R/equacheck.R

In artedison/ensRadaptor: Metabolic model creator for ensemble method

#' check equalabration
#'
#' this function check the trend of chi^2 and parameters
#' this is prefered before accumulation run
#' it can check the chi^2~sweeps, initial_concentration~time, and kinetic parameters~time
#'
#' @param o02data list. o02 data struct. must be provided
#' @param sweeps numeric. the last n sweeps that should be included in the drawing. must be provided
#' @param dir.res string. result directory. must be provided
#' @param addon string. addon string for names. default ""
#' @param comp string. whether plot parameter with sweep?
#'       "chi2": only plot chi2. default
#'       "all": plot all
#' @return no return just plot
#' @export
equa_check<-function(o02data=NULL,sweeps=NULL,dir.res=NULL,addon="",comp="chi2"){
  if(is.null(o02data)){
    stop("please provide input data")
  }
  if(is.null(sweeps)){
    stop("please state explicitly the presenting sweeps")
  }
  if(is.null(dir.res)){
    stop("please provide the output path")
  }
  len=length(o02data[["ids"]])
  rang=(len-sweeps+1):len
  ##chi^2
  tab=cbind(o02data[["ids"]][rang],2*o02data[["chisq"]][rang])
  draw_sweep(tab,ylab="chi^2",
      loci=paste0(dir.res,"chi2-sweep.check",addon,".pdf"),linethick=FALSE)
  if(comp=="all"){
    ##ini concentration
    inis=names(o02data[["theta_spec_ini"]][[1]])
    tabchose=Reduce("rbind",o02data[["theta_spec_ini"]][rang])
    for(ini in inis){
      tab=cbind(o02data[["ids"]][rang],tabchose[,ini])
      draw_sweep(tab,ylab=ini,
          loci=paste0(dir.res,"iniconec-sweep.check",ini,".",addon,".pdf"),linethick=FALSE)
    }
    ##kinetic parameter
    paras=names(o02data[["theta_reac_para"]][[1]])
    tabchose=Reduce("rbind",o02data[["theta_reac_para"]][rang])
    for(para in paras){
      tab=cbind(o02data[["ids"]][rang],tabchose[,para])
      draw_sweep(tab,ylab=para,
          loci=paste0(dir.res,"kinepara-sweep.check",para,".",addon,".pdf"),linethick=FALSE)
    }
  }
}