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httk (version 1.3)

High-Throughput Toxicokinetics

Description

Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").

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Version

Install

install.packages('httk')

Monthly Downloads

588

Version

1.3

License

GPL-3

Maintainer

John Wambaugh

Last Published

October 14th, 2015

Functions in httk (1.3)

calc_stats

Calculate the statistics.
calc_analytic_css

Calculate the analytic steady state concentration.
get_wetmore_cheminfo

Get Wetmore Chemical Information.
calc_hepatic_clearance

Calculate the hepatic clearance.
export_pbtk_jarnac

Export model to jarnac.
predict_partitioning_schmitt

Predict partition coefficients using the method from Schmitt (2008).
in.list

Convenience Boolean (yes/no) functions to idnetify chemical membership in several key lists.
get_wetmore_oral_equiv

Get Wetmore Oral Equivalent Dose
calc_rblood2plasma

Calculate the constant ratio of the blood concentration to the plasma concentration.
calc_css

Find the steady state concentration and the day it is reached.
chem.invivo.PK.data

Published toxicokinetic time course measurements
Wetmore.data

Published toxicokinetic predictions based on in vitro data
get_wetmore_css

Get Wetmore Css
chem.physical_and_invitro.data

Physico-chemical properties and in vitro measurements for toxicokinetics
add_chemtable

Add a table of chemical information for use in making httk predictions.
calc_elimination_rate

Calculate the elimination rate for a one compartment model.
calc_vdist

Calculate the volume of distribution for a one compartment model.
parameterize_3comp

Parameterize_3comp
chem.lists

Chemical membership in different research projects
calc_mc_oral_equiv

Calculate Monte Carlo Oral Equivalent Dose
calc_ionization

Calculate the ionization.
parameterize_1comp

Parameterize_1comp
parameterize_steadystate

Parameterize_SteadyState
calc_total_clearance

Calculate the total clearance.
export_pbtk_sbml

Export model to sbml.
chem.invivo.PK.summary.data

Summary of published toxicokinetic time course experiments
tissue.data

Tissue composition and species-specific physiology parameters
parameterize_schmitt

Parameterize Schmitt's method.
PK.physiology.data

Species-specific physiology parameters
solve_3comp

Solve_3comp
monte_carlo

Monte Carlo for pharmacokinetic models
solve_pbtk

Solve_PBTK
solve_1comp

Solve one compartment TK model
parameterize_pbtk

Parameterize_PBTK
get_cheminfo

Retrieve chemical information from HTTK package
calc_mc_css

Find the monte carlo steady state concentration.