update.brmsfit: Update 'brms' models

In brms: Bayesian Regression Models using 'Stan'

Update brms models

Description

This method allows to update an existing brmsfit object.

Usage

## S3 method for class 'brmsfit'
update(object, formula., newdata = NULL, recompile = NULL, ...)

Arguments

object	An object of class brmsfit.
formula.	Changes to the formula; for details see update.formula and brmsformula.
newdata	Optional data.frame to update the model with new data. Data-dependent default priors will not be updated automatically.
recompile	Logical, indicating whether the Stan model should be recompiled. If NULL (the default), update tries to figure out internally, if recompilation is necessary. Setting it to FALSE will cause all Stan code changing arguments to be ignored.
...	Other arguments passed to brm.

Details

When updating a brmsfit created with the cmdstanr backend in a different R session, a recompilation will be triggered because by default, cmdstanr writes the model executable to a temporary directory. To avoid that, set option "cmdstanr_write_stan_file_dir" to a nontemporary path of your choice before creating the original brmsfit (see section 'Examples' below).

Examples

## Not run: 
fit1 <- brm(time | cens(censored) ~ age * sex + disease + (1|patient),
            data = kidney, family = gaussian("log"))
summary(fit1)

## remove effects of 'disease'
fit2 <- update(fit1, formula. = ~ . - disease)
summary(fit2)

## remove the group specific term of 'patient' and
## change the data (just take a subset in this example)
fit3 <- update(fit1, formula. = ~ . - (1|patient),
               newdata = kidney[1:38, ])
summary(fit3)

## use another family and add population-level priors
fit4 <- update(fit1, family = weibull(), init = "0",
               prior = set_prior("normal(0,5)"))
summary(fit4)

## to avoid a recompilation when updating a 'cmdstanr'-backend fit in a fresh
## R session, set option 'cmdstanr_write_stan_file_dir' before creating the
## initial 'brmsfit'
## CAUTION: the following code creates some files in the current working
## directory: two 'model_<hash>.stan' files, one 'model_<hash>(.exe)'
## executable, and one 'fit_cmdstanr_<some_number>.rds' file
set.seed(7)
fname <- paste0("fit_cmdstanr_", sample.int(.Machine$integer.max, 1))
options(cmdstanr_write_stan_file_dir = getwd())
fit_cmdstanr <- brm(rate ~ conc + state,
                    data = Puromycin,
                    backend = "cmdstanr",
                    file = fname)
# now restart the R session and run the following (after attaching 'brms')
set.seed(7)
fname <- paste0("fit_cmdstanr_", sample.int(.Machine$integer.max, 1))
fit_cmdstanr <- brm(rate ~ conc + state,
                    data = Puromycin,
                    backend = "cmdstanr",
                    file = fname)
upd_cmdstanr <- update(fit_cmdstanr,
                       formula. = rate ~ conc)

## End(Not run)

brms documentation built on Sept. 23, 2024, 5:08 p.m.