Statistical Rethinking 2022 Lecture 13

Course materials: https://github.com/rmcelreath/stat_rethinking_2022

Transcript

1. Statistical Rethinking 13: Multi-Multilevel Models 2022
3. complete pooling partial pooling no pooling S i ∼ Binomial(D i , p i ) logit(p i ) = α T[i] ¯ α ∼ Normal(0,1.5) α j ∼ Normal( ¯ α, σ) σ ∼ Exponential(1) 200 400 600 sigma PSIS score 0.1 0.15 0.23 0.34 0.52 0.78 1.18 1.79 2.7 4.07
4. Practical Difficulties Varying effects are a good default, but… (1) How to use more than one cluster type at the same time? For example stories and participants (2) How to calculate predictions (3) How to sample chains efficiently 2 4 6 8 10 12 1 2 3 4 5 6 7 Story Response 0 10 20 30 40 50 1 2 3 4 5 6 7 Participant Response
5. Clusters & features Clusters: Kinds of groups in the data Features: Aspects of the model (parameters) that vary by cluster 2 4 6 8 10 12 1 2 3 4 5 6 7 Story Response 0 10 20 30 40 50 1 2 3 4 5 6 7 Participant Response Cluster
 tanks
 stories
 individuals
 departments Features
 survival
 treatment effect
 average response
 admission rate, bias
6. 2 4 6 8 10 12 1 2 3 4 5 6 7 Story Response 0 10 20 30 40 50 1 2 3 4 5 6 7 Participant Response Add clusters: More index variables, more population priors (this lecture) Add features: More parameters, more dimensions in each population prior (next lecture) Cluster
 tanks
 stories
 individuals
 departments Features
 survival
 treatment effect
 average response
 admission rate, bias
7. focal actor right lever left lever food empty
8. partner food food food empty to actor to partner “prosocial option”
9.  #*/0. Prosocial chimpanzees data(chimpanzees) 504 trials, 7 actors, 6 blocks 4 treatments: (1) right, no partner
 (2) left, no partner
 (3) right, partner
 (4) left, partner
10. Prosocial chimpanzees data(chimpanzees) 504 trials, 7 actors, 6 blocks 4 treatments: (1) right, no partner
 (2) left, no partner
 (3) right, partner
 (4) left, partner P T A B block actor pulled left side condition
11. Prosocial chimpanzees P i ∼ Bernoulli(p i ) logit(p i ) = β T[i],B[i] + α A[i] block actor treatment pulled left P T A B block actor pulled left side condition
12. Prosocial chimpanzees P T A B block actor pulled left side condition P i ∼ Bernoulli(p i ) logit(p i ) = β T[i],B[i] + α A[i]
13. Prosocial chimpanzees Probability of left lever P i ∼ Bernoulli(p i ) log-odds of left lever logit(p i ) = β T[i],B[i] + α A[i]
14. Prosocial chimpanzees Probability of left lever P i ∼ Bernoulli(p i ) α j ∼ Normal( ¯ α, σ A ) log-odds of left lever Prior for actor effects (handedness) logit(p i ) = β T[i],B[i] + α A[i]
15. Prosocial chimpanzees Probability of left lever P i ∼ Bernoulli(p i ) α j ∼ Normal( ¯ α, σ A ) log-odds of left lever Prior treatment/block effects Prior for actor effects (handedness) logit(p i ) = β T[i],B[i] + α A[i] β j,k ∼ Normal(0,σ B )
