This function calculates an elimination rate from the three compartment steady state model where elimination is entirely due to metablism by the liver and glomerular filtration in the kidneys.
calc_elimination_rate(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
parameters = NULL,
model = "3compartmentss",
species = "Human",
suppress.messages = TRUE,
default.to.human = FALSE,
class.exclude = TRUE,
restrictive.clearance = TRUE,
adjusted.Funbound.plasma = TRUE,
adjusted.Clint = TRUE,
regression = TRUE,
well.stirred.correction = TRUE,
clint.pvalue.threshold = 0.05,
minimum.Funbound.plasma = 1e-04
)Units of 1/h.
Either the cas number or the chemical name must be specified.
Either the chemical name or the cas number must be specified.
EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard) the chemical must be identified by either CAS, name, or DTXSIDs
Chemical parameters from parameterize_steadystate or 1compartment function, overrides chem.name and chem.cas.
The model used to calculate total clearance (defaults to "3compartmentss")
Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").
Whether or not the output message is suppressed.
Substitutes missing animal values with human values if true.
Exclude chemical classes identified as outside of domain of applicability by relevant modelinfo_[MODEL] file (default TRUE).
In calculating elimination rate, protein binding is not taken into account (set to 1) in liver clearance if FALSE.
Uses adjusted Funbound.plasma when set to TRUE along with partition coefficients calculated with this value.
Uses Kilford et al. (2008) hepatocyte incubation binding adjustment for Clint when set to TRUE (Default).
Whether or not to use the regressions in calculating partition coefficients.
Uses correction in calculation of hepatic clearance for -stirred model if TRUE. This assumes clearance relative to amount unbound in whole blood instead of plasma, but converted to use with plasma concentration.
Hepatic clearance for chemicals where the in vitro clearance assay result has a p-values 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
Elimination rate calculated by dividing the total clearance (using the default -stirred hepatic model) by the volume of distribution. When species is specified as rabbit, dog, or mouse, the function uses the appropriate physiological data(volumes and flows) but substitues human fraction unbound, partition coefficients, and intrinsic hepatic clearance.
Schmitt, Walter. "General approach for the calculation of tissue to plasma partition coefficients." Toxicology in vitro 22.2 (2008): 457-467.
dawson2021qsarhttk
kilford2008hepatocellularhttk
calc_total_clearance for calculation of total clearance
calc_vdist for calculation of volume of distribution
calc_elimination_rate(chem.name="Bisphenol A")
if (FALSE) {
calc_elimination_rate(chem.name="Bisphenol A",species="Rat")
calc_elimination_rate(chem.cas="80-05-7")
}
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