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#' Calculate the analytic steady state concentration for the one compartment model.
#'
#' This function calculates the analytic steady state plasma or venous blood
#' concentrations as a result of infusion dosing.
#'
#' @param chem.name Either the chemical name, CAS number, or the parameters must
#' be specified.
#'
#' @param chem.cas Either the chemical name, CAS number, or the parameters must
#' be specified.
#'
#' @param dtxsid EPA's 'DSSTox Structure ID (\url{https://comptox.epa.gov/dashboard})
#' the chemical must be identified by either CAS, name, or DTXSIDs
#'
#' @param parameters Chemical parameters from parameterize_pbtk (for model =
#' 'pbtk'), parameterize_3comp (for model = '3compartment),
#' parameterize_1comp(for model = '1compartment') or parameterize_steadystate
#' (for model = '3compartmentss'), overrides chem.name and chem.cas.
#'
#' @param hourly.dose Hourly dose rate mg/kg BW/h.
#'
#' @param concentration Desired concentration type, 'blood' or default 'plasma'.
#'
#' @param suppress.messages Whether or not the output message is suppressed.
#'
#' @param recalc.blood2plasma Recalculates the ratio of the amount of chemical
#' in the blood to plasma using the input parameters. Use this if you have
#' altered hematocrit, Funbound.plasma, or Krbc2pu.
#'
#' @param tissue Desired tissue conentration (defaults to whole body
#' concentration.)
#'
#' @param restrictive.clearance If TRUE (default), then only the fraction of
#' chemical not bound to protein is available for metabolism in the liver. If
#' FALSE, then all chemical in the liver is metabolized (faster metabolism due
#' to rapid off-binding).
#'
#' @param bioactive.free.invivo If FALSE (default), then the total concentration is treated
#' as bioactive in vivo. If TRUE, the the unbound (free) plasma concentration is treated as
#' bioactive in vivo. Only works with tissue = NULL in current implementation.
#'
#' @param dosing List of dosing metrics used in simulation, which includes
#' the namesake entries of a model's associated dosing.params. For steady-state
#' calculations this is likely to be either "daily.dose" for oral exposures or
#' "Cinhaled" for inhalation.
#'
#' @param dose.units The units associated with the dose received.
#'
#' @param Caco2.options A list of options to use when working with Caco2 apical to
#' basolateral data \code{Caco2.Pab}, default is Caco2.options = list(Caco2.Pab.default = 1.6,
#' Caco2.Fabs = TRUE, Caco2.Fgut = TRUE, overwrite.invivo = FALSE, keepit100 = FALSE). Caco2.Pab.default sets the default value for
#' Caco2.Pab if Caco2.Pab is unavailable. Caco2.Fabs = TRUE uses Caco2.Pab to calculate
#' fabs.oral, otherwise fabs.oral = \code{Fabs}. Caco2.Fgut = TRUE uses Caco2.Pab to calculate
#' fgut.oral, otherwise fgut.oral = \code{Fgut}. overwrite.invivo = TRUE overwrites Fabs and Fgut in vivo values from literature with
#' Caco2 derived values if available. keepit100 = TRUE overwrites Fabs and Fgut with 1 (i.e. 100 percent) regardless of other settings.
#' See \code{\link{get_fbio}} for further details.
#'
#' @param ... Additional parameters passed to parameterize function if
#' parameters is NULL.
#'
#' @return Steady state plasma concentration in mg/L units
#'
#' @seealso \code{\link{calc_analytic_css}}
#'
#' @seealso \code{\link{parameterize_1comp}}
#'
#' @author Robert Pearce and John Wambaugh
#'
#' @keywords 1compartment
calc_analytic_css_1comp <- function(chem.name=NULL,
chem.cas = NULL,
dtxsid = NULL,
parameters=NULL,
dosing=list(daily.dose=1),
hourly.dose = NULL,
dose.units = "mg",
concentration='plasma',
suppress.messages=FALSE,
recalc.blood2plasma=FALSE,
tissue=NULL,
restrictive.clearance=TRUE,
bioactive.free.invivo = FALSE,
Caco2.options = list(),
...)
