R/NMsim_typical.R

In NMsim: Seamless 'Nonmem' Simulation Platform

##' Typical subject simiulation method
##' 
##' Like \code{NMsim_default} but with all ETAs=0, giving a
##' "typical subject" simulation. Do not confuse this with a
##' "reference subject" simulation which has to do with covariate
##' values. Technically all ETAs=0 is obtained by replacing
##' \code{$OMEGA} by a zero matrix.
##' 
##' @param file.sim See \code{?NMsim}.
##' @param file.mod See \code{?NMsim}.
##' @param data.sim See \code{?NMsim}.
##' @param return.text If TRUE, just the text will be returned, and
##'     resulting control stream is not written to file.
##' @import NMdata
##' @return Path to simulation control stream
##' @export


NMsim_typical <- function(file.sim,file.mod,data.sim,return.text=FALSE){

    message("NMsim_typical() is deprecated. Use `typical=TRUE` in combination with other simulation methods instead. The old `method.sim=NMsim_typical` is equivalent to combining `typical=TRUE` with the default simulation method `method.sim=NMsim_default`.")
    
#### Section start: Dummy variables, only not to get NOTE's in pacakge checks ####

    par.type <- NULL
    i <- NULL

### Section end: Dummy variables, only not to get NOTE's in pacakge checks


    files.needed.def <- NMsim_default(file.sim=file.sim,file.mod,data.sim)
    lines.sim <- readLines(file.sim)

### this introduces dependency on file.ext or Netas as
### arguments. Better keep deprecated NMsim_typical as is. Used in typicalize() instead. 

    ## if(missing(Netas)) Netas <- NULL
    ## if(missing(file.ext)) file.ext <- NULL
    
    ## if(is.null(Netas)){        
    ##     if(is.null(file.ext)){
    ##         file.ext <- fnExtension(file.mod,"ext")    
    ##         if(!file.exists(file.ext)){
    ##             stop("ext file not found and number of Etas not provided. See arguments file.ext and Netas.")
    ##         } else {
    ##             extres <- NMreadExt(file.ext,return="pars",as.fun="data.table")
    ##             Netas <- extres[par.type=="OMEGA",max(i)]
    ##         }
    ##     }
    ## }


    extres <- NMreadExt(fnExtension(file.mod,"ext"),return="pars",as.fun="data.table")
    Netas <- extres[par.type=="OMEGA",max(i)]
    
    lines.omega <- paste(c("$OMEGA",rep("0 FIX",Netas),""),collapse="\n")
    lines.sim <- NMdata:::NMwriteSectionOne(lines=lines.sim,section="omega",newlines=lines.omega,backup=FALSE,quiet=TRUE)

    if(return.text){
        return(lines.sim)            
    }

    writeTextFile(lines=lines.sim,file=file.sim)

    return(file.sim)
}