Nothing
#' Update \pkg{brms} models
#'
#' This method allows to update an existing \code{brmsfit} object.
#'
#' @param object An object of class \code{brmsfit}.
#' @param formula. Changes to the formula; for details see
#' \code{\link{update.formula}} and \code{\link{brmsformula}}.
#' @param newdata Optional \code{data.frame} to update the model with new data.
#' Data-dependent default priors will not be updated automatically.
#' @param recompile Logical, indicating whether the Stan model should
#' be recompiled. If \code{NULL} (the default), \code{update} tries
#' to figure out internally, if recompilation is necessary.
#' Setting it to \code{FALSE} will cause all Stan code changing
#' arguments to be ignored.
#' @param ... Other arguments passed to \code{\link{brm}}.
#'
#' @details When updating a \code{brmsfit} created with the \pkg{cmdstanr}
#' backend in a different \R session, a recompilation will be triggered
#' because by default, \pkg{cmdstanr} writes the model executable to a
#' temporary directory. To avoid that, set option
#' \code{"cmdstanr_write_stan_file_dir"} to a nontemporary path of your choice
#' before creating the original \code{brmsfit} (see section 'Examples' below).
#'
#' @examples
#' \dontrun{
#' 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)
#' }
#'
#' @export
update.brmsfit <- function(object, formula., newdata = NULL,
recompile = NULL, ...) {
dots <- list(...)
testmode <- isTRUE(dots[["testmode"]])
dots$testmode <- NULL
if ("silent" %in% names(dots)) {
dots$silent <- validate_silent(dots$silent)
} else {
dots$silent <- object$stan_args$silent %||% 1L
}
silent <- dots$silent
object <- restructure(object)
if (isTRUE(object$version$brms < "2.0.0")) {
warning2("Updating models fitted with older versions of brms may fail.")
}
object$file <- NULL
if ("data" %in% names(dots)) {
# otherwise the data name cannot be found by substitute
stop2("Please use argument 'newdata' to update the data.")
}
if (!is.null(newdata)) {
dots$data <- newdata
data_name <- substitute_name(newdata)
} else {
dots$data <- object$data
data_name <- get_data_name(object$data)
}
if (missing(formula.) || is.null(formula.)) {
dots$formula <- object$formula
if (!is.null(dots[["family"]])) {
dots$formula <- bf(dots$formula, family = dots$family)
}
if (!is.null(dots[["autocor"]])) {
dots$formula <- bf(dots$formula, autocor = dots$autocor)
}
} else {
# TODO: restructure updating of the model formula
if (is.mvbrmsformula(formula.) || is.mvbrmsformula(object$formula)) {
stop2("Updating formulas of multivariate models is not yet possible.")
}
if (is.brmsformula(formula.)) {
nl <- get_nl(formula.)
} else {
formula. <- as.formula(formula.)
nl <- get_nl(formula(object))
}
family <- get_arg("family", formula., dots, object)
autocor <- get_arg("autocor", formula., dots, object)
dots$formula <- bf(formula., family = family, autocor = autocor, nl = nl)
if (is_nonlinear(object)) {
if (length(setdiff(all.vars(dots$formula$formula), ".")) == 0L) {
dots$formula <- update(object$formula, dots$formula, mode = "keep")
} else {
dots$formula <- update(object$formula, dots$formula, mode = "replace")
if (silent < 2) {
message("Argument 'formula.' will completely replace the ",
"original formula in non-linear models.")
}
}
} else {
mvars <- all.vars(dots$formula$formula)
mvars <- setdiff(mvars, c(names(object$data), "."))
if (length(mvars) && is.null(newdata)) {
stop2("New variables found: ", collapse_comma(mvars),
"\nPlease supply your data again via argument 'newdata'.")
}
dots$formula <- update(formula(object), dots$formula)
}
}
# update response categories and ordinal thresholds
dots$formula <- validate_formula(dots$formula, data = dots$data)
if (is.null(dots$prior)) {
dots$prior <- object$prior
} else {
if (!is.brmsprior(dots$prior)) {
stop2("Argument 'prior' needs to be a 'brmsprior' object.")
