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.
  
      extra.args <- list(...)
      calc.hep.clear.args <- extra.args[names(extra.args) %in%
                                          names(formals(calc_hep_clearance))]
      parameters.dt[, Clmetabolismc := 
        as.numeric(do.call(calc_hep_clearance,
                           args=purrr::compact(
                             c(
                               list(
                             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))), # L/h/kgBW^(3/4)
                             suppress.messages=TRUE),
                             calc.hep.clear.args))))]

  return(parameters.dt)
}