Computes log marginal likelihood via bridge sampling.
bridge_sampler(samples, ...)# S3 method for stanfit
bridge_sampler(
samples = NULL,
stanfit_model = samples,
repetitions = 1,
method = "normal",
cores = 1,
use_neff = TRUE,
maxiter = 1000,
silent = FALSE,
verbose = FALSE,
...
)
# S3 method for mcmc.list
bridge_sampler(
samples = NULL,
log_posterior = NULL,
...,
data = NULL,
lb = NULL,
ub = NULL,
repetitions = 1,
param_types = rep("real", ncol(samples[[1]])),
method = "normal",
cores = 1,
use_neff = TRUE,
packages = NULL,
varlist = NULL,
envir = .GlobalEnv,
rcppFile = NULL,
maxiter = 1000,
silent = FALSE,
verbose = FALSE
)
# S3 method for mcmc
bridge_sampler(
samples = NULL,
log_posterior = NULL,
...,
data = NULL,
lb = NULL,
ub = NULL,
repetitions = 1,
method = "normal",
cores = 1,
use_neff = TRUE,
packages = NULL,
varlist = NULL,
envir = .GlobalEnv,
rcppFile = NULL,
maxiter = 1000,
param_types = rep("real", ncol(samples)),
silent = FALSE,
verbose = FALSE
)
# S3 method for matrix
bridge_sampler(
samples = NULL,
log_posterior = NULL,
...,
data = NULL,
lb = NULL,
ub = NULL,
repetitions = 1,
method = "normal",
cores = 1,
use_neff = TRUE,
packages = NULL,
varlist = NULL,
envir = .GlobalEnv,
rcppFile = NULL,
maxiter = 1000,
param_types = rep("real", ncol(samples)),
silent = FALSE,
verbose = FALSE
)
# S3 method for stanreg
bridge_sampler(
samples,
repetitions = 1,
method = "normal",
cores = 1,
use_neff = TRUE,
maxiter = 1000,
silent = FALSE,
verbose = FALSE,
...
)
# S3 method for rjags
bridge_sampler(
samples = NULL,
log_posterior = NULL,
...,
data = NULL,
lb = NULL,
ub = NULL,
repetitions = 1,
method = "normal",
cores = 1,
use_neff = TRUE,
packages = NULL,
varlist = NULL,
envir = .GlobalEnv,
rcppFile = NULL,
maxiter = 1000,
silent = FALSE,
verbose = FALSE
)
# S3 method for runjags
bridge_sampler(
samples = NULL,
log_posterior = NULL,
...,
data = NULL,
lb = NULL,
ub = NULL,
repetitions = 1,
method = "normal",
cores = 1,
use_neff = TRUE,
packages = NULL,
varlist = NULL,
envir = .GlobalEnv,
rcppFile = NULL,
maxiter = 1000,
silent = FALSE,
verbose = FALSE
)
# S3 method for MCMC_refClass
bridge_sampler(
samples,
repetitions = 1,
method = "normal",
cores = 1,
use_neff = TRUE,
maxiter = 1000,
silent = FALSE,
verbose = FALSE,
...
)
an mcmc.list object, a fitted stanfit object, a
stanreg object, an rjags object, a runjags object, or a
matrix with posterior samples (colnames need to correspond to
parameter names in lb and ub) with posterior samples.
additional arguments passed to log_posterior. Ignored for
the stanfit and stanreg methods.
for the stanfit method, an additional object of
class "stanfit" with the same model as samples, which will be
used for evaluating the log_posterior (i.e., it does not need to
contain any samples). The default is to use samples. In case
samples was compiled in a different R session or on another computer
with a different OS or setup, the samples model usually cannot be
used for evaluation. In this case, one can compile the model on the current
computer with iter = 0 and pass it here (this usually needs to be
done before samples is loaded).
number of repetitions.
either "normal" or "warp3".
number of cores used for evaluating log_posterior. On
unix-like systems (where .Platform$OS.type == "unix" evaluates to
TRUE; e.g., Linux and Mac OS) forking via mclapply is
used. Hence elements needed for evaluation should be in the
.GlobalEnv. For other systems (e.g., Windows)
makeCluster is used and further arguments specified below will
be used.
Boolean which determines whether the effective sample size is
used in the optimal bridge function. Default is TRUE. If FALSE, the number
of samples is used instead. If samples is a matrix, it is
assumed that the matrix contains the samples of one chain in order.
