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").

Install the latest version of this package by entering the following in R:
install.packages("httk")
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 publication2017-03-03 18:16:04
MaintainerJohn Wambaugh <wambaugh.john@epa.gov>
LicenseGPL-3
Version1.5

View on CRAN

Man pages

add_chemtable: Add a table of chemical information for use in making httk...

age_dist_smooth: Smoothed age distributions by race and gender.

age_draw_smooth: Draws ages from a smoothed distribution for a given...

blood_mass_correct: Find average blood masses by age.

blood_weight: Predict blood mass.

bmiage: CDC BMI-for-age charts

body_surface_area: Predict body surface area.

bone_mass_age: Predict bone mass.

brain_mass: Predict brain mass.

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...

ckd_epi_eq: CKD-EPI equation for GFR.

convert_httk: Converts HTTK-Pop virtual population into parameters relevant...

draw_fup_clint: Draw Funbound.plasma and Clint from censored or non-censored...

estimate_gfr: Predict GFR.

estimate_gfr_ped: Predict GFR in children.

estimate_hematocrit: Predict hematocrit using smoothing spline.

export_pbtk_jarnac: Export model to jarnac.

export_pbtk_sbml: Export model to sbml.

gen_age_height_weight: Generate ages, heights, and weights for a virtual population...

gen_height_weight: Generate heights and weights for a virtual population.

get_cheminfo: Retrieve chemical information from HTTK package

get_gfr_category: Categorize kidney function by GFR.

get_httk_params: Converts the HTTK-Pop population data table to a table of the...

get_rblood2plasma: Get ratio of the blood concentration to the plasma...

get_weight_class: Given vectors of age, BMI, recumbent length, weight, and...

get_wetmore_cheminfo: Get Wetmore Chemical Information.

hematocrit_infants: Predict hematocrit in infants under 1 year old.

howgate: Howgate 2006

httkpop: httkpop: Virtual population generator for HTTK.

httkpop_bio: Convert HTTK-Pop-generated parameters to HTTK physiological...

httkpop_direct_resample: Generate a virtual population by directly resampling the...

httkpop_direct_resample_inner: Inner loop function called by 'httkpop_direct_resample'.

httkpop_generate: Generate a virtual population

httkpop_virtual_indiv: Generate a virtual population by the virtual individuals...

in_list: Convenience Boolean (yes/no) functions to idnetify chemical...

is_in_inclusive: Checks whether a value, or all values in a vector, is within...

johnson: Johnson 2006

kidney_mass_children: Predict kidney mass for children.

liver_mass_children: Predict liver mass for children.

lump_tissues: Lump tissue parameters

lung_mass_children: Predict lung mass for children.

mcnally_dt: Reference tissue masses and flows from tables in McNally et...

monte_carlo: Monte Carlo for pharmacokinetic models

nhanes_mec_svy: Pre-processed NHANES data.

Obach2008: Published Pharmacokinetic Parameters from Obach et al. 2008

onlyp: NHANES Exposure Data

pancreas_mass_children: Predict pancreas mass for children.

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...

rfun: Randomly draws from a one-dimensional KDE

r_left_censored_norm: Returns draws from a normal distribution with a lower...

skeletal_muscle_mass: Predict skeletal muscle mass.

skeletal_muscle_mass_children: Predict skeletal muscle mass for children.

skin_mass_bosgra: Predict skin mass.

solve_1comp_pk: Solve one compartment TK model

solve_3comp_pbpk: Solve_3comp

solve_pbtk: Solve_PBTK

spleen_mass_children: Predict spleen mass for children.

spline_heightweight: Smoothing splines for log height vs. age and log body weight...

spline_hematocrit: Smoothing splines for log hematocrit vs. age in months, and...

spline_serumcreat: Smoothing splines for log serum creatinine vs. age in months,...

tc.dt: Toxcast Data

tissue_data: Tissue composition and species-specific physiology parameters

tissue_masses_flows: Given a data.table describing a virtual population by the...

tissue_scale: Allometric scaling.

Wetmore2012: Published toxicokinetic predictions based on in vitro data...