16. Prosocial chimpanzees Probability of left lever P i ∼ Bernoulli(p i ) α j ∼ Normal( ¯ α, σ A ) σ A , σ B ∼ Exponential(1) log-odds of left lever Prior treatment/block effects Prior for actor effects (handedness) Prior for “variance components” logit(p i ) = β T[i],B[i] + α A[i] β j,k ∼ Normal(0,σ B )
17. Pooling treatment effects?! Why is it reasonable to partially pool treatment effects? Because treatments are not completely different Because there are many possible treatments, you used a few Because it results in better estimates If parameters get the same prior, usually better to learn the prior from the sample β j,k ∼ Normal(0,σ B )
18. data(chimpanzees) d <- chimpanzees d$treatment <- 1 + d$prosoc_left + 2*d$condition dat <- list( P = d$pulled_left, A = d$actor, B = d$block, T = d$treatment ) # block interactions mBT <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- b[T,B] + a[A], ## adaptive priors matrix[T,B]:b ~ dnorm( 0 , sigma_B ), a[A] ~ dnorm( a_bar , sigma_A ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1) ) , data=dat , chains=4 , cores=4 ) > precis(mBT,3) mean sd 5.5% 94.5% n_eff Rhat4 b[1,1] -0.23 0.37 -0.85 0.34 1301 1.00 b[1,2] -0.01 0.34 -0.56 0.51 2716 1.00 b[1,3] 0.32 0.36 -0.22 0.92 919 1.00 b[1,4] 0.11 0.35 -0.44 0.68 1790 1.00 b[1,5] -0.36 0.37 -0.98 0.17 922 1.00 b[1,6] -0.24 0.35 -0.85 0.28 1327 1.01 b[2,1] 0.09 0.35 -0.44 0.67 2071 1.00 b[2,2] -0.01 0.36 -0.58 0.56 1689 1.00 b[2,3] -0.12 0.34 -0.69 0.41 1738 1.00 b[2,4] 0.32 0.38 -0.21 0.98 1120 1.00 b[2,5] 0.20 0.35 -0.32 0.79 1769 1.00 b[2,6] 0.67 0.45 0.02 1.42 333 1.01 b[3,1] -0.36 0.38 -1.01 0.17 735 1.00 b[3,2] -0.03 0.36 -0.61 0.53 2061 1.00 b[3,3] -0.21 0.35 -0.79 0.33 1464 1.00 b[3,4] -0.46 0.38 -1.11 0.06 527 1.01 b[3,5] 0.03 0.37 -0.53 0.62 2478 1.00 b[3,6] -0.34 0.37 -0.99 0.19 883 1.00 b[4,1] -0.37 0.40 -1.06 0.20 873 1.01 b[4,2] 0.28 0.36 -0.24 0.88 1205 1.00 b[4,3] 0.27 0.35 -0.24 0.86 1105 1.00 b[4,4] 0.08 0.37 -0.49 0.68 1828 1.00 b[4,5] 0.06 0.34 -0.48 0.60 2025 1.00 b[4,6] 0.45 0.41 -0.13 1.17 597 1.01 a[1] -0.35 0.27 -0.78 0.09 1408 1.00 a[2] 4.70 1.25 3.09 7.01 1214 1.00 a[3] -0.62 0.27 -1.08 -0.20 1481 1.00 a[4] -0.64 0.27 -1.07 -0.20 1424 1.00 a[5] -0.36 0.27 -0.78 0.06 1237 1.00 a[6] 0.60 0.26 0.18 1.04 1654 1.00 a[7] 2.15 0.39 1.56 2.82 1436 1.00 a_bar 0.62 0.69 -0.47 1.71 1635 1.00 sigma_A 2.02 0.66 1.17 3.17 1482 1.00 sigma_B 0.46 0.18 0.18 0.74 198 1.02
19. data(chimpanzees) d <- chimpanzees d$treatment <- 1 + d$prosoc_left + 2*d$condition dat <- list( P = d$pulled_left, A = d$actor, B = d$block, T = d$treatment ) # block interactions mBT <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- b[T,B] + a[A], ## adaptive priors matrix[T,B]:b ~ dnorm( 0 , sigma_B ), a[A] ~ dnorm( a_bar , sigma_A ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1) ) , data=dat , chains=4 , cores=4 ) > precis(mBT,3) mean