If samples come from more than one chain, we recommend to use an
mcmc.list object for optimal performance.
maximum number of iterations for the iterative updating scheme. Default is 1,000 to avoid infinite loops.
Boolean which determines whether to print the number of iterations of the updating scheme to the console. Default is FALSE.
Boolean. Should internal debug information be printed to
console? Default is FALSE.
function or name of function that takes a parameter
vector and the data as input and returns the log of the unnormalized
posterior density (i.e., a scalar value). If the function name is passed,
the function should exist in the .GlobalEnv. For special behavior if
cores > 1 see Details.
data object which is used in log_posterior.
named vector with lower bounds for parameters.
named vector with upper bounds for parameters.
character vector of length ncol(samples) with
"real", "simplex" or "circular". For all regular
bounded or unbounded continuous parameters, this should just be
"real". However, if there are parameters which lie on a simplex or on
the circle, this should be noted here. Simplex parameters are parameters
which are bounded below by zero and collectively sum to one, such as weights
in a mixture model. For these, the stick-breaking transformation is
performed as described in the Stan reference manual. The circular variables
are given a numerical representation to which the normal distribution is
most likely a good fit. Only possible to use with
bridge_sampler.matrix.
character vector with names of packages needed for evaluating
log_posterior in parallel (only relevant if cores > 1 and
.Platform$OS.type != "unix").
character vector with names of variables needed for evaluating
log_posterior (only needed if cores > 1 and
.Platform$OS.type != "unix" as these objects will be exported to the
nodes). These objects need to exist in envir.
specifies the environment for varlist (only needed if
cores > 1 and .Platform$OS.type != "unix" as these objects
will be exported to the nodes). Default is .GlobalEnv.
in case cores > 1 and log_posterior is an
Rcpp function, rcppFile specifies the path to the cpp file
(will be compiled on all cores).
if repetitions = 1, returns a list of class "bridge"
with components:
logml: estimate of log marginal
likelihood.
niter: number of iterations of the iterative
updating scheme.
method: bridge sampling method that was used
to obtain the estimate.
q11: log posterior evaluations for
posterior samples.
q12: log proposal evaluations for posterior
samples.
q21: log posterior evaluations for samples from
proposal.
q22: log proposal evaluations for samples from
proposal.
if repetitions > 1, returns a list of class
"bridge_list" with components:
logml: numeric
vector with estimates of log marginal likelihood.
niter:
numeric vector with number of iterations of the iterative updating scheme
for each repetition.
method: bridge sampling method that was
used to obtain the estimates.
repetitions: number of
repetitions.
Note that the results depend strongly on the parameter priors. Therefore, it is strongly advised to think carefully about the priors before calculating marginal likelihoods. For example, the prior choices implemented in rstanarm or brms might not be optimal from a testing point of view. We recommend to use priors that have been chosen from a testing and not a purely estimation perspective.
Also note that for testing, the number of posterior samples usually needs to be substantially larger than for estimation.
Bridge sampling is implemented as described in Meng and Wong (1996,
see equation 4.1) using the "optimal" bridge function. When method =
"normal", the proposal distribution is a multivariate normal distribution
with mean vector equal to the sample mean vector of samples and
covariance matrix equal to the sample covariance matrix of samples.
For a recent tutorial on bridge sampling, see Gronau et al. (in press).
When method = "warp3", the proposal distribution is a standard
multivariate normal distribution and the posterior distribution is "warped"
(Meng & Schilling, 2002) so that it has the same mean vector, covariance
matrix, and skew as the samples. method = "warp3" takes approximately
twice as long as method = "normal".
Note that for the matrix method, the lower and upper bound of a
parameter cannot be a function of the bounds of another parameter.
Furthermore, constraints that depend on multiple parameters of the model are
not supported. This usually excludes, for example, parameters that
constitute a covariance matrix or sets of parameters that need to sum to
one.
However, if the retransformations are part of the model itself and the
log_posterior accepts parameters on the real line and performs the
appropriate Jacobian adjustments, such as done for stanfit and
stanreg objects, such constraints are obviously possible (i.e., we
currently do not know of any parameter supported within Stan that does not
work with the current implementation through a stanfit object).
mclapply. Hence elements needed for evaluation of
log_posterior should be in the .GlobalEnv.On other OSes (e.g., Windows), things can get more complicated. For normal
parallel computation, the log_posterior function can be passed as
both function and function name. If the latter, it needs to exist in the
environment specified in the envir argument. For parallel computation
when using an Rcpp function, log_posterior can only be passed
as the function name (i.e., character). This function needs to result from
calling sourceCpp on the file specified in rcppFile.
