View source: R/parameterize_1comp.R
parameterize_1comp | R Documentation |
This function initializes the parameters needed in the function solve_1comp. Volume of distribution is estimated by using a modified Schmitt (2008) method to predict tissue particition coefficients (Pearce et al., 2017) and then lumping the compartments weighted by tissue volume:
parameterize_1comp(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
species = "Human",
default.to.human = FALSE,
adjusted.Funbound.plasma = TRUE,
adjusted.Clint = TRUE,
regression = TRUE,
restrictive.clearance = TRUE,
well.stirred.correction = TRUE,
suppress.messages = FALSE,
clint.pvalue.threshold = 0.05,
minimum.Funbound.plasma = 1e-04,
Caco2.options = list()
)
chem.cas |
Chemical Abstract Services Registry Number (CAS-RN) – the chemical must be identified by either CAS, name, or DTXISD |
chem.name |
Chemical name (spaces and capitalization ignored) – the chemical must be identified by either CAS, name, or DTXISD |
dtxsid |
EPA's DSSTox Structure ID (https://comptox.epa.gov/dashboard) – the chemical must be identified by either CAS, name, or DTXSIDs |
species |
Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human"). |
default.to.human |
Substitutes missing rat values with human values if true. |
adjusted.Funbound.plasma |
Uses Pearce et al. (2017) lipid binding adjustment for Funbound.plasma (which impacts volume of distribution) when set to TRUE (Default). |
adjusted.Clint |
Uses Kilford et al. (2008) hepatocyte incubation binding adjustment for Clint when set to TRUE (Default). |
regression |
Whether or not to use the regressions in calculating partition coefficients in volume of distribution calculation. |
restrictive.clearance |
In calculating elimination rate and hepatic bioavailability, protein binding is not taken into account (set to 1) in liver clearance if FALSE. |
well.stirred.correction |
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. |
suppress.messages |
Whether or not to suppress messages. |
clint.pvalue.threshold |
Hepatic clearance for chemicals where the in vitro clearance assay result has a p-value greater than the threshold are set to zero. |
minimum.Funbound.plasma |
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). |
Caco2.options |
A list of options to use when working with Caco2 apical to
basolateral data |
V_d,steady-state = Sum over all tissues (K_i * V_i) + V_plasma
where K_i is the tissue:unbound plasma concentration partition coefficient for tissue i.
Vdist |
Volume of distribution, units of L/kg BW. |
Fabsgut |
Fraction of the oral dose absorbed and surviving gut metabolism, i.e. the fraction of the dose that enters the gutlumen. |
kelim |
Elimination rate, units of 1/h. |
hematocrit |
Percent volume of red blood cells in the blood. |
Fabsgut |
Fraction of the oral dose absorbed, i.e. the fraction of the dose that enters the gutlumen. |
Fhep.assay.correction |
The fraction of chemical unbound in hepatocyte assay using the method of Kilford et al. (2008) |
kelim |
Elimination rate, units of 1/h. |
hematocrit |
Percent volume of red blood cells in the blood. |
kgutabs |
Rate chemical is absorbed, 1/h. |
million.cells.per.gliver |
Millions cells per gram of liver tissue. |
MW |
Molecular Weight, g/mol. |
Rblood2plasma |
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. |
hepatic.bioavailability |
Fraction of dose remaining after first pass clearance, calculated from the corrected well-stirred model. |
BW |
Body Weight, kg. |
John Wambaugh and Robert Pearce
pearce2017httkhttk
\insertRefschmitt2008generalhttk
\insertRefpearce2017evaluationhttk
\insertRefkilford2008hepatocellularhttk
solve_1comp
calc_analytic_css_1comp
calc_vdist
parameterize_steadystate
apply_clint_adjustment
tissue.data
physiology.data
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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