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DataCamp Bayesian Modeling with RJAGS BAYESIAN MODELING WITH RJAGS A simple Bayesian regression model Alicia Johnson Associate Professor, Macalester College DataCamp Bayesian Modeling with RJAGS Chapter 3 goals Engineer a simple Bayesian

  1. DataCamp Bayesian Modeling with RJAGS BAYESIAN MODELING WITH RJAGS A simple Bayesian regression model Alicia Johnson Associate Professor, Macalester College

  2. DataCamp Bayesian Modeling with RJAGS Chapter 3 goals Engineer a simple Bayesian regression model Define, compile, and simulate regression models in RJAGS Use Markov chain simulation output for posterior inference & prediction

  3. DataCamp Bayesian Modeling with RJAGS Modeling weight Y = weight of adult i (kg) i Model 2 Y ∼ N ( m , s ) i

  4. DataCamp Bayesian Modeling with RJAGS Modeling weight by height Y = weight of adult i (kg) i Model 2 Y ∼ N ( m , s ) i

  5. DataCamp Bayesian Modeling with RJAGS Modeling weight by height Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i

  6. DataCamp Bayesian Modeling with RJAGS Modeling weight by height Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i m = a + bX i i

  7. DataCamp Bayesian Modeling with RJAGS Modeling weight by height Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i m = a + bX i i

  8. DataCamp Bayesian Modeling with RJAGS Modeling weight by height Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i m = a + bX i i

  9. DataCamp Bayesian Modeling with RJAGS Modeling weight by height Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i m = a + bX i i

  10. DataCamp Bayesian Modeling with RJAGS Modeling weight by height Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i m = a + bX i i

  11. DataCamp Bayesian Modeling with RJAGS Bayesian regression model 2 Y ∼ N ( m , s ) i i m = a + bX i i a = y-intercept value of m when X = 0 i i b = slope rate of change in weight (kg) per 1 cm increase in height s = residual standard deviation individual deviation from trend m i

  12. DataCamp Bayesian Modeling with RJAGS Priors for the intercept & slope

  13. DataCamp Bayesian Modeling with RJAGS Priors for the intercept & slope

  14. DataCamp Bayesian Modeling with RJAGS Priors for the intercept & slope

  15. DataCamp Bayesian Modeling with RJAGS Prior for the residual standard deviation

  16. DataCamp Bayesian Modeling with RJAGS Prior for the residual standard deviation

  17. DataCamp Bayesian Modeling with RJAGS Bayesian regression model 2 Y ∼ N ( m , s ) i i m = a + bX i i 2 a ∼ N (0,200 ) 2 b ∼ N (1,0.5 ) s ∼ Unif (0,20)

  18. DataCamp Bayesian Modeling with RJAGS BAYESIAN MODELING WITH RJAGS Let's practice!

  19. DataCamp Bayesian Modeling with RJAGS BAYESIAN MODELING WITH RJAGS Bayesian regression in RJAGS Alicia Johnson Associate Professor, Macalester College

  20. DataCamp Bayesian Modeling with RJAGS Bayesian regression model Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i m = a + bX i i 2 a ∼ N (0,200 ) 2 b ∼ N (1,0.5 ) s ∼ Unif (0,20)

  21. DataCamp Bayesian Modeling with RJAGS Prior insight

  22. DataCamp Bayesian Modeling with RJAGS Insight from the observed weight & height data 2 Y ∼ N ( m , s ) i i m = a + bX i i > wt_mod <- lm(wgt ~ hgt, bdims) > coef(wt_mod) (Intercept) hgt -105.011254 1.017617 > summary(wt_mod)$sigma [1] 9.30804

  23. DataCamp Bayesian Modeling with RJAGS DEFINE the regression model weight_model <- "model{ # Likelihood model for Y[i] # Prior models for a, b, s }"

  24. DataCamp Bayesian Modeling with RJAGS DEFINE the regression model weight_model <- "model{ 2 Y ∼ N ( m , s ) for i from 1 to 507 i i # Likelihood model for Y[i] for(i in 1:length(Y)) { } # Prior models for a, b, s }"

  25. DataCamp Bayesian Modeling with RJAGS DEFINE the regression model weight_model <- "model{ 2 Y ∼ N ( m , s ) for i from 1 to 507 i i # Likelihood model for Y[i] for(i in 1:length(Y)) { Y[i] ~ dnorm(m[i], s^(-2)) } # Prior models for a, b, s }"

  26. DataCamp Bayesian Modeling with RJAGS DEFINE the regression model weight_model <- "model{ # Likelihood model for Y[i] 2 Y ∼ N ( m , s ) for i from 1 to 507 for(i in 1:length(Y)) { i i Y[i] ~ dnorm(m[i], s^(-2)) m = a + bX m[i] <- a + b * X[i] i i } NOTE: use " <- " not " ~ " # Prior models for a, b, s }"

  27. DataCamp Bayesian Modeling with RJAGS DEFINE the regression model weight_model <- "model{ # Likelihood model for Y[i] 2 Y ∼ N ( m , s ) for i from 1 to 507 for(i in 1:length(Y)) { i i Y[i] ~ dnorm(m[i], s^(-2)) m = a + bX m[i] <- a + b * X[i] i i } # Prior models for a, b, s 2 a ∼ N (0,200 ) a ~ dnorm(0, 200^(-2)) b ~ dnorm(1, 0.5^(-2)) 2 b ∼ N (1,0.5 ) s ~ dunif(0, 20) s ∼ Unif (0,20) }"

