R/update_sso.R

In shinystan: Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models

# shinystan is free software; you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation; either version 3 of the License, or (at your option) any later
# version.
# 
# shinystan is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License along with
# this program; if not, see <http://www.gnu.org/licenses/>.


#' Update an object created by the previous version of shinystan
#' 
#' If you encounter any errors when using a shinystan object (\code{sso}) 
#' created by a previous version of \pkg{shinystan}, you might need to run
#' \code{update_sso}. If \code{update_sso} does not resolve the problem and 
#' you still have the object (e.g. stanfit,  stanreg, mcmc.list) from which 
#' \code{sso} was originally created, you can create a new shinystan object 
#' using \code{\link{as.shinystan}}.
#' 
#' @export
#' @template args-sso
#' @return If \code{sso} is already compatible with your version of
#'   \pkg{shinystan} then \code{sso} itself is returned and a message is printed
#'   indicating that \code{sso} is already up-to-date. Otherwise an updated
#'   version of \code{sso} is returned unless an error is encountered.
#'   
#' @template seealso-as.shinystan
#'   
#' @examples 
#' \dontrun{
#' sso_new <- update_sso(sso)
#' }
#' 
update_sso <- function(sso) {
  stopifnot(is.shinystan(sso))
  sso_ver <- sso_version(sso)
  shinystan_ver <- utils::packageVersion("shinystan")
  if (sso_ver == shinystan_ver) {
    message(deparse(substitute(sso)), " already up-to-date.")
    return(sso)
  } else if (sso_ver > shinystan_ver) {
    stop(
      deparse(substitute(sso)),
      " was created using a more recent version ",
      "of shinystan than the one you are currently using. ",
      "Please update your version of the shinystan package."
    )
  }
  
  slot(sso, "sampler_params") <-
    .rename_sampler_param(slot(sso, "sampler_params"),
                          oldname = "n_divergent__",
                          newname = "divergent__")
  sso_new <- shinystan()
  for (sn in slotNames(sso_new)) {
    if (.hasSlot(sso, sn)) {
      slot(sso_new, sn) <- slot(sso, sn)
    } else {
      new_slots <- c("posterior_sample", "n_chain", "n_iter", "n_warmup")
      old_slots <- c("samps_all", "nChains", "nIter", "nWarmup")
      j <- which(new_slots == sn)
      if (!length(j))
        stop("Bug found. Slot ", sn, " can't be updated.")
      if (.hasSlot(sso, old_slots[j])) {
        slot(sso_new, sn) <- slot(sso, old_slots[j])
      } else {
        stop("slot ", sn, " not found in ", deparse(substitute(sso))) 
      }
    }
  }
  sso_new@misc[["sso_version"]] <- utils::packageVersion("shinystan")
  message("shinystan object updated.")
  sso_new
}