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#' Parameters for a three-compartment toxicokinetic model (dynamic)
#'
#' This function generates the chemical- and species-specific parameters needed
#' for model '3compartment', for example \code{\link{solve_3comp}}. A call is
#' masde to \code{\link{parameterize_pbtk}} to use Schmitt (2008)'s method
#' as modified by Pearce et al. (2017) to predict partition coefficients based
#' on descriptions in \code{\link{tissue.data}}. Organ volumes and flows are
#' retrieved from table \code{\link{physiology.data}}.
#'
#' @param chem.cas Chemical Abstract Services Registry Number (CAS-RN) -- the
#' chemical must be identified by either CAS, name, or DTXISD
#'
#' @param chem.name Chemical name (spaces and capitalization ignored) -- the
#' chemical must be identified by either CAS, name, or DTXISD
#'
#' @param dtxsid EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard)
#' -- the chemical must be identified by either CAS, name, or DTXSIDs
#'
#' @param species Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or
#' default "Human").
#'
#' @param default.to.human Substitutes missing animal values with human values
#' if true.
#'
#' @param force.human.clint.fup Forces use of human values for hepatic
#' intrinsic clearance and fraction of unbound plasma if true.
#'
#' @param clint.pvalue.threshold Hepatic clearances with clearance assays
#' having p-values greater than the threshold are set to zero.
#'
#' @param adjusted.Funbound.plasma Uses Pearce et al. (2017) lipid binding adjustment
#' for Funbound.plasma (which impacts partition coefficients) when set to TRUE (Default).
#'
#' @param adjusted.Clint Uses Kilford et al. (2008) hepatocyte incubation
#' binding adjustment for Clint when set to TRUE (Default).
#'
#' @param regression Whether or not to use the regressions in calculating
#' partition coefficients.
#'
#' @param suppress.messages Whether or not the output message is suppressed.
#'
#' @param restrictive.clearance In calculating hepatic.bioavailability, protein
#' binding is not taken into account (set to 1) in liver clearance if FALSE.
#'
#' @param minimum.Funbound.plasma Monte Carlo draws less than this value are set
#' equal to this value (default is 0.0001 -- half the lowest measured Fup in our
#' dataset).
#'
#' @return
#' \item{BW}{Body Weight, kg.}
#' \item{Clmetabolismc}{Hepatic Clearance, L/h/kg BW.}
#' \item{Fgutabs}{Fraction of the oral dose absorbed, i.e. the
#' fraction of the dose that enters the gutlumen.}
#' \item{Funbound.plasma}{Fraction of plasma that is not bound.}
#' \item{Fhep.assay.correction}{The fraction of chemical unbound in hepatocyte
#' assay using the method of Kilford et al. (2008)}
#' \item{hematocrit}{Percent volume of red blood cells in the blood.}
#' \item{Kgut2pu}{Ratio of concentration of chemical in gut tissue to unbound
#' concentration in plasma.}
#' \item{Kliver2pu}{Ratio of concentration of
#' chemical in liver tissue to unbound concentration in plasma.}
#' \item{Krbc2pu}{Ratio of concentration of chemical in red blood cells to
#' unbound concentration in plasma.}
#' \item{Krest2pu}{Ratio of concentration of
#' chemical in rest of body tissue to unbound concentration in plasma.}
#' \item{million.cells.per.gliver}{Millions cells per gram of liver tissue.}
#' \item{MW}{Molecular Weight, g/mol.}
#' \item{Qcardiacc}{Cardiac Output, L/h/kg
#' BW^3/4.} \item{Qgfrc}{Glomerular Filtration Rate, L/h/kg BW^3/4, volume of
#' fluid filtered from kidney and excreted.}
#' \item{Qgutf}{Fraction of cardiac output flowing to the gut.}
#' \item{Qliverf}{Fraction of cardiac output flowing to the liver.}
#' \item{Rblood2plasma}{The ratio of the concentration
#' of the chemical in the blood to the concentration in the plasma.}
#' \item{Vgutc}{Volume of the gut per kg body weight, L/kg BW.}
#' \item{Vliverc}{Volume of the liver per kg body weight, L/kg BW.}
#' \item{Vrestc}{ Volume of the rest of the body per kg body weight, L/kg BW.}
#'
#' @author Robert Pearce and John Wambaugh
#'
#' @references
#' Pearce, Robert G., et al. "Httk: R package for high-throughput
#' toxicokinetics." Journal of statistical software 79.4 (2017): 1.
#'
#' Schmitt, Walter. "General approach for the calculation of tissue
#' to plasma partition coefficients." Toxicology in vitro 22.2 (2008): 457-467.
#'
#' Pearce, Robert G., et al. "Evaluation and calibration of high-throughput
#' predictions of chemical distribution to tissues." Journal of pharmacokinetics
#' and pharmacodynamics 44.6 (2017): 549-565.
#'
#' Kilford, P. J., Gertz, M., Houston, J. B. and Galetin, A.
#' (2008). Hepatocellular binding of drugs: correction for unbound fraction in
#' hepatocyte incubations using microsomal binding or drug lipophilicity data.
#' Drug Metabolism and Disposition 36(7), 1194-7, 10.1124/dmd.108.020834.
#'
#' @keywords Parameter 3compartment
#'
#' @seealso \code{\link{solve_3comp}}
#'
#' @seealso \code{\link{calc_analytic_css_3comp}}
#'
#' @seealso \code{\link{parameterize_pbtk}}
#'
#' @seealso \code{\link{apply_clint_adjustment}}
#'
#' @seealso \code{\link{tissue.data}}
#'
#' @seealso \code{\link{physiology.data}}
#'
#' @examples
#'
#' parameters <- parameterize_3comp(chem.name='Bisphenol-A',species='Rat')
#' parameters <- parameterize_3comp(chem.cas='80-05-7',
#' species='rabbit',default.to.human=TRUE)
#' out <- solve_3comp(parameters=parameters,plots=TRUE)
#'
#' @export parameterize_3comp
parameterize_3comp<- function(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
species = "Human",
default.to.human = FALSE,
force.human.clint.fup = FALSE,
clint.pvalue.threshold = 0.05,
adjusted.Funbound.plasma = TRUE,
adjusted.Clint = TRUE,
regression = TRUE,
suppress.messages = FALSE,
restrictive.clearance = TRUE,
minimum.Funbound.plasma = 0.0001)
{
parms <- parameterize_pbtk(
chem.cas = chem.cas,
chem.name = chem.name,
dtxsid = dtxsid,
species = species,
default.to.human = default.to.human,
tissuelist = list(
liver=c("liver"),
gut=c("gut")),
force.human.clint.fup = force.human.clint.fup,
clint.pvalue.threshold = clint.pvalue.threshold,
adjusted.Funbound.plasma = adjusted.Funbound.plasma,
adjusted.Clint=adjusted.Clint,
regression = regression,
suppress.messages = suppress.messages,
restrictive.clearance = restrictive.clearance,
minimum.Funbound.plasma = minimum.Funbound.plasma)
parms$Qkidneyf <- parms$Vvenc <- parms$Vartc <- NULL
return(lapply(parms[order(tolower(names(parms)))],set_httk_precision))
}
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