}
# update existing priors manually and keep only user-specified ones
# default priors are recomputed base on newdata if provided
old_user_prior <- subset2(object$prior, source = "user")
dots$prior <- rbind(dots$prior, old_user_prior)
dupl_priors <- duplicated(dots$prior[, rcols_prior()])
dots$prior <- dots$prior[!dupl_priors, ]
}
# make sure potentially updated priors pass 'validate_prior'
attr(dots$prior, "allow_invalid_prior") <- TRUE
if (!"sample_prior" %in% names(dots)) {
dots$sample_prior <- attr(object$prior, "sample_prior")
if (is.null(dots$sample_prior)) {
has_prior_pars <- any(grepl("^prior_", variables(object)))
dots$sample_prior <- if (has_prior_pars) "yes" else "no"
}
}
# do not use 'is.null' to allow updating arguments to NULL
if (!"data2" %in% names(dots)) {
dots$data2 <- object$data2
}
if (!"stanvars" %in% names(dots)) {
dots$stanvars <- object$stanvars
}
if (!"algorithm" %in% names(dots)) {
dots$algorithm <- object$algorithm
}
if (!"backend" %in% names(dots)) {
dots$backend <- object$backend
}
if (!"threads" %in% names(dots)) {
dots$threads <- object$threads
}
if (!"save_pars" %in% names(dots)) {
dots$save_pars <- object$save_pars
}
if (!"knots" %in% names(dots)) {
dots$knots <- get_knots(object$data)
}
if (!"drop_unused_levels" %in% names(dots)) {
dots$drop_unused_levels <- get_drop_unused_levels(object$data)
}
if (!"normalize" %in% names(dots)) {
dots$normalize <- is_normalized(object$model)
}
# update arguments controlling the sampling process
if (is.null(dots$iter)) {
# only keep old 'warmup' if also keeping old 'iter'
dots$warmup <- first_not_null(dots$warmup, object$fit@sim$warmup)
}
dots$iter <- first_not_null(dots$iter, object$fit@sim$iter)
dots$chains <- first_not_null(dots$chains, object$fit@sim$chains)
dots$thin <- first_not_null(dots$thin, object$fit@sim$thin)
dots$backend <- match.arg(dots$backend, backend_choices())
same_backend <- is_equal(dots$backend, object$backend)
if (same_backend) {
# reusing control arguments in other backends may cause errors #1259
control <- attr(object$fit@sim$samples[[1]], "args")$control
control <- control[setdiff(names(control), names(dots$control))]
dots$control[names(control)] <- control
# reuse backend arguments originally passed to brm #1373
names_old_stan_args <- setdiff(names(object$stan_args), names(dots))
dots[names_old_stan_args] <- object$stan_args[names_old_stan_args]
}
if (is.null(recompile)) {
# only recompile if new and old stan code do not match
new_stancode <- suppressMessages(do_call(make_stancode, dots))
# stan code may differ just because of the version number (#288)
new_stancode <- sub("^[^\n]+\n", "", new_stancode)
old_stancode <- stancode(object, version = FALSE)
recompile <- needs_recompilation(object) || !same_backend ||
!is_equal(new_stancode, old_stancode)
if (recompile && silent < 2) {
message("The desired updates require recompiling the model")
}
}
recompile <- as_one_logical(recompile)
if (recompile) {
# recompliation is necessary
dots$fit <- NA
if (!testmode) {
object <- do_call(brm, dots)
}
} else {
# refit the model without compiling it again
if (!is.null(dots$formula)) {
object$formula <- dots$formula
dots$formula <- NULL
}
bterms <- brmsterms(object$formula)
object$data2 <- validate_data2(dots$data2, bterms = bterms)
object$data <- validate_data(
dots$data, bterms = bterms, data2 = object$data2,
knots = dots$knots, drop_unused_levels = dots$drop_unused_levels
)
object$prior <- .validate_prior(
dots$prior, bterms = bterms, data = object$data,
sample_prior = dots$sample_prior
)
object$family <- get_element(object$formula, "family")
object$autocor <- get_element(object$formula, "autocor")
object$ranef <- tidy_ranef(bterms, data = object$data)
object$stanvars <- validate_stanvars(dots$stanvars)
object$threads <- validate_threads(dots$threads)
if ("sample_prior" %in% names(dots)) {
dots$sample_prior <- validate_sample_prior(dots$sample_prior)
attr(object$prior, "sample_prior") <- dots$sample_prior
}
object$save_pars <- validate_save_pars(
save_pars = dots$save_pars,
save_ranef = dots$save_ranef,
save_mevars = dots$save_mevars,
save_all_pars = dots$save_all_pars
)
object$basis <- standata_basis(bterms, data = object$data)
algorithm <- match.arg(dots$algorithm, algorithm_choices())
dots$algorithm <- object$algorithm <- algorithm
# can only avoid recompilation when using the old backend
dots$backend <- object$backend
if (!testmode) {
dots$fit <- object
object <- do_call(brm, dots)
}
}
attr(object$data, "data_name") <- data_name
object
}
#' Update \pkg{brms} models based on multiple data sets
#'
#' This method allows to update an existing \code{brmsfit_multiple} object.