sd 5.5% 94.5% n_eff Rhat4 b[1,1] -0.23 0.37 -0.85 0.34 1301 1.00 b[1,2] -0.01 0.34 -0.56 0.51 2716 1.00 b[1,3] 0.32 0.36 -0.22 0.92 919 1.00 b[1,4] 0.11 0.35 -0.44 0.68 1790 1.00 b[1,5] -0.36 0.37 -0.98 0.17 922 1.00 b[1,6] -0.24 0.35 -0.85 0.28 1327 1.01 b[2,1] 0.09 0.35 -0.44 0.67 2071 1.00 b[2,2] -0.01 0.36 -0.58 0.56 1689 1.00 b[2,3] -0.12 0.34 -0.69 0.41 1738 1.00 b[2,4] 0.32 0.38 -0.21 0.98 1120 1.00 b[2,5] 0.20 0.35 -0.32 0.79 1769 1.00 b[2,6] 0.67 0.45 0.02 1.42 333 1.01 b[3,1] -0.36 0.38 -1.01 0.17 735 1.00 b[3,2] -0.03 0.36 -0.61 0.53 2061 1.00 b[3,3] -0.21 0.35 -0.79 0.33 1464 1.00 b[3,4] -0.46 0.38 -1.11 0.06 527 1.01 b[3,5] 0.03 0.37 -0.53 0.62 2478 1.00 b[3,6] -0.34 0.37 -0.99 0.19 883 1.00 b[4,1] -0.37 0.40 -1.06 0.20 873 1.01 b[4,2] 0.28 0.36 -0.24 0.88 1205 1.00 b[4,3] 0.27 0.35 -0.24 0.86 1105 1.00 b[4,4] 0.08 0.37 -0.49 0.68 1828 1.00 b[4,5] 0.06 0.34 -0.48 0.60 2025 1.00 b[4,6] 0.45 0.41 -0.13 1.17 597 1.01 a[1] -0.35 0.27 -0.78 0.09 1408 1.00 a[2] 4.70 1.25 3.09 7.01 1214 1.00 a[3] -0.62 0.27 -1.08 -0.20 1481 1.00 a[4] -0.64 0.27 -1.07 -0.20 1424 1.00 a[5] -0.36 0.27 -0.78 0.06 1237 1.00 a[6] 0.60 0.26 0.18 1.04 1654 1.00 a[7] 2.15 0.39 1.56 2.82 1436 1.00 a_bar 0.62 0.69 -0.47 1.71 1635 1.00 sigma_A 2.02 0.66 1.17 3.17 1482 1.00 sigma_B 0.46 0.18 0.18 0.74 198 1.02 n_eff = 198 sigma_B b[2,6]
20. -2 -1 0 1 2 treatment log-odds R/N L/N R/P L/P treatment/block effects actor effects 0.0 0.2 0.4 0.6 0.8 1.0 actor probability pull left 1 2 3 4 5 6 7
21. -2 -1 0 1 2 treatment log-odds R/N L/N R/P L/P 0 1 2 3 4 5 0.0 0.4 0.8 sigma_A Density 0 1 2 3 4 5 0.0 1.5 sigma_B Density 0.0 0.2 0.4 0.6 0.8 1.0 actor probability pull left 1 2 3 4 5 6 7 actor variation treatment/block variation
22. Variance does not add! In linear models, variance components are additive Total variation in outcome is sum of the components Not true for generalized linear models Link function breaks additivity Variation in one component moderates variation in the others 0 1 2 3 4 5 0.0 0.4 0.8 sigma_A Density 0 1 2 3 4 5 0.0 1.5 sigma_B Density actor variation treatment/block variation
23. Multilevel predictions & effects How to compute predictions and interventions (causal effects)? Predict for same groups: Use varying effect estimates for each group Predict for new groups: Ignore varying effect estimates, marginalize over population distribution 0 1 2 3 4 5 0.0 0.4 0.8 sigma_A Density 0 1 2 3 4 5 0.0 1.5 sigma_B Density actor variation treatment/block variation
24. New groups Reedfrog intervention Target population 50% predation, 25% large tadpoles What is causal effect of increasing size to 75% large? library(rethinking) data(reedfrogs) d <- reedfrogs dat <- list( S = d$surv, D = d$density, T = 1:nrow(d), P = ifelse(d$pred=="no",1L,2L), G = ifelse(d$size=="small",1L,2L) ) mSPG <- ulam( alist( S ~ binomial( D , p ), logit(p) <- a[T] + b[P,G], a[T] ~ normal( 0 , sigma ), matrix[P,G]:b ~ normal( 0 , 1 ), sigma ~ exponential( 1 ) ), data=dat , chains=4 , cores=4 )
