clint_PREJAGS: Clint Level-4 PREJAGS arguments
In invitroTKstats: In Vitro Toxicokinetic Data Processing and Analysis Pipeline

clint_PREJAGS

R Documentation

Clint Level-4 PREJAGS arguments

Description

The arguments given to JAGS for the tested compound during level-4 processing of mass spectrometry measurements of intrinsic hepatic clearance (Clint) for cryopreserved pooled human hepatocytes. Chemicals were per- and poly-fluorinated alkyl substance (PFAS) samples. The experiments were led by Dr.s Marci Smeltz and Barbara Wetmore \insertCitesmeltz2023plasmainvitroTKstats. This list is overwritten for each tested compound. Therefore, only contains arguments given to JAGS for the last tested compound.

Usage

clint_PREJAGS

Format

A named list with 26 elements:

obs: Response of the "Cvst" sample types for the tested compound
Test.Nominal.Conc: Unique Test.Nominal.Conc values (expected initial concentration) of "Cvst" sample types
Num.cal: Unique number of Calibration values
Num.obs: Number of Response of the "Cvst" sample types for the tested compound
obs.conc: Indices of the Test.Nominal.Conc values that corresponds to the "Cvst" sample types' Test.Nominal.Conc
obs.time: Time of the "Cvst" sample types for the tested compound
obs.cal: Indices of the unique "Cvst" Calibration values that corresponds to the "Cvst" sample types' Calibration
obs.Dilution.Factor: Dilution Factor of the "Cvst" sample types for the tested compound (number of times the sample was diluted)
Num.blank.obs: Number of "Blank" sample types for the tested compound
Blank.obs: Response of the "Blank" sample types for the tested compound
Blank.cal: Indices of the unique "Blank" Calibration values that corresponds to the "Blank" sample types' Calibration
Blank.Dilution.Factor: Dilution Factor of the "Blank" sample types for the tested compound (number of times the sample was diluted)
Num.cc: Number of "CC" sample types with non-NA Test.Compound.Conc values for the tested compound
cc.obs.conc: Test.Compound.Conc (non-NA) of the "CC" sample types for the tested compound
cc.obs: Response of the "CC" sample types with non-NA Test.Compound.Conc for the tested compound
cc.obs.cal: Indices of the unique "CC" Calibration values that corresponds to the "CC" sample types' Calibration
cc.obs.Dilution.Factor: Dilution Factor of the "CC" sample types (number of times the sample was diluted) with non-NA Test.Compound.Conc for the tested compound
Num.abio.obs: Number of "Inactive" samples types for the tested compound
abio.obs: Response of the "Inactive" sample types for the tested compound
abio.obs.conc: Indices of the Test.Nominal.Conc values that corresponds to the "Inactive" sample types' Test.Nominal.Conc
abio.obs.time: Time of the "Inactive" sample types for the tested compound
abio.obs.cal: Indices of the unique "Inactive" Calibration values that corresponds to the "Inactive" sample types' Calibration
abio.obs.Dilution.Factor: Dilution Factor of the "Inactive" sample types for the tested compound (number of times the sample was diluted)
DECREASE.PROB: Prior probability that a chemical will decrease in the assay. (Defaults to 0.5.)
SATURATE.PROB: Prior probability that a chemicals rate of metabolism will decrease between 1 and 10 uM. (Defaults to 0.25.)
DEGRADE.PROB: Prior probability that a chemical will be unstable (degrade abiotically) in the assay. (Defaults to 0.05.)