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").

AuthorJohn 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 publication2016-02-03 01:14:25
MaintainerJohn Wambaugh <wambaugh.john@epa.gov>
LicenseGPL-3
Version1.4

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

Functions

add_chemtable Man page
calc_analytic_css Man page
calc_css Man page
calc_elimination_rate Man page
calc_hepatic_clearance Man page
calc_ionization Man page
calc_mc_css Man page
calc_mc_oral_equiv Man page
calc_rblood2plasma Man page
calc_stats Man page
calc_total_clearance Man page
calc_vdist Man page
chem.invivo.PK.data Man page
chem.invivo.PK.summary.data Man page
chem.lists Man page
chem.physical_and_invitro.data Man page
export_pbtk_jarnac Man page
export_pbtk_sbml Man page
get_cheminfo Man page
get_wetmore_cheminfo Man page
get_wetmore_css Man page
get_wetmore_oral_equiv Man page
in.list Man page
is.expocast Man page
is.httk Man page
is.nhanes Man page
is.nhanes.blood.analyte Man page
is.nhanes.blood.parent Man page
is.nhanes.serum.analyte Man page
is.nhanes.serum.parent Man page
is.nhanes.urine.analyte Man page
is.nhanes.urine.parent Man page
is.tox21 Man page
is.toxcast Man page
lump_tissues Man page
monte_carlo Man page
parameterize_1comp Man page
parameterize_3comp Man page
parameterize_pbtk Man page
parameterize_schmitt Man page
parameterize_steadystate Man page
physiology.data Man page
predict_partitioning_schmitt Man page
solve_1comp Man page
solve_3comp Man page
solve_pbtk Man page
tissue.data Man page
Wetmore.data Man page

Files

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

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