25. post <- extract.samples(mSPG) # sim under status quo n_groups <- 1000 n_samples <- 2000 S1 <- matrix(0,nrow=n_samples,ncol=n_groups) for ( s in 1:n_groups ) { # sim a tank from posterior population aT <- rnorm(n_samples,0,post$sigma) # sample P and G for this group P <- sample( 1:2 , size=1 , prob=c(0.5,0.5) ) # 50% pred G <- sample( 1:2 , size=1 , prob=c(0.75,0.25) ) # 25% large # sim survival p <- inv_logit( aT + post$b[,P,G] ) S1[,s] <- rbinom(2000,35,p) }
26. post <- extract.samples(mSPG) # sim under status quo n_groups <- 1000 n_samples <- 2000 S1 <- matrix(0,nrow=n_samples,ncol=n_groups) for ( s in 1:n_groups ) { # sim a tank from posterior population aT <- rnorm(n_samples,0,post$sigma) # sample P and G for this group P <- sample( 1:2 , size=1 , prob=c(0.5,0.5) ) # 50% pred G <- sample( 1:2 , size=1 , prob=c(0.75,0.25) ) # 25% large # sim survival p <- inv_logit( aT + post$b[,P,G] ) S1[,s] <- rbinom(2000,35,p) }
27. post <- extract.samples(mSPG) # sim under status quo n_groups <- 1000 n_samples <- 2000 S1 <- matrix(0,nrow=n_samples,ncol=n_groups) for ( s in 1:n_groups ) { # sim a tank from posterior population aT <- rnorm(n_samples,0,post$sigma) # sample P and G for this group P <- sample( 1:2 , size=1 , prob=c(0.5,0.5) ) # 50% pred G <- sample( 1:2 , size=1 , prob=c(0.75,0.25) ) # 25% large # sim survival p <- inv_logit( aT + post$b[,P,G] ) S1[,s] <- rbinom(2000,35,p) }
28. post <- extract.samples(mSPG) # sim under status quo n_groups <- 1000 n_samples <- 2000 S1 <- matrix(0,nrow=n_samples,ncol=n_groups) for ( s in 1:n_groups ) { # sim a tank from posterior population aT <- rnorm(n_samples,0,post$sigma) # sample P and G for this group P <- sample( 1:2 , size=1 , prob=c(0.5,0.5) ) # 50% pred G <- sample( 1:2 , size=1 , prob=c(0.75,0.25) ) # 25% large # sim survival p <- inv_logit( aT + post$b[,P,G] ) S1[,s] <- rbinom(2000,35,p) }
29. post <- extract.samples(mSPG) # sim under status quo n_groups <- 1000 n_samples <- 2000 S1 <- matrix(0,nrow=n_samples,ncol=n_groups) for ( s in 1:n_groups ) { # sim a tank from posterior population aT <- rnorm(n_samples,0,post$sigma) # sample P and G for this group P <- sample( 1:2 , size=1 , prob=c(0.5,0.5) ) # 50% pred G <- sample( 1:2 , size=1 , prob=c(0.75,0.25) ) # 25% large # sim survival p <- inv_logit( aT + post$b[,P,G] ) S1[,s] <- rbinom(2000,35,p) } 0 50000 100000 150000 number surviving Frequency 0 3 6 9 13 18 23 28 33 Reedfrog status quo
30. # intervention - 50% large S2 <- matrix(0,nrow=n_samples,ncol=n_groups) for ( s in 1:n_groups ) { # sim a tank from posterior population aT <- rnorm(n_samples,0,post$sigma) # sample P and G for this group P <- sample( 1:2 , size=1 , prob=c(0.5,0.5) ) # 50% pred G <- sample( 1:2 , size=1 , prob=c(0.25,0.75) ) # 75% large # sim survival p <- inv_logit( aT + post$b[,P,G] ) S2[,s] <- rbinom(n_samples,35,p) } 0 50000 100000 150000 number surviving Frequency 0 3 6 9 13 18 23 28 33 Reedfrog intervention