  28. DataCamp Bayesian Modeling with RJAGS COMPILE the regression model # COMPILE the model weight_jags <- jags.model(textConnection(weight_model), data = list(X = bdims$hgt, Y = bdims$wgt), inits = list(.RNG.name = "base::Wichmann-Hill", .RNG.seed = 2018)) > dim(bdims) [1] 507 25 > head(bdims$hgt) [1] 174.0 175.3 193.5 186.5 187.2 181.5 > head(bdims$wgt) [1] 65.6 71.8 80.7 72.6 78.8 74.8

  29. DataCamp Bayesian Modeling with RJAGS SIMULATE the regression model # COMPILE the model weight_jags <- jags.model(textConnection(weight_model), data = list(X = bdims$hgt, Y = bdims$wgt), inits = list(.RNG.name = "base::Wichmann-Hill", .RNG.seed = 2018)) # SIMULATE the posterior weight_sim <- coda.samples(model = weight_jags, variable.names = c("a", "b", "s"), n.iter = 10000)

  30. DataCamp Bayesian Modeling with RJAGS

  31. DataCamp Bayesian Modeling with RJAGS Addressing Markov chain instability Standardize the height predictor (subtract the mean and divide by the standard deviation). Increase chain length.

  32. DataCamp Bayesian Modeling with RJAGS

  33. DataCamp Bayesian Modeling with RJAGS Posterior insights

  34. DataCamp Bayesian Modeling with RJAGS BAYESIAN MODELING WITH RJAGS Let's practice!

  35. DataCamp Bayesian Modeling with RJAGS BAYESIAN MODELING WITH RJAGS Posterior estimation & inference Alicia Johnson Associate Professor, Macalester College

  36. DataCamp Bayesian Modeling with RJAGS Bayesian regression model Y = weight of adult i (kg) i X = height of adult i (cm) i Model 2 Y ∼ N ( m , s ) i i m = a + bX i i 2 a ∼ N (0,200 ) 2 b ∼ N (1,0.5 ) s ∼ Unif (0,20)

  37. DataCamp Bayesian Modeling with RJAGS Posterior point estimation

  38. DataCamp Bayesian Modeling with RJAGS Posterior point estimation

  39. DataCamp Bayesian Modeling with RJAGS Posterior point estimation > summary(weight_sim_big) 1. Empirical mean and standard deviation for each variable, plus standard error of the mean: Mean SD Naive SE Time-series SE a -104.038 7.85296 0.0248332 0.661515 b 1.012 0.04581 0.0001449 0.003849 s 9.331 0.29495 0.0009327 0.001216 2. Quantiles for each variable: 2.5% 25% 50% 75% 97.5% a -118.6843 -109.5171 -104.365 -99.036 -87.470 b 0.9152 0.9828 1.014 1.044 1.098 s 8.7764 9.1284 9.322 9.524 9.933 posterior mean of a ≈ -104.038 posterior mean of b ≈ 1.012

  40. DataCamp Bayesian Modeling with RJAGS Posterior point estimation Posterior mean trend: m = −104.038 + 1.012 X i i Markov chain output: > head(weight_chains) a b s [1,] -113.9029 1.072505 8.772007 [2,] -115.0644 1.077914 8.986393 [3,] -114.6958 1.077130 9.679812 [4,] -115.0568 1.072668 8.814403 [5,] -114.0782 1.071775 8.895299 [6,] -114.3271 1.069477 9.016185

  41. DataCamp Bayesian Modeling with RJAGS Posterior uncertainty Posterior mean trend: m = −104.038 + 1.012 X i i Markov chain output: > head(weight_chains) a b s [1,] -113.9029 1.072505 8.772007 [2,] -115.0644 1.077914 8.986393 [3,] -114.6958 1.077130 9.679812 [4,] -115.0568 1.072668 8.814403 [5,] -114.0782 1.071775 8.895299 [6,] -114.3271 1.069477 9.016185

  42. DataCamp Bayesian Modeling with RJAGS Posterior credible intervals

  43. DataCamp Bayesian Modeling with RJAGS Posterior credible intervals > summary(weight_sim_big) 1. Empirical mean and standard deviation for each variable, plus standard error of the mean: Mean SD Naive SE Time-series SE a -104.038 7.85296 0.0248332 0.661515 b 1.012 0.04581 0.0001449 0.003849 s 9.331 0.29495 0.0009327 0.001216 2. Quantiles for each variable: 2.5% 25% 50% 75% 97.5% a -118.6843 -109.5171 -104.365 -99.036 -87.470 b 0.9152 0.9828 1.014 1.044 1.098 s 8.7764 9.1284 9.322 9.524 9.933 95% posterior credible interval for a : (-118.6843, -87.470) 95% posterior credible interval for b : (0.9152, 1.098)

  44. DataCamp Bayesian Modeling with RJAGS Posterior credible intervals Interpretation In light of our priors & observed data, there's a 95% (posterior) chance that b is between 0.9152 & 1.098 kg/cm.

  45. DataCamp Bayesian Modeling with RJAGS Posterior probabilities > table(weight_chains$b > 1.1) FALSE TRUE 97835 2165 > mean(weight_chains$b > 1.1) [1] 0.02165 Interpretation: There's a 2.165% posterior chance that b exceeds 1.1 kg/cm.

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