In Vitro Toxicokinetic Data Processing and Analysis Pipeline
Caco-2 Chemical Information Example Data set
Clint Chemical Information Example Data set
Fup UC Level-4 PREJAGS arguments
Heaviside
Set Initial Values for Intrinsic Hepatic Clearance (Clint) Bayesian Mo...
Set Initial Values for Fup RED Bayesian Model
Set Initial Values for Fup UC Bayesian Model
Common Columns in Level-1
Merge Multiple Level-0 files into a Single Table for Processing
Check the character columns are correctly of character class.
Check there is no missing data for specified columns.
Check the numeric columns are correctly of numeric class.
Check the standard column names are in the data.
Function to Check Level 0 Data Catalog
Build Data Object for Fup UC Bayesian Model
Calculate Intrinsic Hepatic Clearance (Clint) with Bayesian Modeling (...
Calculate Point Estimates of Fraction Unbound in Plasma (Fup) with Rap...
Calculate Fraction Unbound in Plasma (Fup) from Rapid Equilibrium Dial...
Calculate Point Estimates of Fraction Unbound in Plasma (Fup) with Ult...
Calculate Fraction Unbound in Plasma (Fup) from Ultracentrifugation (U...
Build Data Object for Intrinsic Hepatic Clearance (Clint) Bayesian Mod...
Build Data Object for Fup RED Bayesian Model
Caco-2 Level-0 Example Data set
Caco-2 Level-1 Example Data set
Caco-2 Level-2 Example Data set
Caco-2 Level-3 Example Data set
Calculate a Point Estimate of Apparent Membrane Permeability (Papp) fr...
Calculate a Point Estimate of Intrinsic Hepatic Clearance (Clint) (Lev...
Clint Level-0 Example Data set
Clint Level-1 Example Data set
Clint Level-2 Heldout Example Data set
Clint Level-2 Example Data set
Clint Level-3 Example Data set
Creates a Standardized Data Table for Chemical Analysis Methods
Clint Level-4 Example Data set
Clint Level-4 PREJAGS arguments
Function to create a catalog of level 0 files to be merged.
Creates a Standardized Data Table of Chemical Identities
Check if all the data is missing for specified columns.
Extract level 1 ultracentrifugation \insertCite redgrave1975separation...
Creates a Standardized Data Frame with Caco-2 Data (Level-1)
Creates a Standardized Data Frame with Hepatocyte Clearance Data (Leve...
Creates a Standardized Data Frame with Rapid Equilibrium Dialysis (RED...
Creates a Standardized Data Frame with Ultracentrifugation (UC) Plasma...
Fup RED Chemical Information Example Data set
Fup RED Level-0 Example Data set
Fup RED Level-1 Example Data set
Fup RED Level-2 Heldout Example Data set
Fup RED Level-2 Example Data set
Fup RED Level-3 Example Data set
Fup RED Level-4 Example Data set
Fup RED Level-4 PREJAGS arguments
Fup UC Chemical Information Example Data set
Fup UC Level-0 Example Data set
Fup UC Level-1 Example Data set
Fup UC Level-2 Heldout Example Data set
Fup UC Level-2 Example Data set
Fup UC Level-3 Example Data set
Fup UC Level-4 Example Data set
Plot Mass Spectrometry Responses from Measurements of Intrinsic Hepati...
Plot Mass Spectrometry Responses for Fraction Unbound in Plasma Data f...
Round Numeric Data (Any Level and Assay)
Convert a runjags-class object to a list
Add Sample Verification Column (Level-2)
Formatting function for X-axis in log10-scale
Creates a Summary Table of Mass-Spectrometry (MS) Data
A set of tools for processing and analyzing in vitro toxicokinetic measurements in a standardized and reproducible pipeline. The package was developed to perform frequentist and Bayesian estimation on a variety of in vitro toxicokinetic measurements including -- but not limited to -- chemical fraction unbound in the presence of plasma (f_up), intrinsic hepatic clearance (Clint, uL/min/million hepatocytes), and membrane permeability for oral absorption (Caco2). The methods provided by the package were described in Wambaugh et al. (2019) <doi:10.1093/toxsci/kfz205>.