31. less survival more survival -30 -20 -10 0 10 20 30 0.00 0.01 0.02 0.03 0.04 change in survival proportion of simulation
32. Multilevel predictions Group variation moderates causal effects Averaging over group variation means simulating groups (or using estimates from observed groups as appropriate) If you have a generative model, you can simulate interventions for new targets 0 50000 100000 150000 number surviving Frequency 0 3 6 9 13 18 23 28 33 0 50000 100000 150000 number surviving Frequency 0 3 6 9 13 18 23 28 33
33. PAUSE
34. v ∼ Normal(0,0.5) x ∼ Normal(0, exp(v))
35. v ∼ Normal(0,_) x ∼ Normal(0, exp(v))
36. v ∼ Normal(0,3) x ∼ Normal(0, exp(v)) divergent transitions
37. Divergent transitions Why? Same step size not optimal everywhere High curvature = simulation cannot follow surface What can we do? (1) use a smaller step size (2) reparameterize! v ∼ Normal(0,3) x ∼ Normal(0, exp(v))
38. v ∼ Normal(0,3) x ∼ Normal(0, exp(v)) Small step size Small step size helps, but makes exploration slow
39. v ∼ Normal(0,3) x ∼ Normal(0, exp(v)) “Centered”
40. v ∼ Normal(0,3) z ∼ Normal(0,1) x = z exp(v) v ∼ Normal(0,3) x ∼ Normal(0, exp(v)) “Centered” “Non-centered”
41. v ∼ Normal(0,3) z ∼ Normal(0,1) x = z exp(v)
42. m13.7 <- ulam( alist( v ~ normal(0,3), x ~ normal(0,exp(v)) ), data=list(N=1) , chains=4 ) m13.7nc <- ulam( alist( v ~ normal(0,3), z ~ normal(0,1), gq> real[1]:x <<- z*exp(v) ), data=list(N=1) , chains=4 )
43. m13.7 <- ulam( alist( v ~ normal(0,3), x ~ normal(0,exp(v)) ), data=list(N=1) , chains=4 ) m13.7nc <- ulam( alist( v ~ normal(0,3), z ~ normal(0,1), gq> real[1]:x <<- z*exp(v) ), data=list(N=1) , chains=4 ) Warning: 112 of 2000 (6.0%) transitions ended with a divergence. > precis( m13.7 ) mean sd 5.5% 94.5% n_eff Rhat4 v 1.41 2.37 -1.84 5.93 7 1.46 x 35.93 168.42 -21.15 258.86 30 1.19 > precis( m13.7nc ) mean sd 5.5% 94.5% n_eff Rhat4 v -0.04 3.12 -5.17 4.84 1380 1 z -0.01 0.96 -1.60 1.51 1495 1 x -19.34 899.98 -30.81 24.86 1874 1
44. 0 200 400 600 800 1000 -5 0 5 10 n_eff = 7 v 0 200 400 600 800 1000 -1000 0 500 n_eff = 30 x
45. 0 200 400 600 800 1000 -10 -5 0 5 10 n_eff = 1380 v 0 200 400 600 800 1000 -3 -2 -1 0 1 2 3 n_eff = 1495 z 0 200 400 600 800 1000 -20000 0 10000 n_eff = 1874 x 0 200 400 600 800 1000 -5 0 5 10 n_eff = 7 v 0 200 400 600 800 1000 -1000 0 500 n_eff = 30 x
46. Non-centered varying effects S i ∼ Binomial(D i , p i ) α j ∼ Normal( ¯ α, σ) σ ∼ Exponential(1) logit(p i ) = α T[i] “Centered” ¯ α ∼ Normal(0,1.5)
47. Non-centered varying effects S i ∼ Binomial(D i , p i ) α j ∼ Normal( ¯ α, σ) logit(p i ) = α T[i] logit(p i ) = ¯ α + z T[i] × σ z j ∼ Normal(0,1) S i ∼ Binomial(D i , p i ) “Centered” “Non-centered” σ ∼ Exponential(1) ¯ α ∼ Normal(0,1.5) σ ∼ Exponential(1) ¯ α ∼ Normal(0,1.5)
