This function initializes the parameters needed in the functions solve_pbtk, calc_css, and others using the multiple compartment model.
parameterize_pbtk(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
species = "Human",
default.to.human = FALSE,
tissuelist = list(liver = c("liver"), kidney = c("kidney"), lung = c("lung"), gut =
c("gut")),
force.human.clint.fup = FALSE,
clint.pvalue.threshold = 0.05,
adjusted.Funbound.plasma = TRUE,
regression = TRUE,
suppress.messages = FALSE,
restrictive.clearance = TRUE,
minimum.Funbound.plasma = 1e-04
)Body Weight, kg.
Hepatic Clearance, L/h/kg BW.
Fraction of the oral dose absorbed, i.e. the fraction of the dose that enters the gutlumen.
Fraction of plasma that is not bound.
The fraction of chemical unbound in hepatocyte assay using the method of Kilford et al. (2008)
Percent volume of red blood cells in the blood.
Ratio of concentration of chemical in gut tissue to unbound concentration in plasma.
Rate that chemical enters the gut from gutlumen, 1/h.
Ratio of concentration of chemical in kidney tissue to unbound concentration in plasma.
Ratio of concentration of chemical in liver tissue to unbound concentration in plasma.
Ratio of concentration of chemical in lung tissue to unbound concentration in plasma.
Ratio of concentration of chemical in red blood cells to unbound concentration in plasma.
Ratio of concentration of chemical in rest of body tissue to unbound concentration in plasma.
Millions cells per gram of liver tissue.
Molecular Weight, g/mol.
Cardiac Output, L/h/kg BW^3/4.
Glomerular Filtration Rate, L/h/kg BW^3/4, volume of fluid filtered from kidney and excreted.
Fraction of cardiac output flowing to the gut.
Fraction of cardiac output flowing to the kidneys.
Fraction of cardiac output flowing to the liver.
The ratio of the concentration of the chemical in the blood to the concentration in the plasma from available_rblood2plasma.
Volume of the arteries per kg body weight, L/kg BW.
Volume of the gut per kg body weight, L/kg BW.
Volume of the kidneys per kg body weight, L/kg BW.
Volume of the liver per kg body weight, L/kg BW.
Volume of the lungs per kg body weight, L/kg BW.
Volume of the rest of the body per kg body weight, L/kg BW.
Volume of the veins per kg body weight, L/kg BW.
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 animal values with human values if true (hepatic intrinsic clearance or fraction of unbound plasma).
Specifies compartment names and tissues groupings. Remaining tissues in tissue.data are lumped in the rest of the body. However, solve_pbtk only works with the default parameters.
Forces use of human values for hepatic intrinsic clearance and fraction of unbound plasma if true.
Hepatic clearance for chemicals where the in vitro clearance assay result has a p-values greater than the threshold are set to zero.
Returns adjusted Funbound.plasma when set to TRUE along with parition coefficients calculated with this value.
Whether or not to use the regressions in calculating partition coefficients.
Whether or not the output message is suppressed.
In calculating hepatic.bioavailability, protein binding is not taken into account (set to 1) in liver clearance if FALSE.
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_pbtk(chem.cas='80-05-7')
parameters <- parameterize_pbtk(chem.name='Bisphenol-A',species='Rat')
# Change the tissue lumping (note, these model parameters will not work with our current solver):
compartments <- list(liver=c("liver"),fast=c("heart","brain","muscle","kidney"),
lung=c("lung"),gut=c("gut"),slow=c("bone"))
parameterize_pbtk(chem.name="Bisphenol a",species="Rat",default.to.human=TRUE,
tissuelist=compartments)
Run the code above in your browser using DataLab