level-2 model: Sampled CLASSROOMS • Level-2 model is for the superordinate level here, Level-1 model is for the subordinate level Variance of classroom intercept is the error variance at Level 2 Residual is the error variance at Level 1
8. 8. Notation • Two models seems confusing. But we can simplify with some algebra… • Model of classroom j: • Model of student i: Student Error Ei(j) = End-of-year math exam score + + Baseline Yi(j) B0j Fixed mindset γ10x1i(j) U0j = Intercept + B0j γ00 Teacher effect for this classroom (Error) LEVEL-1 MODEL (Student) LEVEL-2 MODEL (Classroom) Overall intercept across everyone
9. 9. Notation • Substitution gives us a single model that combines level-1 and level-2 • Mixed effects model • Combined model: Student Error Ei(j) = End-of-year math exam score + + Yi(j) Fixed mindset γ10x1i(j) U0j + Overall intercept γ00 Teacher effect for this classroom (Error)
10. 10. Notation • Just two slightly different ways of writing the same thing. Notation difference, not statistical! • Mixed effects model: • Hierarchical linear model: Ei(j) = + + Yi(j) γ10x1i(j) U0j + γ00 Ei(j) = Yi(j) B0j γ10x1i(j) U0j = + B0j γ00 + +
11. 11. Notation • lme4 always uses the mixed-effects model notation • lmer( FinalMathScore ~ 1 + TOI + (1|Classroom) ) • (Level-1 error is always implied, don’t have to include) Student Error Ei(j) = End-of-year math exam score + + Yi(j) Fixed mindset γ10x1i(j) U0j + Overall intercept γ00 Teacher effect for this class (Error)
12. 12. Week 5.1: Level-2 Variables ! Notation ! Multiple Random Effects ! Combining Datasets in R ! Modeling ! Level-2 Variables ! Including Level-2 Variables in R ! Modeling Consequences ! Cross-Level Interactions ! Lab
13. 13. ! We’re continuing our study of naïve theories of intelligence & math performance ! We’ve now collected data at three different schools ! math1.csv from Jefferson Middle School ! math2.csv from Highland Middle School ! math3.csv from Hoover Middle School Combining Datasets in R
14. 14. Combining Datasets in R ! Look at the math1, math2, math3 dataframes ! How are they similar? How are they different? ! TOI and final math score for each student
15. 15. Combining Datasets in R ! Look at the math1, math2, math3 dataframes ! How are they similar? How are they different? ! TOI and final math score for each student Columns not always in same order
16. 16. Combining Datasets in R ! Look at the math1, math2, math3 dataframes ! How are they similar? How are they different? ! TOI and final math score for each student Only Hoover has GPA reported
17. 17. Combining Datasets in R ! Overall, this is similar information, so let’s combine it all ! Paste together the rows from two (or more) dataframes to create a new one: ! bind_rows(math1, math2, math3) -> math ! Useful when observations are spread across files ! Or, to create a dataframe that combines 2 filtered dataframes math1 math2 math3 math
18. 18. bind_rows(): Results ! Resulting dataframe: ! nrow(math) is 720 – all three combined math1 math2 math3 math
19. 19. ! Resulting dataframe: ! bind_rows() is smart! ! Not a problem that column order varies across dataframes ! Looks at the column names ! Not a problem that GPA column only existed in one of the original dataframes ! NA (missing data) for the students at the other schools bind_rows(): Results
20. 20. bind_rows(): Results ! Resulting dataframe: ! You can also add the optional .id argument ! bind_rows(math1, math2, math3, .id='OriginalDataframe’) -> math ! Adds another column that tracks which of the original dataframes (by number) each observation came from
21. 21. Other, Similar Functions ! bind_rows() pastes together every row from every dataframe, even if there are duplicates ! If you want to skip duplicates, use union() ! Same syntax as bind_rows(), just different function name ! Other related functions: ! intersect(): Keep only the rows that appear in all of the source dataframes ! setdiff(): Keep only the rows that appear in a single source dataframe—if duplicates, delete both copies
22. 22. Week 5.1: Level-2 Variables ! Notation ! Multiple Random Effects ! Combining Datasets in R ! Modeling ! Level-2 Variables ! Including Level-2 Variables in R ! Modeling Consequences ! Cross-Level Interactions ! Lab
23. 23. Multiple Random Effects • Schools could differ in math achievement—let’s add School to the model to control for that • Is SCHOOL a fixed effect or a random effect? • These schools are just a sample of possible schools of interest " Random effect. School 1 School 2 Sampled SCHOOLS Sampled CLASSROOMS Sampled STUDENTS LEVEL 3 LEVEL 2 LEVEL 1 Student 1 Student 2 Student 3 Student 4 Mr. Wagner’s Class Ms. Fulton’s Class Ms. Green’s Class Ms. Cornell’s Class
24. 24. Multiple Random Effects • No problem to have more than 1 random effect in the model! Let’s a random intercept for School. School 1 School 2 Sampled SCHOOLS Sampled CLASSROOMS Sampled STUDENTS LEVEL 3 LEVEL 2 LEVEL 1 Student 1 Student 2 Student 3 Student 4 Mr. Wagner’s Class Ms. Fulton’s Class Ms. Green’s Class Ms. Cornell’s Class
25. 25. Multiple Random Effects • model2 <- lmer(FinalMathScore ~ 1 + TOI + (1|Classroom) + (1|School), data=math) School 1 School 2 Sampled SCHOOLS Sampled CLASSROOMS Sampled STUDENTS LEVEL 3 LEVEL 2 LEVEL 1 Student 1 Student 2 Student 3 Student 4 Mr. Wagner’s Class Ms. Fulton’s Class Ms. Green’s Class Ms. Cornell’s Class