{
if (!is.null(hourly.dose))
{
warning("calc_analytic_css_3compss deprecated argument hourly.dose replaced with new argument dose, value given assigned to dose")
dosing <- list(daily.dose = 24*hourly.dose)
}
# Load from modelinfo file:
THIS.MODEL <- "1compartment"
param.names <- model.list[[THIS.MODEL]]$param.names
param.names.schmitt <- model.list[["schmitt"]]$param.names
parameterize_function <- model.list[[THIS.MODEL]]$parameterize.func
# We need to describe the chemical to be simulated one way or another:
if (is.null(chem.cas) &
is.null(chem.name) &
is.null(dtxsid) &
is.null(parameters))
stop('parameters, chem.name, chem.cas, or dtxsid must be specified.')
# Look up the chemical name/CAS, depending on what was provide:
if (is.null(parameters))
{
out <- get_chem_id(
chem.cas=chem.cas,
chem.name=chem.name,
dtxsid=dtxsid)
chem.cas <- out$chem.cas
chem.name <- out$chem.name
dtxsid <- out$dtxsid
parameters <- do.call(what=parameterize_function,
args=purrr::compact(c(
list(chem.cas=chem.cas,
chem.name=chem.name,
suppress.messages=suppress.messages,
Caco2.options = Caco2.options,
restrictive.clearance = restrictive.clearance
),
...)))
if (recalc.blood2plasma)
{
warning("Argument recalc.blood2plasma=TRUE ignored because parameters is NULL.")
}
} else {
if (!all(param.names %in% names(parameters)))
{
stop(paste("Missing parameters:",
paste(param.names[which(!param.names %in% names(parameters))],
collapse=', '),
". Use parameters from parameterize_1comp."))
}
if (!restrictive.clearance)
{
warning("Argument restrictive.clearance=FALSE ignored by model 1comp when parameters!=NULL.")
}
}
# one compartment Css is dose.rate / clearance:
# Dose rate:
hourly.dose <- dosing[["daily.dose"]] /
parameters[["BW"]] /
24 *
convert_units(MW = parameters[["MW"]],
dose.units,
"mg") # mg/kg/h
Css <- hourly.dose *
# Oral bioavailability:
parameters[["Fabsgut"]] * parameters[["hepatic.bioavailability"]] /
# Clearance:
parameters[["kelim"]] / parameters[["Vdist"]]
# Convert to plasma concentration:
Css <- Css/parameters[["Rblood2plasma"]]
# Check to see if a specific tissue was asked for:
if (!is.null(tissue))
{
# Need to convert to Schmitt parameters:
#The parameters used in predict_partitioning_schmitt may be a compound
#data.table/data.frame or list object, however, depending on the source
#of the parameters. In calc_mc_css, for example, parameters is received
#as a "data.table" object. Screen for processing appropriately.
if (any(class(parameters) == "data.table")){
pcs <- predict_partitioning_schmitt(parameters =
parameters[, param.names.schmitt[param.names.schmitt %in%
names(parameters)], with = F])
}else if (is(parameters,"list")) {
pcs <- predict_partitioning_schmitt(parameters =
parameters[param.names.schmitt[param.names.schmitt %in%
names(parameters)]])
}else stop('httk is only configured to process parameters as objects of
class list or class compound data.table/data.frame.')
if (!paste0('K',tolower(tissue)) %in%
substr(names(pcs),1,nchar(names(pcs))-3))
{
stop(paste("Tissue",tissue,"is not available."))
}
Css <- Css *
pcs[[names(pcs)[substr(names(pcs),2,nchar(names(pcs))-3)==tissue]]] *
parameters$Funbound.plasma
}
if(tolower(concentration) != 'tissue'){
if (tolower(concentration)=='blood')
{
Css <- Css * parameters[['Rblood2plasma']]
}else if(bioactive.free.invivo == TRUE & tolower(concentration) == 'plasma'){
Css <- Css * parameters[['Funbound.plasma']]
} else if (tolower(concentration)!='plasma')
{
stop("Only blood and plasma concentrations are calculated.")
}
}
return(Css)
}
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