Due to the way rstan currently works, parallel computations with
stanfit and stanreg objects only work with forking (i.e., NOT
on Windows).
Gronau, Q. F., Singmann, H., & Wagenmakers, E.-J. (2020). bridgesampling: An R Package for Estimating Normalizing Constants. Journal of Statistical Software, 92. 10.18637/jss.v092.i10
Gronau, Q. F., Sarafoglou, A., Matzke, D., Ly, A., Boehm, U.,
Marsman, M., Leslie, D. S., Forster, J. J., Wagenmakers, E.-J., &
Steingroever, H. (in press). A tutorial on bridge sampling. Journal of
Mathematical Psychology. https://arxiv.org/abs/1703.05984
vignette("bridgesampling_tutorial")
Gronau, Q. F., Wagenmakers, E.-J., Heck, D. W., & Matzke, D. (2017). A simple method for comparing complex models: Bayesian model comparison for hierarchical multinomial processing tree models using Warp-III bridge sampling. Manuscript submitted for publication. https://psyarxiv.com/yxhfm
Meng, X.-L., & Wong, W. H. (1996). Simulating ratios of normalizing constants via a simple identity: A theoretical exploration. Statistica Sinica, 6, 831-860. http://www3.stat.sinica.edu.tw/statistica/j6n4/j6n43/j6n43.htm
Meng, X.-L., & Schilling, S. (2002). Warp bridge sampling. Journal of Computational and Graphical Statistics, 11(3), 552-586. 10.1198/106186002457
Overstall, A. M., & Forster, J. J. (2010). Default Bayesian model determination methods for generalised linear mixed models. Computational Statistics & Data Analysis, 54, 3269-3288. 10.1016/j.csda.2010.03.008
bf allows the user to calculate Bayes factors and
post_prob allows the user to calculate posterior model
probabilities from bridge sampling estimates. bridge-methods
lists some additional methods that automatically invoke the
error_measures function.
# NOT RUN {
## ------------------------------------------------------------------------
## Example 1: Estimating the Normalizing Constant of a Two-Dimensional
## Standard Normal Distribution
## ------------------------------------------------------------------------
library(bridgesampling)
library(mvtnorm)
samples <- rmvnorm(1e4, mean = rep(0, 2), sigma = diag(2))
colnames(samples) <- c("x1", "x2")
log_density <- function(samples.row, data) {
-.5*t(samples.row) %*% samples.row
}
lb <- rep(-Inf, 2)
ub <- rep(Inf, 2)
names(lb) <- names(ub) <- colnames(samples)
bridge_result <- bridge_sampler(samples = samples, log_posterior = log_density,
data = NULL, lb = lb, ub = ub, silent = TRUE)
# compare to analytical value
analytical <- log(2*pi)
print(cbind(bridge_result$logml, analytical))
# }
# NOT RUN {
## ------------------------------------------------------------------------
## Example 2: Hierarchical Normal Model
## ------------------------------------------------------------------------
# for a full description of the example, see
vignette("bridgesampling_example_jags")
library(R2jags)
### generate data ###
set.seed(12345)
mu <- 0
tau2 <- 0.5
sigma2 <- 1
n <- 20
theta <- rnorm(n, mu, sqrt(tau2))
y <- rnorm(n, theta, sqrt(sigma2))
### set prior parameters
alpha <- 1
beta <- 1
mu0 <- 0
tau20 <- 1
### functions to get posterior samples ###
### H0: mu = 0
getSamplesModelH0 <- function(data, niter = 52000, nburnin = 2000, nchains = 3) {
model <- "
model {
for (i in 1:n) {
theta[i] ~ dnorm(0, invTau2)
y[i] ~ dnorm(theta[i], 1/sigma2)
}
invTau2 ~ dgamma(alpha, beta)
tau2 <- 1/invTau2
}"
s <- jags(data, parameters.to.save = c("theta", "invTau2"),
model.file = textConnection(model),
n.chains = nchains, n.iter = niter,
n.burnin = nburnin, n.thin = 1)
return(s)
}
### H1: mu != 0
getSamplesModelH1 <- function(data, niter = 52000, nburnin = 2000,