#'
#' @param object An object of class \code{brmsfit_multiple}.
#' @param formula. Changes to the formula; for details see
#' \code{\link{update.formula}} and \code{\link{brmsformula}}.
#' @param newdata List of \code{data.frames} to update the model with new data.
#' Currently required even if the original data should be used.
#' @param ... Other arguments passed to \code{\link{update.brmsfit}}
#' and \code{\link{brm_multiple}}.
#'
#' @examples
#' \dontrun{
#' library(mice)
#' imp <- mice(nhanes2)
#'
#' # initially fit the model
#' fit_imp1 <- brm_multiple(bmi ~ age + hyp + chl, data = imp, chains = 1)
#' summary(fit_imp1)
#'
#' # update the model using fewer predictors
#' fit_imp2 <- update(fit_imp1, formula. = . ~ hyp + chl, newdata = imp)
#' summary(fit_imp2)
#' }
#'
#' @export
update.brmsfit_multiple <- function(object, formula., newdata = NULL, ...) {
dots <- list(...)
if ("data" %in% names(dots)) {
# otherwise the data name cannot be found by substitute
stop2("Please use argument 'newdata' to update the data.")
}
if (is.null(newdata)) {
stop2("'newdata' is required when updating a 'brmsfit_multiple' object.")
}
data_name <- substitute_name(newdata)
if (inherits(newdata, "mids")) {
require_package("mice", version = "3.0.0")
newdata <- lapply(seq_len(newdata$m), mice::complete, data = newdata)
} else if (!(is.list(newdata) && is.vector(newdata))) {
stop2("'newdata' must be a list of data.frames.")
}
# update the template model using all arguments
if (missing(formula.)) {
formula. <- NULL
}
args <- c(nlist(object, formula., newdata = newdata[[1]]), dots)
args$file <- NULL
args$chains <- 0
fit <- do_call(update.brmsfit, args)
# arguments later passed to brm_multiple
args <- c(nlist(fit, data = newdata), dots)
# update arguments controlling the sampling process
# they cannot be accessed directly from the template model
# as it does not contain any draws (chains = 0)
if (is.null(args$iter)) {
# only keep old 'warmup' if also keeping old 'iter'
args$warmup <- first_not_null(args$warmup, object$fit@sim$warmup)
}
if (is.null(args$chains)) {
# chains were combined across all submodels
args$chains <- object$fit@sim$chains / max(NROW(object$rhats), 1)
}
args$iter <- first_not_null(args$iter, object$fit@sim$iter)
args$thin <- first_not_null(args$thin, object$fit@sim$thin)
control <- attr(object$fit@sim$samples[[1]], "args")$control
control <- control[setdiff(names(control), names(args$control))]
args$control[names(control)] <- control
args$recompile <- NULL
out <- do_call(brm_multiple, args)
attr(out$data, "data_name") <- data_name
out
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.