Package: invitroTKstats 0.0.14

Caroline Ring

invitroTKstats: In Vitro Toxicokinetic Data Processing and Analysis Pipeline

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>.

Authors:John Wambaugh [aut], Caroline Ring [cre], Sarah E. Davidson-Fritz [aut], Lindsay Knupp [ctb], Barbara A. Wetmore [ctb], Zhao Zhihui [ctb], Chantel Nicolas [ctb], Anna Kreutz [ctb], U.S. Federal Government [cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
invitroTKstats/json (API)

# Install 'invitroTKstats' in R:
install.packages('invitroTKstats', repos = c('https://usepa.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/usepa/invitrotkstats/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

jagscpp

6.88 score 2 stars 73 scripts 171 downloads 21 exports 37 dependencies

Last updated from:43cb092157. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK169
source / vignettesOK264
linux-release-x86_64OK216
macos-release-arm64OK139
macos-oldrel-arm64OK121
windows-develOK125
windows-releaseOK126
windows-oldrelOK125
wasm-releaseOK138

Exports:calc_caco2_pointcalc_clintcalc_clint_pointcalc_fup_redcalc_fup_red_pointcalc_fup_uccalc_fup_uc_pointcheck_catalogcreate_catalogcreate_chem_tablecreate_method_tableformat_caco2format_clintformat_fup_redformat_fup_ucmerge_level0plot_clintplot_fup_ucround_outputsample_verificationsummarize_table

Dependencies:cellrangerclicodacpp11crayondplyrfarvergenericsggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrpillarpkgconfigprettyunitsprogressR6rbibutilsRColorBrewerRdpackreadxlrematchrlangrunjagsS7scalestibbletidyselectutf8vctrsviridisLitewithr

Apparent Membrane Permeability (Caco-2)
Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Best Practices: Food for thought | References
Rendered fromCaco2_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-07-24

Intrinsic Hepatic Clearance (Cl~int~)
Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Level 4 processing | Best Practices: Food for thought | Appendix | L4 Bayesian Modeling Information | Measurement Model | Estimation of Blanks | Estimation of Calibration Curve | Clearance Model | Estimation of Metabolic Clearance | Estimation of Abiotic Clearance | Post-MCMC Estimates | JAGS to L4 Equation Notation Tables | References
Rendered fromClint_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-07-24

Fraction Unbound in Plasma - Rapid Equilibrium Dialysis (f~up~ RED)
Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Level 4 processing | Best Practices: Food for thought | Appendix | L4 Bayesian Modeling Information | Measurement Model | Estimation for Blanks with No Plasma | Estimation for Blanks with Plasma | Estimation for Initial Time (T0) | Estimation for the Calibration Curve | Estimation for the RED Plasma Protein Binding Assay | Concentrations for Replicates | Estimation for PBS | Estimation for Plasma | Post-MCMC Estimates | Fraction of Chemical Unbound in Plasma (Bayesian Estimates) | Fraction Unbound in Plasma (Empirical Point Estimate) | JAGS to L4 Equation Notation Tables | References
Rendered fromFupRED_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-07-24

Fraction Unbound in Plasma - Ultracentrifugation (f~up~ UC)
Introduction | Suggested packages for use with this vignette | Load Data | Level 1 processing | Level 2 processing | Level 3 processing | Level 4 processing | Best Practices: Food for thought | Appendix | L4 Bayesian Modeling Information | Measurement Model | Estimation of Response Observations | Binding Model | Post-MCMC Estimates | Fraction of Chemical Stability | Fraction of Chemical Unbound in Plasma (Bayesian Estimates) | Fraction Unbound in Plasma (Empirical Point Estimate) | JAGS to L4 Equation Notation Tables | References
Rendered fromFupUC_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-07-24

Appendix
Introduction | Data Notation | Function Notation
Rendered fromAppendix_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-07-24
Started: 2025-07-24

Data Guide Creation and Level-0 Data Compilation
Overview | Suggested packages for use with this vignette | Raw Data File Exploration | Data Catalog | Chemical ID Map | Level-0 (L0) Data Compilation | Best Practices for Data Processing | References
Rendered fromData-guide-and-L0_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-07-24
Started: 2025-07-24

Plotting Functions
Introduction | Set Up | plot_clint.R | plot_fup_uc.R | References
Rendered fromplotting-invitroTKstats.Rmdusingknitr::rmarkdown

