Fit a Bayesian measurement model using brms as a backend interface to Stan.
Usage
bmm(
formula,
data,
model,
prior = NULL,
sort_data = getOption("bmm.sort_data", "check"),
silent = getOption("bmm.silent", 1),
backend = getOption("brms.backend", NULL),
...
)
fit_model(
formula,
data,
model,
prior = NULL,
sort_data = getOption("bmm.sort_data", "check"),
silent = getOption("bmm.silent", 1),
backend = getOption("brms.backend", NULL),
...
)
Arguments
- formula
An object of class
bmmformula
. A symbolic description of the model to be fitted.- data
An object of class data.frame, containing data of all variables used in the model. The names of the variables must match the variable names passed to the
bmmodel
object for required argurments.- model
A description of the model to be fitted. This is a call to a
bmmodel
such asmixture3p()
function. Every model function has a number of required arguments which need to be specified within the function call. Callsupported_models()
to see the list of supported models and their required arguments- prior
One or more
brmsprior
objects created bybrms::set_prior()
or related functions and combined using the c method or the + operator. See alsodefault_prior()
for more help. Not necessary for the default model fitting, but you can provide prior constraints to model parameters- sort_data
Logical. If TRUE, the data will be sorted by the predictor variables for faster sampling. If FALSE, the data will not be sorted, but sampling will be slower. If "check" (the default),
bmm()
will check if the data is sorted, and ask you via a console prompt if it should be sorted. You can set the default value for this option using globaloptions(bmm.sort_data = TRUE/FALSE/"check)
)or via
bmm_options(sort_data)`- silent
Verbosity level between 0 and 2. If 1 (the default), most of the informational messages of compiler and sampler are suppressed. If 2, even more messages are suppressed. The actual sampling progress is still printed. Set refresh = 0 to turn this off as well. If using backend = "rstan" you can also set open_progress = FALSE to prevent opening additional progress bars.
- backend
Character. The backend to use for fitting the model. Can be "rstan" or "cmdstanr". If NULL (the default), "cmdstanr" will be used if the cmdstanr package is installed, otherwise "rstan" will be used. You can set the default backend using global
options(brms.backend = "rstan"/"cmdstanr")
- ...
Further arguments passed to
brms::brm()
or Stan. See the description ofbrms::brm()
for more details
Value
An object of class brmsfit which contains the posterior draws along with many other useful information about the model. Use methods(class = "brmsfit") for an overview on available methods.
Supported Models
The following models are supported:
imm(resp_error, nt_features, nt_distances, set_size, regex, links, version)
mixture2p(resp_error, links)
mixture3p(resp_error, nt_features, set_size, regex, links)
sdm(resp_error, links, version)
Type ?modelname to get information about a specific model, e.g. ?imm
bmmformula syntax
see vignette("bmm_bmmformula", package = "bmm")
for a detailed description of the syntax and how
it differs from the syntax for brmsformula
Default priors, Stan code and Stan data
For more information about the default priors in bmm and about who to extract the Stan code and data generated by bmm and #' brms, see vignette("bmm_extract_info", package = "bmm")
.
Miscellaneous
Type help(package=bmm)
for a full list of available help topics.
fit_model() is a deprecated alias for bmm().
References
Frischkorn, G. T., & Popov, V. (2023). A tutorial for estimating mixture models for visual working memory tasks in brms: Introducing the Bayesian Measurement Modeling (bmm) package for R. https://doi.org/10.31234/osf.io/umt57
Examples
if (FALSE) {
# generate artificial data from the Signal Discrimination Model
dat <- data.frame(y = rsdm(2000))
# define formula
ff <- bmmformula(c ~ 1, kappa ~ 1)
# fit the model
fit <- bmm(formula = ff,
data = dat,
model = sdm(resp_error = "y"),
cores = 4,
backend = 'cmdstanr')
}