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# Add the 3compartment steady-state model with inhalation to the list of models:
# Model identifier for the model.list:
THIS.MODEL <- "sumclearances"
# Dose this model work with Monte Carlo parameter sampling?
model.list[[THIS.MODEL]]$monte.carlo <- TRUE
#Analytic expression for steady-state plasma concentration.
model.list[[THIS.MODEL]]$analytic.css.func <- "calc_analytic_css_sumclearances"
# What units does the analytic function return:
model.list[[THIS.MODEL]]$steady.state.units <- "mg/L"
# Function used for generating model parameters:
model.list[[THIS.MODEL]]$parameterize.func <- "parameterize_sumclearances"
# These are all the parameters returned by the R model parameterization function.
# Some of these parameters are not directly used to solve the model, but describe
# how other parameters were calculated:
model.list[[THIS.MODEL]]$param.names <- c("BW",
"Caco2.Pab",
"Caco2.Pab.dist",
"Clint",
"Clint.dist",
"Dow74",
"Fabsgut",
"Fhep.assay.correction",
"Funbound.plasma",
"Funbound.plasma.dist",
"Funbound.plasma.adjustment",
"hepatic.bioavailability",
"liver.density",
"logHenry",
"million.cells.per.gliver",
"MW",
"pKa_Accept",
"pKa_Donor",
"Pow",
"Qtotal.liverc",
"Qgfrc",
"Rblood2plasma",
"Vliverc",
"Qalvc",
"Kblood2air")
# Allowable units (and whether they are for amounts or concentration):
model.list[[THIS.MODEL]]$conc.units <- c('um', 'mg/l')
model.list[[THIS.MODEL]]$amount.units <- c('umol', 'mg')
#Parameters needed to make a prediction (this is used by get_cheminfo):
model.list[[THIS.MODEL]]$required.params <- c(
"Clint",
"Funbound.plasma",
"Pow",
"pKa_Donor",
"pKa_Accept",
"MW",
"logHenry"
)
# If httk-pop is enabled:
# We want all the standard physiological calculations performed:
model.list[[THIS.MODEL]]$calc.standard.httkpop2httk <- TRUE
# These are the model parameters that are impacted by httk-pop:
model.list[[THIS.MODEL]]$httkpop.params <- c(
"BW",
"Fabsgut",
"hepatic.bioavailability",
"liver.density",
"million.cells.per.gliver",
"Qtotal.liverc",
"Qgfrc",
"Rblood2plasma",
"Vliverc",
"Qalvc")
# Do we need to recalculate partition coefficients when doing Monte Carlo?
model.list[[THIS.MODEL]]$calcpc <- FALSE
# Do we need to recalculate first pass metabolism when doing Monte Carlo?
model.list[[THIS.MODEL]]$firstpass <- TRUE
# These model parameters are impacted by the in vitro measurements:
model.list[[THIS.MODEL]]$invitro.params <- c("BW",
"Clint",
"Clint.dist",
"Fhep.assay.correction",
"Funbound.plasma",
"Funbound.plasma.dist",
"Funbound.plasma.adjustment",
"hepatic.bioavailability",
"Rblood2plasma")
# Do we ignore the Fups where the alue was below the limit of detection?
model.list[[THIS.MODEL]]$exclude.fup.zero <- FALSE
# Filter out compounds belonging to select chemical classes
model.list[[THIS.MODEL]]$chem.class.filt <- c("PFAS")
# These are the parameter names needed to describe steady-state dosing:
model.list[[THIS.MODEL]]$css.dosing.params <- c("hourly.dose")
model.list[[THIS.MODEL]]$routes <- list(
"oral" = list(
"dosing.params" = c("daily.dose")),
"inhalation" = list(
"dosing.params" = c("Cinhppmv"))
)
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