httk: High-Throughput Toxicokinetics

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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

View on CRAN

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