26. 26. Multiple Random Effects • model2 <- lmer(FinalMathScore ~ 1 + TOI + (1|Classroom) + (1|School), data=math) • Less variability across schools than classrooms in a school
27. 27. Multiple Random Effects • This is an example of nested random effects. • Each classroom is always in the same school. • We’ll look at crossed random effects next week School 1 School 2 Sampled SCHOOLS Sampled CLASSROOMS Sampled STUDENTS LEVEL 3 LEVEL 2 LEVEL 1 Student 1 Student 2 Student 3 Student 4 Mr. Wagner’s Class Ms. Fulton’s Class Ms. Green’s Class Ms. Cornell’s Class
28. 28. Week 5.1: Level-2 Variables ! Notation ! Multiple Random Effects ! Combining Datasets in R ! Modeling ! Level-2 Variables ! Including Level-2 Variables in R ! Modeling Consequences ! Cross-Level Interactions ! Lab
29. 29. Level-2 Variables • So far, all our model says about classrooms is that they’re different • Some classrooms have a large intercept • Some classrooms have a small intercept • But, we might also have some interesting variables that characterize classrooms • They might even be our main research interest! • How about teacher theories of intelligence? • Might affect how they interact with & teach students
30. 30. Level-2 Variables Student 1 Student 2 Student 3 Student 4 Sampled STUDENTS Mr. Wagner’s Class Ms. Fulton’s Class Ms. Green’s Class Ms. Cornell’s Class Sampled CLASSROOMS • TeacherTheory characterizes Level 2 • All students in the same classroom will experience the same TeacherTheory LEVEL 2 LEVEL 1 TeacherTheory TOI
31. 31. Level-2 Variables • Is TeacherTheory a fixed effect or random effect? • Teacher mindset is a fixed-effect variable • We ARE interested in the effects of teacher mindset on student math achievement … a research question, not just something to control for • Even if we ran this with a new random sample of 30 teachers, we WOULD hope to replicate whatever regression slope for teacher mindset we observe (whereas we wouldn’t get the same 30 teachers back)
32. 32. Level-2 Variables • This becomes another variable in the level-2 model of classroom differences • Tells us what we can expect this classroom to be like Student Error Ei(j) = End-of-year math exam score + + Baseline Yi(j) B0j Growth mindset γ10x1i(j) U0j = Intercept + Overall intercept B0j γ00 Teacher effect for this classroom (Error) LEVEL-1 MODEL (Student) LEVEL-2 MODEL (Classroom) Teacher mindset + γ20x20j
33. 33. Level-2 Variables • Since R uses mixed effects notation, we don’t have to do anything special to add a level-2 variable to the model • model3 <- lmer(FinalMathScore ~ 1 + TOI + TeacherTheory + (1|Classroom) + (1|School), data=math) • R automatically figures out TeacherTheory is a level-2 variable because it’s invariant for each classroom • We keep the random intercept for Classroom because we don’t expect TeacherTheory will explain all of the classroom differences. Intercept captures residual differences.
34. 34. Week 5.1: Level-2 Variables ! Notation ! Multiple Random Effects ! Combining Datasets in R ! Modeling ! Level-2 Variables ! Including Level-2 Variables in R ! Modeling Consequences ! Cross-Level Interactions ! Lab
35. 35. What Changes? What Doesn’t? • Random classroom & school variance is reduced. • Teacher theories of intelligence accounts for some of the variance among classrooms (and among the schools those classrooms are in). • TeacherTheory explains some of the “Class j” effect we’re substituting into the level 1 equation. No longer just a random intercept. WITHOUT TEACHERTHEORY WITH TEACHERTHEORY
36. 36. What Changes? What Doesn’t? • Residual error at level 1 essentially unchanged. • Describes how students vary from the class average • Divergence from the class average cannot be explained by teacher • Regardless of what explains the “Class j” effect, you’re still substituting it into the same Lv 1 model WITHOUT TEACHERTHEORY WITH TEACHERTHEORY
37. 37. What Changes? What Doesn’t? • Similarly, our level-1 fixed effect is essentially unchanged • Explaining where level-2 variation comes from does not change our level-1 model • Note that average student TOI and TeacherTheory are very slightly correlated (due to random chance); otherwise, there’d be no change. WITHOUT TEACHERTHEORY WITH TEACHERTHEORY
38. 38. Week 5.1: Level-2 Variables ! Notation ! Multiple Random Effects ! Combining Datasets in R ! Modeling ! Level-2 Variables ! Including Level-2 Variables in R ! Modeling Consequences ! Cross-Level Interactions ! Lab
39. 39. Cross-Level Interactions • Because R uses mixed effects notation, it’s also very easy to add interactions between level-1 and level-2 variables • model4 <- lmer(FinalMathScore ~ 1 + TOI + TeacherTheory + TOI:TeacherTheory + (1|Classroom) + (1|School), data=math) • Does the effect of a student’s theory of intelligence depend on what the teacher’s theory is? • e.g., maybe matching theories is beneficial
40. 40. Cross-Level Interactions • Because R uses mixed effects notation, it’s also very easy to add interactions between level-1 and level-2 variables • In this case, the interaction is not significant
41. 41. Week 5.1: Level-2 Variables ! Notation ! Multiple Random Effects ! Combining Datasets in R ! Modeling ! Level-2 Variables ! Including Level-2 Variables in R ! Modeling Consequences ! Cross-Level Interactions ! Lab