#' Change elements of the Model based on inputs
#'
#' @param parsedObject R object containing parsed NONMEM objects
#' @param problem $Problem (NONMEM $PROB) list within the R Model Object
#' @param theta $Theta list (NONEMM $THETA) within the R Model Object
#' @param omega $Omega list (NONMEM $OMEGA) within the R Model Object
#' @param sigma $Sigma list (NONMEM $SIGMA) within the R Model Object
#' @param task $Estimates list (NONMEM $EST, $SIM) within the R Model Object
#' @param data $Data list (NONMEM $DATA) within the R Model Object
#' @param dataNames $Input list (NONMEM $INPUT) within the R Model Object
#' @param tables $Tables list (NONMEM $TABLES) within the R Model Object
#' @param addPsNHeader Logical - whether to include PsN Header information.
#' Default FALSE.
#' @return NONMEM estimation output files
#' @examples
#' @export
updateModel <- function(parsedObject, problem = parsedObject$Problem,
theta = parsedObject$Theta, omega = parsedObject$Omega,
sigma = parsedObject$Sigma, task = parsedObject$Estimates,
data = parsedObject$Data, dataNames = parsedObject$Input,
tables = parsedObject$Tables,
addPsNHeader = F, runno = 0, ...) {
newObject <- parsedObject
newObject$Problem <- problem
newObject$Theta <- theta
newObject$Omega <- omega
newObject$Sigma <- sigma
newObject$Estimates <- task
newObject$Data <- data
newObject$Input <- dataNames
newObject$Tables <- tables
newObject$Tables$File <- gsub("[0:9]", runno, parsedObject$Tables$File)
if (addPsNHeader)
newObject$Problem <- PsNHeader(parsedObject, ...)
return(newObject)
}
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