This function initializes the parameters needed in the function solve_1comp.
parameterize_1comp(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
species = "Human",
default.to.human = FALSE,
adjusted.Funbound.plasma = TRUE,
regression = TRUE,
restrictive.clearance = TRUE,
well.stirred.correction = TRUE,
suppress.messages = FALSE,
clint.pvalue.threshold = 0.05,
minimum.Funbound.plasma = 1e-04
)Volume of distribution, units of L/kg BW.
Fraction of the oral dose absorbed, i.e. the fraction of the dose that enters the gutlumen.
The fraction of chemical unbound in hepatocyte assay using the method of Kilford et al. (2008)
Elimination rate, units of 1/h.
Percent volume of red blood cells in the blood.
Rate chemical is absorbed, 1/h.
Millions cells per gram of liver tissue.
Molecular Weight, g/mol.
The ratio of the concentration of the chemical in the blood to the concentration in the plasma. Not used in calculations but included for the conversion of plasma outputs.
Fraction of dose remaining after first pass clearance, calculated from the corrected well-stirred model.
Body Weight, kg.
Chemical Abstract Services Registry Number (CAS-RN) -- the chemical must be identified by either CAS, name, or DTXISD
Chemical name (spaces and capitalization ignored) -- the chemical must be identified by either CAS, name, or DTXISD
EPA's DSSTox Structure ID (https://comptox.epa.gov/dashboard) -- the chemical must be identified by either CAS, name, or DTXSIDs
Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").
Substitutes missing rat values with human values if true.
Uses adjusted Funbound.plasma when set to TRUE along with volume of distribution calculated with this value.
Whether or not to use the regressions in calculating partition coefficients in volume of distribution calculation.
In calculating elimination rate and hepatic bioavailability, protein binding is not taken into account (set to 1) in liver clearance if FALSE.
Uses correction in calculation of hepatic clearance for well-stirred model if TRUE. This assumes clearance relative to amount unbound in whole blood instead of plasma, but converted to use with plasma concentration.
Whether or not to suppress messages.
Hepatic clearance for chemicals where the in vitro clearance assay result has a p-value greater than the threshold are set to zero.
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).
John Wambaugh and Robert Pearce
Pearce, Robert G., et al. "Httk: R package for high-throughput toxicokinetics." Journal of statistical software 79.4 (2017): 1.
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.
parameters <- parameterize_1comp(chem.name='Bisphenol-A',species='Rat')
parameters <- parameterize_1comp(chem.cas='80-05-7',
restrictive.clearance=FALSE,
species='rabbit',
default.to.human=TRUE)
out <- solve_1comp(parameters=parameters)
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