# httk: High-Throughput Toxicokinetics

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").

- Author
- John Wambaugh and Robert Pearce, Schmitt method implementation by Jimena Davis, dynamic model adapted from code by R. Woodrow Setzer, Rabbit parameters from Nisha Sipes
- Date of publication
- 2016-02-03 01:14:25
- Maintainer
- John Wambaugh <wambaugh.john@epa.gov>
- License
- GPL-3
- Version
- 1.4

## Man pages

- add_chemtable
- Add a table of chemical information for use in making httk...
- calc_analytic_css
- Calculate the analytic steady state concentration.
- calc_css
- Find the steady state concentration and the day it is...
- Calc_elimination_rate
- Calculate the elimination rate for a one compartment model.
- calc_hepatic_clearance
- Calculate the hepatic clearance.
- calc_ionization
- Calculate the ionization.
- calc_mc_css
- Find the monte carlo steady state concentration.
- calc_mc_oral_equiv
- Calculate Monte Carlo Oral Equivalent Dose
- Calc_ratioblood2plasma
- Calculate the constant ratio of the blood concentration to...
- calc_stats
- Calculate the statistics.
- calc_total_clearance
- Calculate the total clearance.
- Calc_volume_of_distriution
- Calculate the volume of distribution for a one compartment...
- chem_invivo_PK_data
- Published toxicokinetic time course measurements
- chem_invivo_PK_summary_data
- Summary of published toxicokinetic time course experiments
- chem.lists
- Chemical membership in different research projects
- chem_physical_and_invitro_data
- Physico-chemical properties and in vitro measurements for...
- export_pbtk_jarnac
- Export model to jarnac.
- export_pbtk_sbml
- Export model to sbml.
- get_cheminfo
- Retrieve chemical information from HTTK package
- get_wetmore_cheminfo
- Get Wetmore Chemical Information.
- in_list
- Convenience Boolean (yes/no) functions to idnetify chemical...
- lump_tissues
- Lump tissue parameters
- monte_carlo
- Monte Carlo for pharmacokinetic models
- parameterize_1comp
- Parameterize_1comp
- parameterize_3comp
- Parameterize_3comp
- Parameterize_PBTK
- Parameterize_PBTK
- parameterize_schmitt
- Parameterize Schmitt's method.
- Parameterize_SteadyState
- Parameterize_SteadyState
- PK_physiology_data
- Species-specific physiology parameters
- predict_partitioning_schmitt
- Predict partition coefficients using the method from Schmitt...
- solve_1comp_pk
- Solve one compartment TK model
- solve_3comp_pbpk
- Solve_3comp
- solve_pbtk
- Solve_PBTK
- tissue_data
- Tissue composition and species-specific physiology parameters
- Wetmore_Css
- Get Wetmore Css
- Wetmore.data
- Published toxicokinetic predictions based on in vitro data
- Wetmore_Oral_Equiv
- Get Wetmore Oral Equivalent Dose

## Files in this package

httk |

httk/tests |

httk/tests/cheminfo_test.R |

httk/tests/cheminfo_test.Rout.save |

httk/tests/other_tests.R |

httk/tests/other_tests.Rout.save |

httk/src |

httk/src/vLiverPBPK.c |

httk/src/3compPBPKmodel.c |

httk/src/pbtk1comp.c |

httk/NAMESPACE |

httk/data |

httk/data/Tables.RData |

httk/R |

httk/R/ionization_functions.R |

httk/R/get_chem_id.R |

httk/R/calc_analytic_css.R |

httk/R/get_Wetmore_Oral_Equiv.R |

httk/R/Parameterize_3comp.r |

httk/R/lump_tissues.R |

httk/R/parameterize_1comp.R |

httk/R/solve_1comp.R |

httk/R/3compPBPKmodel_inits.R |

httk/R/solve_pbtk.R |

httk/R/r_left_censored_norm.R |

httk/R/monte_carlo.R |

httk/R/get_Wetmore_cheminfo.R |

httk/R/get_cheminfo.R |

httk/R/Calc_Hepatic_Clearance.r |

httk/R/Calc_ratioblood2plasma.R |

httk/R/calc_mc_oral_equiv.R |

httk/R/parameterize_schmitt.R |

httk/R/solve_3comp.R |

httk/R/Export_PBTK_Jarnac.R |

httk/R/Get_invitroPK_param.r |

httk/R/get_param.r |

httk/R/add_chemtable.R |

httk/R/calc_fu_hep.R |

httk/R/Parameterize_PBTK.r |

httk/R/Calc_elimination_rate.R |

httk/R/calc_chem_stats.R |

httk/R/Calc_volume_of_distribution.R |

httk/R/get_Wetmore_Css.R |

httk/R/Predict_partitioning_Schmitt.R |

httk/R/Calc_timecourse_peak.r |

httk/R/Calc_total_clearance.R |

httk/R/pbtk1comp_inits.R |

httk/R/in.list.R |

httk/R/Parameterize_SteadyState.R |

httk/R/calc_mc_css.R |

httk/R/Export_PBTK_SBML.R |

httk/R/calc_stats.R |

httk/R/vLiverPBPK_inits.R |

httk/R/Get_physchem_param.r |

httk/R/calc_css.R |

httk/MD5 |

httk/DESCRIPTION |

httk/man |

httk/man/Calc_elimination_rate.Rd |

httk/man/chem_physical_and_invitro_data.Rd |

httk/man/get_cheminfo.Rd |

httk/man/lump_tissues.Rd |

httk/man/add_chemtable.Rd |

httk/man/calc_stats.Rd |

httk/man/Parameterize_PBTK.Rd |

httk/man/parameterize_schmitt.Rd |

httk/man/Wetmore_Oral_Equiv.Rd |

httk/man/calc_total_clearance.Rd |

httk/man/chem.lists.Rd |

httk/man/monte_carlo.Rd |

httk/man/tissue_data.Rd |

httk/man/Wetmore.data.Rd |

httk/man/export_pbtk_jarnac.Rd |

httk/man/calc_mc_css.Rd |

httk/man/get_wetmore_cheminfo.Rd |

httk/man/calc_ionization.Rd |

httk/man/chem_invivo_PK_summary_data.Rd |

httk/man/parameterize_3comp.Rd |

httk/man/in_list.Rd |

httk/man/calc_css.Rd |

httk/man/calc_hepatic_clearance.Rd |

httk/man/PK_physiology_data.Rd |

httk/man/Calc_volume_of_distriution.Rd |

httk/man/Wetmore_Css.Rd |

httk/man/calc_analytic_css.Rd |

httk/man/export_pbtk_sbml.Rd |

httk/man/chem_invivo_PK_data.Rd |

httk/man/parameterize_1comp.Rd |

httk/man/Calc_ratioblood2plasma.Rd |

httk/man/solve_1comp_pk.Rd |

httk/man/predict_partitioning_schmitt.Rd |

httk/man/Parameterize_SteadyState.Rd |

httk/man/solve_3comp_pbpk.Rd |

httk/man/solve_pbtk.Rd |

httk/man/calc_mc_oral_equiv.Rd |