R/propagate_invitrouv_pbtk.R

In httk: High-Throughput Toxicokinetics

#' Propagates uncertainty and variability in in vitro HTTK data into PBPK
#' model parameters
#'
#' @param parameters.dt The data table of parameters being used by the Monte
#' Carlo sampler
#' @param ... Additional arguments passed to \code{\link{calc_hep_clearance}}
#'
#'@return A data.table whose columns are the parameters of the HTTK model
#'  specified in \code{model}.
#'
#' @author John Wambaugh
#'
#' @keywords monte-carlo pbtk
propagate_invitrouv_pbtk <- function(
                             parameters.dt,
                             ...)
{
  #R CMD CHECK throws notes about "no visible binding for global variable", for
  #each time a data.table column name is used without quotes. To appease R CMD
  #CHECK, a variable has to be created for each of these column names and set to
  #NULL. Note that within the data.table, these variables will not be NULL! Yes,
  #this is pointless and annoying.
  Clmetabolismc<-Clint<-Funbound.plasma<-Fhep.assay.correction<-Qgutf<-NULL
  liver.density<-million.cells.per.gliver<-BW<-Vliverc<-Qliverf<-NULL
  Qcardiacc<- NULL
  #End R CMD CHECK appeasement.
  
      #Compute Vdist, volume of distribution
      parameters.dt[, Clmetabolismc := 
        as.numeric(calc_hep_clearance(
          hepatic.model="unscaled",
          parameters=list(
            Clint=Clint, #uL/min/10^6 cells
            Funbound.plasma=Funbound.plasma, # unitless fraction
            Fhep.assay.correction=
              Fhep.assay.correction, 
            million.cells.per.gliver= million.cells.per.gliver, # 10^6 cells/g-liver
            liver.density= liver.density, # g/mL
            Dn=0.17,
            BW=BW,
            Vliverc=Vliverc, #L/kg
            Qtotal.liverc=
              ((Qgutf+Qliverf)*as.numeric(Qcardiacc))/1000*60),
          suppress.messages=TRUE,
          ...))]

  return(parameters.dt)
}