48. Non-centered varying effects S i ∼ Binomial(D i , p i ) α j ∼ Normal( ¯ α, σ) logit(p i ) = α T[i] logit(p i ) = ¯ α + z T[i] × σ z j ∼ Normal(0,1) S i ∼ Binomial(D i , p i ) “Centered” “Non-centered” σ ∼ Exponential(1) ¯ α ∼ Normal(0,1.5) σ ∼ Exponential(1) ¯ α ∼ Normal(0,1.5)
49. Non-centered chimpanzees P i ∼ Bernoulli(p i ) α j ∼ Normal( ¯ α, σ A ) σ A , σ B ∼ Exponential(1) logit(p i ) = β T[i],B[i] + α A[i] β j,k ∼ Normal(0,σ B ) ¯ α ∼ Normal(0,1.5) “Centered”
50. Non-centered chimpanzees P i ∼ Bernoulli(p i ) α j ∼ Normal( ¯ α, σ A ) σ A , σ B ∼ Exponential(1) logit(p i ) = β T[i],B[i] + α A[i] β j,k ∼ Normal(0,σ B ) P i ∼ Bernoulli(p i ) logit(p i ) = ¯ α + (z α,A[i] )σ A + (z β,T[i],B[i] )σ B z α,j ∼ Normal(0,1) z β,j ∼ Normal(0,1) σ A , σ B ∼ Exponential(1) ¯ α ∼ Normal(0,1.5) ¯ α ∼ Normal(0,1.5) “Centered” “Non-centered”
51. Non-centered chimpanzees P i ∼ Bernoulli(p i ) α j ∼ Normal( ¯ α, σ A ) σ A , σ B ∼ Exponential(1) logit(p i ) = β T[i],B[i] + α A[i] β j,k ∼ Normal(0,σ B ) P i ∼ Bernoulli(p i ) logit(p i ) = ¯ α + (z α,A[i] )σ A + (z β,T[i],B[i] )σ B z α,j ∼ Normal(0,1) z β,j ∼ Normal(0,1) σ A , σ B ∼ Exponential(1) ¯ α ∼ Normal(0,1.5) ¯ α ∼ Normal(0,1.5) “Centered” “Non-centered”
52. Non-centered chimpanzees P i ∼ Bernoulli(p i ) α j ∼ Normal( ¯ α, σ A ) σ A , σ B ∼ Exponential(1) logit(p i ) = β T[i],B[i] + α A[i] β j,k ∼ Normal(0,σ B ) P i ∼ Bernoulli(p i ) logit(p i ) = ¯ α + (z α,A[i] )σ A + (z β,T[i],B[i] )σ B z α,j ∼ Normal(0,1) z β,j ∼ Normal(0,1) σ A , σ B ∼ Exponential(1) ¯ α ∼ Normal(0,1.5) ¯ α ∼ Normal(0,1.5) “Centered” “Non-centered”
53. mBT <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- b[T,B] + a[A], ## adaptive priors matrix[T,B]:b ~ dnorm( 0 , sigma_B ), a[A] ~ dnorm( a_bar , sigma_A ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1) ) , data=dat , chains=4 , cores=4 ) mBTnc <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- a_bar + z_a[A]*sigma_A + z_b[T,B]*sigma_B , ## adaptive priors matrix[T,B]:z_b ~ dnorm( 0 , 1 ), z_a[A] ~ dnorm( 0 , 1 ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1), gq> vector[A]:a <<- a_bar + z_a*sigma_A, gq> matrix[T,B]:b <<- z_b*sigma_B ) , data=dat , chains=4 , cores=4 ) P i ∼ Bernoulli(p i ) logit(p i ) = ¯ α + (z α,A[i] )σ A + (z β,T[i],B[i] )σ B z α,j ∼ Normal(0,1) z β,j ∼ Normal(0,1) σ A , σ B ∼ Exponential(1) ¯ α ∼ Normal(0,1.5)
54. mBT <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- b[T,B] + a[A], ## adaptive priors matrix[T,B]:b ~ dnorm( 0 , sigma_B ), a[A] ~ dnorm( a_bar , sigma_A ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1) ) , data=dat , chains=4 , cores=4 ) mBTnc <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- a_bar + z_a[A]*sigma_A + z_b[T,B]*sigma_B , ## adaptive priors matrix[T,B]:z_b ~ dnorm( 0 , 1 ), z_a[A] ~ dnorm( 0 , 1 ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1), gq> vector[A]:a <<- a_bar + z_a*sigma_A, gq> matrix[T,B]:b <<- z_b*sigma_B ) , data=dat , chains=4 , cores=4 ) P i ∼ Bernoulli(p i ) logit(p i ) = ¯ α + (z α,A[i] )σ A + (z β,T[i],B[i] )σ B z α,j ∼ Normal(0,1) z β,j ∼ Normal(0,1) σ A , σ B ∼ Exponential(1) ¯ α ∼ Normal(0,1.5)
