calc_half_life {httk} | R Documentation |
Calculates the half-life for a one compartment model.
Description
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.
Usage
calc_half_life(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
parameters = NULL,
species = "Human",
model = "3compartmentss",
suppress.messages = TRUE,
...
)
Arguments
chem.cas |
Either the cas number or the chemical name must be specified. |
chem.name |
Either the chemical name or the cas number must be specified. |
dtxsid |
EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard) the chemical must be identified by either CAS, name, or DTXSIDs |
parameters |
Chemical parameters from parameterize_steadystate or 1compartment function, overrides chem.name and chem.cas. |
species |
Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human"). |
model |
The model used to calculate elimination rate (defaults to "3compartmentss") |
suppress.messages |
Whether or not the output message is suppressed. |
... |
Additional parameters passed to parameterize function if parameters is NULL. |
Details
Half life is calculated by dividing the natural-log of 2 by the elimination rate from the one compartment model.
Value
Half life |
Units of h. |
Author(s)
Sarah E. Davidson
See Also
Examples
calc_half_life(chem.name="Bisphenol A")
calc_half_life(chem.name="Bisphenol A",species="Rat")
calc_half_life(chem.cas="80-05-7")
# Volatiles are outside the domain of default model:
try(calc_half_life(
chem.name="toluene"))
# We can turn off physchem checking:
calc_half_life(
chem.name="toluene",
physchem.exclude=FALSE)
# Or use an appropriate model for volatiles:
calc_half_life(
chem.name="toluene",
model="sumclearances")
# PFAS are outside the domain:
try(calc_half_life(
dtxsid="DTXSID8031865",
model="sumclearances"))
# Can turn off chemical class checking:
calc_half_life(
dtxsid="DTXSID8031865",
model="sumclearances",
class.exclude=FALSE,
suppress.messages=TRUE)
# For a metabolized compound, non-restrictive clearance should be faster:
h1 <- calc_half_life(
chem.name="toluene",
model="sumclearances",
suppress.messages=TRUE)
h2 <- calc_half_life(
chem.name="toluene",
model="sumclearances",
restrictive.clearance=FALSE,
suppress.messages=TRUE)
# Check that h2 < h1:
if (!(h2 < h1)) stop("h2 not less than h1")
# Change species:
calc_half_life(
dtxsid="DTXSID8031865",
species="rat",
model="sumclearances",
default.to.human=TRUE,
class.exclude=FALSE,
physchem.exclude=FALSE,
suppress.messages=TRUE)