This function calculates the half life from the three compartment steady state model where elimination is entirely due to metabolism by the liver and glomerular filtration in the kidneys.
calc_half_life(
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,
regression = TRUE,
well.stirred.correction = TRUE,
clint.pvalue.threshold = 0.05,
minimum.Funbound.plasma = 1e-04
)Units of 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 elimination rate (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.
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).
Sarah E. Davidson
Half life is calculated by dividing the natural-log of 2 by the elimination rate from the one compartment model.
calc_elimination_rate
calc_half_life(chem.name="Bisphenol A")
# \donttest{
calc_half_life(chem.name="Bisphenol A",species="Rat")
calc_half_life(chem.cas="80-05-7")
# }
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