R/fit_peel.R

In timjmiller/wham: Woods Hole Assessment Model (WHAM)

#' Fit model peeling off \emph{i} years of data
#'
#' Internal function called by \code{\link{retro}} for \emph{i} in 1--\code{n.peels}.
#' Fits the model peeling off \emph{i} years of data (calls \code{\link{fit_tmb}}).
#'
#' @param peel Integer, number of years of data to remove before model fitting.
#' @param input input with same structure as that provided by \code{\link{prepare_wham_input}}. May want to use input$par = model$parList to start at MLEs.
#' @param do.sdrep T/F, calculate standard deviations of model parameters? Default = \code{FALSE}.
#' @param n.newton integer, number of additional Newton steps after optimizafit_tmbtion for each peel. Default = \code{3}.
#' @param MakeADFun.silent T/F, Passed to silent argument of \code{\link[TMB:MakeADFun]{TMB::MakeADFun}}. Default = \code{FALSE}.
#' @param retro.silent T/F, Passed to argument of internal fit_peel function. Determines whether peel number is printed to screen. Default = \code{FALSE}.
#' @param save.input T/F, should modified input list be saved? Necessary to project from a peel but increases model object size. Default = \code{FALSE}.
#'
#' @return \code{out}, output of \code{\link{fit_tmb}} for peel \emph{i}
#'
#' @export
#' 
#' @seealso \code{\link{fit_wham}}, \code{\link{retro}}, \code{\link{fit_tmb}}
#'
fit_peel = function(peel, input, do.sdrep = FALSE, n.newton = 3, MakeADFun.silent = FALSE, retro.silent = FALSE, save.input = FALSE)
{
  out = list()
  if(!retro.silent) print(paste0("Retro Peel: ", peel))
  temp <- reduce_input(input, tail(input$years,peel))
  temp.mod <- TMB::MakeADFun(temp$data, temp$par, DLL="wham", random = temp$random, map = temp$map, silent = MakeADFun.silent)

   out <- fit_tmb(temp.mod, do.sdrep = do.sdrep, n.newton = n.newton, do.check=FALSE)
   out$peel <- peel
   if(save.input){
     out$input <- temp
     out$input$model_name <- paste0(input$model_name, " peel ",peel)
     out$ages.lab <- input$ages.lab
     out$model_name <- paste0(input$model_name, " peel ",peel)
   }

  return(out)
}