Last update: 2025-07-24
Started: 2025-07-24

Readme and manuals

Help Manual

Help pageTopics
Check if all the data is missing for specified columns..check_all_miss_cols
Check the character columns are correctly of character class..check_char_cols
Check there is no missing data for specified columns..check_no_miss_cols
Check the numeric columns are correctly of numeric class..check_num_cols
Check the standard column names are in the data..check_std_colnames_in_data
Build Data Object for Intrinsic Hepatic Clearance (Clint) Bayesian Modelbuild_mydata_clint
Build Data Object for Fup RED Bayesian Modelbuild_mydata_fup_red
Build Data Object for Fup UC Bayesian Modelbuild_mydata_fup_uc
Caco-2 Chemical Information Example Data setcaco2_cheminfo
Caco-2 Level-0 Example Data setcaco2_L0
Caco-2 Level-1 Example Data setcaco2_L1
Caco-2 Level-2 Example Data setcaco2_L2
Caco-2 Level-3 Example Data setcaco2_L3
Calculate a Point Estimate of Apparent Membrane Permeability (Papp) from Caco-2 data (Level-3)calc_caco2_point
Calculate Intrinsic Hepatic Clearance (Clint) with Bayesian Modeling (Level-4)calc_clint
Calculate a Point Estimate of Intrinsic Hepatic Clearance (Clint) (Level-3)calc_clint_point
Calculate Fraction Unbound in Plasma (Fup) from Rapid Equilibrium Dialysis (RED) Data with Bayesian Modeling (Level-4)calc_fup_red
Calculate Point Estimates of Fraction Unbound in Plasma (Fup) with Rapid Equilibrium Dialysis (RED) Data (Level-3)calc_fup_red_point
Calculate Fraction Unbound in Plasma (Fup) from Ultracentrifugation (UC) Data with Bayesian Modeling (Level-4)calc_fup_uc
Calculate Point Estimates of Fraction Unbound in Plasma (Fup) with Ultracentrifugation (UC) Data (Level-3)calc_fup_uc_point
Function to Check Level 0 Data Catalogcheck_catalog
Clint Chemical Information Example Data setclint_cheminfo
Clint Level-0 Example Data setclint_L0
Clint Level-1 Example Data setclint_L1
Clint Level-2 Example Data setclint_L2
Clint Level-2 Heldout Example Data setclint_L2_heldout
Clint Level-3 Example Data setclint_L3
Clint Level-4 Example Data setclint_L4
Clint Level-4 PREJAGS argumentsclint_PREJAGS
Function to create a catalog of level 0 files to be merged.create_catalog
Creates a Standardized Data Table of Chemical Identitiescreate_chem_table
Creates a Standardized Data Table for Chemical Analysis Methodscreate_method_table
Extract level 1 ultracentrifugation (Redgrave et al. 1975) data from wide level 0 fileextract_level1_fup_uc
Creates a Standardized Data Frame with Caco-2 Data (Level-1)format_caco2
Creates a Standardized Data Frame with Hepatocyte Clearance Data (Level-1)format_clint
Creates a Standardized Data Frame with Rapid Equilibrium Dialysis (RED) Plasma Protein Binding (PPB) Data (Level-1)format_fup_red
Creates a Standardized Data Frame with Ultracentrifugation (UC) Plasma Protein Binding (PPB) Data (Level-1)format_fup_uc
Fup RED Chemical Information Example Data setfup_red_cheminfo
Fup RED Level-0 Example Data setfup_red_L0
Fup RED Level-1 Example Data setfup_red_L1
Fup RED Level-2 Example Data setfup_red_L2
Fup RED Level-2 Heldout Example Data setfup_red_L2_heldout
Fup RED Level-3 Example Data setfup_red_L3
Fup RED Level-4 Example Data setfup_red_L4
Fup RED Level-4 PREJAGS argumentsfup_red_PREJAGS
Fup UC Chemical Information Example Data setfup_uc_cheminfo
Fup UC Level-0 Example Data setfup_uc_L0
Fup UC Level-1 Example Data setfup_uc_L1
Fup UC Level-2 Example Data setfup_uc_L2
Fup UC Level-2 Heldout Example Data setfup_uc_L2_heldout
Fup UC Level-3 Example Data setfup_uc_L3
Fup UC Level-4 Example Data setfup_uc_L4
Fup UC Level-4 PREJAGS argumentsfup_uc_PREJAGS
HeavisideHeaviside
Set Initial Values for Intrinsic Hepatic Clearance (Clint) Bayesian Modelinitfunction_clint
Set Initial Values for Fup RED Bayesian Modelinitfunction_fup_red
Set Initial Values for Fup UC Bayesian Modelinitfunction_fup_uc
Common Columns in Level-1L1.common.col L1.common.cols
Merge Multiple Level-0 files into a Single Table for Processingmerge_level0
Plot Mass Spectrometry Responses from Measurements of Intrinsic Hepatic Clearanceplot_clint
Plot Mass Spectrometry Responses for Fraction Unbound in Plasma Data from Ultracentrifugation (UC)plot_fup_uc
Round Numeric Data (Any Level and Assay)round_output
Convert a runjags-class object to a listrunjagsdata.to.list
Add Sample Verification Column (Level-2)sample_verification
Formatting function for X-axis in log10-scalescientific_10
Standard Data Catalog (Data Guide) Columnsstd.catcols
Creates a Summary Table of Mass-Spectrometry (MS) Datasummarize_table