The goal of yodel is to provide a general framework to do baYesian mODEL averaging. Models are fit separately and model weights are then calculated based on the log posterior predictive density of the observed data. See Ando & Tsay (2010) and Gould (2019) for references.
We will begin by doing Bayesian model averaging of some simple linear regression. We will generate data, and the analyze it separately with a linear and quadratic Bayesian model.
library(rjags)
#> Loading required package: coda
#> Linked to JAGS 4.3.0
#> Loaded modules: basemod,bugs
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
linear_jags <- "
model {
for(i in 1:n) {
y[i] ~ dnorm(b1 + b2 * z[i], tau2)
y_log_density[i] <- log(dnorm(y[i], b1 + b2 * z[i], tau2))
}
b1 ~ dnorm(0, .001)
b2 ~ dnorm(0, .001)
tau2 ~ dgamma(1, .001)
}
"
quad_jags <- "
model {
for(i in 1:n) {
y[i] ~ dnorm(b1 + b2 * z[i]+ b3 * z[i] * z[i], tau2)
y_log_density[i] <- log(dnorm(y[i], b1 + b2 * z[i] + b3 * z[i] * z[i], tau2))
}
b1 ~ dnorm(0, .001)
b2 ~ dnorm(0, .001)
b3 ~ dnorm(0, .001)
tau2 ~ dgamma(1, .001)
}
"
set.seed(85)
n <- 100
z <- runif(n, 0, 10)
b1 <- 2
b2 <- 1.5
b3 <- .01
y <- b1 + b2 * z + b3 * z ^ 2 + rnorm(n, 0, .75)
jags_data <- list(z = z, y = y, n = n)
jmod_linear <- jags.model(
file = textConnection(linear_jags),
data = jags_data,
n.chains = 2
)
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 100
#> Unobserved stochastic nodes: 3
#> Total graph size: 607
#>
#> Initializing model
samples_linear <- coda.samples(
jmod_linear,
variable.names = c("b1", "b2", "tau2", "y_log_density"),
n.iter = 1e3
)
jmod_quad <- jags.model(
file = textConnection(quad_jags),
data = jags_data,
n.chains = 2
)
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 100
#> Unobserved stochastic nodes: 4
#> Total graph size: 708
#>
#> Initializing model
samples_quad <- coda.samples(
jmod_quad,
variable.names = c("b1", "b2", "b3", "tau2", "y_log_density"),
n.iter = 1e3
)To calculate the posterior weight of each model, we need to calculate the log-likelihood of each observation for each iteration of the MCMC. The jags code above already calculated it (“y_log_density”), so we’ll put it into a matrix form. We also want the MCMC samples in a dataframe/tibble.
mcmc_linear <- as_tibble(as.matrix(samples_linear))
log_post_pred_linear <- mcmc_linear %>%
dplyr::select(contains("y_log_density")) %>%
as.matrix()
mcmc_quad <- as_tibble(as.matrix(samples_quad))
log_post_pred_quad <- mcmc_quad %>%
dplyr::select(contains("y_log_density")) %>%
as.matrix()To calculate the Bayesian model averaging of a quantity of interest (in our case, the mean at a particular value of z), we need to define functions which calculate the mean at a given value of z for each iteration of the MCMC. The functions for calculating a posterior quantity of interest must take the MCMC samples as the first argument, and output a dataframe with a column named “iter” which identifies the MCMC iteration. There is no restriction on the number of rows or columns of the output of the function, which provides flexibility for a number of modeling scenarios. There is also no restriction on the number of arguments, so long as the first argument is the MCMC samples.
linear_fun <- function(mcmc, z) {
data.frame(
iter = 1:nrow(mcmc),
z = z,
mean = mcmc$b1 + mcmc$b2 * z
)
}
quad_fun <- function(mcmc, z) {
data.frame(
iter = 1:nrow(mcmc),
z = z,
mean = mcmc$b1 + mcmc$b2 * z + mcmc$b3 * z ^ 2
)
}The following code calculates the posterior weights for each model.
Note that the mcmc and fun arguments are
optional if weights are all that are desired. If obtaining posterior
samples for a quantity of interest are wanted (using the
posterior() function), then then these arguments must be
specified.
library(yodel)
bma_fit <- bma(
linear = model_bma_predictive(
log_post_pred = log_post_pred_linear,
adjustment = - 3 / 2,
w_prior = .5,
mcmc = mcmc_linear,
fun = linear_fun
),
quad = model_bma_predictive(
log_post_pred = log_post_pred_quad,
adjustment = - 4 / 2,
w_prior = .5,
mcmc = mcmc_quad,
fun = quad_fun
)
)The bma() function returns the prior weights, posterior
weights, models (lists from model_bma()) and a model index
of which model is to be used on which iteration.
names(bma_fit)
#> [1] "w_prior" "w_post" "models" "seed"
bma_fit$w_prior
#> linear quad
#> 0.5 0.5
bma_fit$w_post
#> linear quad
#> 0.2886865 0.7113135The posterior() function will provide posterior samples
for a quantity of interest. In our case, this is the posterior mean at a
particular value of z. The posterior function takes the output from
bma() as well as other arguments which are needed for the
calculation (specified in the fun arguments of
model_bma()).
The output provides the estimated mean for each iteration of the MCMC, and also specified which model the estimate came from.
bma_fit$w_post
#> linear quad
#> 0.2886865 0.7113135
post <- posterior(bma_fit, z = 5)
head(post)
#> iter z mean model
#> 1 1 5 12.377548 quad
#> 2 2 5 11.643794 quad
#> 3 3 5 10.602492 quad
#> 4 4 5 9.961733 quad
#> 5 5 5 9.805239 quad
#> 6 6 5 10.051760 linearOnce posterior samples are obtained, the user can then calculate statistics of interest, e.g., the posterior mean and credible intervals.
post %>%
group_by(z) %>%
summarize(
lb = quantile(mean, .025),
ub = quantile(mean, .975),
mean = mean(mean),
.groups = "drop"
)
#> # A tibble: 1 × 4
#> z lb ub mean
#> <dbl> <dbl> <dbl> <dbl>
#> 1 5 9.38 9.89 9.66install.packages("yodel")Ando, T., & Tsay, R. (2010). Predictive likelihood for Bayesian model selection and averaging. International Journal of Forecasting, 26(4), 744-763.
Gould, A. L. (2019). BMA‐Mod: A Bayesian model averaging strategy for determining dose‐response relationships in the presence of model uncertainty. Biometrical Journal, 61(5), 1141-1159.