get_fbio: Retrieve or calculate fraction of chemical absorbed from the...
In httk: High-Throughput Toxicokinetics

get_fbio

R Documentation

Retrieve or calculate fraction of chemical absorbed from the gut

Description

This function checks for chemical-specific in vivo measurements of the fraction absorbed from the gut in the chem.physical_and_invitro.data table. If in vivo data are unavailable (or keepit100 == TRUE) we attempt to use in vitro Caco-2 membrane permeability to predict the fractions according to calc_fbio.oral.

Usage

get_fbio(
  parameters = NULL,
  chem.cas = NULL,
  chem.name = NULL,
  dtxsid = NULL,
  species = "Human",
  default.to.human = FALSE,
  Caco2.Pab.default = 1.6,
  Caco2.Fgut = TRUE,
  Caco2.Fabs = TRUE,
  overwrite.invivo = FALSE,
  keepit100 = FALSE,
  suppress.messages = FALSE
)

Arguments

`parameters`	A list of the parameters (Caco2.Pab, Funbound.Plasma, Rblood2plasma, Clint, BW, Qsmallintestine, Fabs, Fgut) used in the calculation, either supplied by user or calculated in parameterize_steady_state.
`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.
`Caco2.Pab.default`	sets the default value for Caco2.Pab if Caco2.Pab is unavailable.
`Caco2.Fgut`	= TRUE uses Caco2.Pab to calculate fgut.oral, otherwise fgut.oral = `Fgut`.
`Caco2.Fabs`	= TRUE uses Caco2.Pab to calculate fabs.oral, otherwise fabs.oral = `Fabs`.
`overwrite.invivo`	= TRUE overwrites Fabs and Fgut in vivo values from literature with Caco2 derived values if available.
`keepit100`	TRUE overwrites Fabs and Fgut with 1 (i.e. 100 percent) regardless of other settings.
`suppress.messages`	Whether or not the output message is suppressed.