nchains = 3) {
model <- "
model {
for (i in 1:n) {
theta[i] ~ dnorm(mu, invTau2)
y[i] ~ dnorm(theta[i], 1/sigma2)
}
mu ~ dnorm(mu0, 1/tau20)
invTau2 ~ dgamma(alpha, beta)
tau2 <- 1/invTau2
}"
s <- jags(data, parameters.to.save = c("theta", "mu", "invTau2"),
model.file = textConnection(model),
n.chains = nchains, n.iter = niter,
n.burnin = nburnin, n.thin = 1)
return(s)
}
### get posterior samples ###
# create data lists for Jags
data_H0 <- list(y = y, n = length(y), alpha = alpha, beta = beta, sigma2 = sigma2)
data_H1 <- list(y = y, n = length(y), mu0 = mu0, tau20 = tau20, alpha = alpha,
beta = beta, sigma2 = sigma2)
# fit models
samples_H0 <- getSamplesModelH0(data_H0)
samples_H1 <- getSamplesModelH1(data_H1)
### functions for evaluating the unnormalized posteriors on log scale ###
log_posterior_H0 <- function(samples.row, data) {
mu <- 0
invTau2 <- samples.row[[ "invTau2" ]]
theta <- samples.row[ paste0("theta[", seq_along(data$y), "]") ]
sum(dnorm(data$y, theta, data$sigma2, log = TRUE)) +
sum(dnorm(theta, mu, 1/sqrt(invTau2), log = TRUE)) +
dgamma(invTau2, data$alpha, data$beta, log = TRUE)
}
log_posterior_H1 <- function(samples.row, data) {
mu <- samples.row[[ "mu" ]]
invTau2 <- samples.row[[ "invTau2" ]]
theta <- samples.row[ paste0("theta[", seq_along(data$y), "]") ]
sum(dnorm(data$y, theta, data$sigma2, log = TRUE)) +
sum(dnorm(theta, mu, 1/sqrt(invTau2), log = TRUE)) +
dnorm(mu, data$mu0, sqrt(data$tau20), log = TRUE) +
dgamma(invTau2, data$alpha, data$beta, log = TRUE)
}
# specify parameter bounds H0
cn <- colnames(samples_H0$BUGSoutput$sims.matrix)
cn <- cn[cn != "deviance"]
lb_H0 <- rep(-Inf, length(cn))
ub_H0 <- rep(Inf, length(cn))
names(lb_H0) <- names(ub_H0) <- cn
lb_H0[[ "invTau2" ]] <- 0
# specify parameter bounds H1
cn <- colnames(samples_H1$BUGSoutput$sims.matrix)
cn <- cn[cn != "deviance"]
lb_H1 <- rep(-Inf, length(cn))
ub_H1 <- rep(Inf, length(cn))
names(lb_H1) <- names(ub_H1) <- cn
lb_H1[[ "invTau2" ]] <- 0
# compute log marginal likelihood via bridge sampling for H0
H0.bridge <- bridge_sampler(samples = samples_H0, data = data_H0,
log_posterior = log_posterior_H0, lb = lb_H0,
ub = ub_H0, silent = TRUE)
print(H0.bridge)
# compute log marginal likelihood via bridge sampling for H1
H1.bridge <- bridge_sampler(samples = samples_H1, data = data_H1,
log_posterior = log_posterior_H1, lb = lb_H1,
ub = ub_H1, silent = TRUE)
print(H1.bridge)
# compute percentage error
print(error_measures(H0.bridge)$percentage)
print(error_measures(H1.bridge)$percentage)
# compute Bayes factor
BF01 <- bf(H0.bridge, H1.bridge)
print(BF01)
# compute posterior model probabilities (assuming equal prior model probabilities)
post1 <- post_prob(H0.bridge, H1.bridge)
print(post1)
# compute posterior model probabilities (using user-specified prior model probabilities)
post2 <- post_prob(H0.bridge, H1.bridge, prior_prob = c(.6, .4))
print(post2)
# }
# NOT RUN {
# }
# NOT RUN {
## ------------------------------------------------------------------------
## Example 3: rstanarm
## ------------------------------------------------------------------------
library(rstanarm)
# N.B.: remember to specify the diagnostic_file
fit_1 <- stan_glm(mpg ~ wt + qsec + am, data = mtcars,
chains = 2, cores = 2, iter = 5000,
diagnostic_file = file.path(tempdir(), "df.csv"))
bridge_1 <- bridge_sampler(fit_1)
fit_2 <- update(fit_1, formula = . ~ . + cyl)
bridge_2 <- bridge_sampler(fit_2, method = "warp3")
bf(bridge_1, bridge_2)
# }
# NOT RUN {
# }
Run the code above in your browser using DataLab