55. mBT <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- b[T,B] + a[A], ## adaptive priors matrix[T,B]:b ~ dnorm( 0 , sigma_B ), a[A] ~ dnorm( a_bar , sigma_A ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1) ) , data=dat , chains=4 , cores=4 ) mBTnc <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- a_bar + z_a[A]*sigma_A + z_b[T,B]*sigma_B , ## adaptive priors matrix[T,B]:z_b ~ dnorm( 0 , 1 ), z_a[A] ~ dnorm( 0 , 1 ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1), gq> vector[A]:a <<- a_bar + z_a*sigma_A, gq> matrix[T,B]:b <<- z_b*sigma_B ) , data=dat , chains=4 , cores=4 ) P i ∼ Bernoulli(p i ) logit(p i ) = ¯ α + (z α,A[i] )σ A + (z β,T[i],B[i] )σ B z α,j ∼ Normal(0,1) z β,j ∼ Normal(0,1) σ A , σ B ∼ Exponential(1) ¯ α ∼ Normal(0,1.5)
56. mBT <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- b[T,B] + a[A], ## adaptive priors matrix[T,B]:b ~ dnorm( 0 , sigma_B ), a[A] ~ dnorm( a_bar , sigma_A ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1) ) , data=dat , chains=4 , cores=4 ) mBTnc <- ulam( alist( P ~ bernoulli( p ) , logit(p) <- a_bar + z_a[A]*sigma_A + z_b[T,B]*sigma_B , ## adaptive priors matrix[T,B]:z_b ~ dnorm( 0 , 1 ), z_a[A] ~ dnorm( 0 , 1 ), ## hyper-priors a_bar ~ dnorm( 0 , 1.5 ), sigma_A ~ dexp(1), sigma_B ~ dexp(1), gq> vector[A]:a <<- a_bar + z_a*sigma_A, gq> matrix[T,B]:b <<- z_b*sigma_B ) , data=dat , chains=4 , cores=4 ) P i ∼ Bernoulli(p i ) logit(p i ) = ¯ α + (z α,A[i] )σ A + (z β,T[i],B[i] )σ B z α,j ∼ Normal(0,1) z β,j ∼ Normal(0,1) σ A , σ B ∼ Exponential(1) ¯ α ∼ Normal(0,1.5)
57. non-centered better centered better n_eff = 672 sigma_A n_eff = 716 sigma_B 500 1500 2500 500 1500 2500 effective sample size (centered) effective sample size (non-centered)
58. Practical Solutions Research problems = technical problems (1) Use more than one cluster type (2) Calculate predictions (3) Sample chains efficiently Practice leads to mastery
59. Course Schedule Week 1 Bayesian inference Chapters 1, 2, 3 Week 2 Linear models & Causal Inference Chapter 4 Week 3 Causes, Confounds & Colliders Chapters 5 & 6 Week 4 Overfitting / MCMC Chapters 7, 8, 9 Week 5 Generalized Linear Models Chapters 10, 11 Week 6 Ordered categories & Multilevel models Chapters 12 & 13 Week 7 More Multilevel models Chapters 13 & 14 Week 8 Multilevel models & Gaussian processes Chapter 14 Week 9 Measurement & Missingness Chapter 15 Week 10 Generalized Linear Madness Chapter 16 https://github.com/rmcelreath/stat_rethinking_2022