Wetmore_Css: Get Wetmore Css

Wetmore.data: Published toxicokinetic predictions based on in vitro data

Wetmore_Oral_Equiv: Get Wetmore Oral Equivalent Dose

wfl: WHO weight-for-length charts

Functions

add_chemtable Man page
age_dist_smooth Man page
age_draw_smooth Man page
blood_mass_correct Man page
blood_weight Man page
bmiage Man page
body_surface_area Man page
bone_mass_age Man page
brain_mass 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
ckd_epi_eq Man page
convert_httk Man page
draw_fup_clint Man page
estimate_gfr Man page
estimate_gfr_ped Man page
estimate_hematocrit Man page
export_pbtk_jarnac Man page
export_pbtk_sbml Man page
gen_age_height_weight Man page
gen_height_weight Man page
get_cheminfo Man page
get_gfr_category Man page
get_httk_params Man page
get_rblood2plasma Man page
get_weight_class Man page
get_wetmore_cheminfo Man page
get_wetmore_css Man page
get_wetmore_oral_equiv Man page
hematocrit_infants Man page
howgate Man page
httkpop Man page
httkpop_bio Man page
httkpop_direct_resample Man page
httkpop_direct_resample_inner Man page
httkpop_generate Man page
httkpop-package Man page
httkpop_virtual_indiv Man page
in.list Man page
is.expocast Man page
is.httk Man page
is_in_inclusive 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
johnson Man page
kidney_mass_children Man page
liver_mass_children Man page
lump_tissues Man page
lung_mass_children Man page
mcnally_dt Man page
monte_carlo Man page
nhanes_mec_svy Man page
Obach2008 Man page
onlyp Man page
pancreas_mass_children 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
rfun Man page
r_left_censored_norm Man page
skeletal_muscle_mass Man page
skeletal_muscle_mass_children Man page
skin_mass_bosgra Man page
solve_1comp Man page
solve_3comp Man page
solve_pbtk Man page
spleen_mass_children Man page
spline_heightweight Man page
spline_hematocrit Man page
spline_serumcreat Man page
tc.dt Man page
tissue.data Man page
tissue_masses_flows Man page
tissue_scale Man page
Wetmore2012 Man page
Wetmore.data Man page
wfl Man page

Files

inst
inst/doc
inst/doc/vignette03_paper_fig2.R
inst/doc/supplemental_vignette_globalsensitivityanalysis.html
inst/doc/vignette_05a_virtualstudypops.Rmd
inst/doc/vignette03_paper_fig2.html
inst/doc/supplemental_vignette_age_dist.Rmd
inst/doc/vignette01_subpopulations.R
inst/doc/supplemental_vignette_globalsensitivityanalysis.Rmd
inst/doc/vignette06_aerplotting.R
inst/doc/vignette_05a_virtualstudypops.html
inst/doc/httk.pdf.asis
inst/doc/vignette01_subpopulations.Rmd
inst/doc/supplemental_vignette_hematocrit_splines.Rmd
inst/doc/vignette05b_plothowgatejohnson.html
inst/doc/httk.pdf
inst/doc/supplemental_vignette_globalsensitivityplot.html
inst/doc/vignette02_evalmodelsubpop.Rmd
inst/doc/supplemental_vignette_heightweight_splines_kde.html
inst/doc/vignette04_paper_fig3.R inst/doc/supplemental_vignette_serumcreat_splines_kde.R inst/doc/vignette_05a_virtualstudypops.R
inst/doc/supplemental_vignette_age_dist.html
inst/doc/vignette02_evalmodelsubpop.R inst/doc/supplemental_vignette_plot_css95.R
inst/doc/supplemental_vignette_plot_css95.html
inst/doc/supplemental_vignette_hematocrit_splines.html
inst/doc/supplemental_vignette_serumcreat_splines_kde.html
inst/doc/supplemental_vignette_hematocrit_splines.R
inst/doc/supplemental_vignette_plot_css95.Rmd
inst/doc/vignette04_paper_fig3.html
inst/doc/supplemental_vignette_heightweight_splines_kde.Rmd
inst/doc/vignette06_aerplotting.html
inst/doc/supplemental_vignette_heightweight_splines_kde.R
inst/doc/vignette06_aerplotting.Rmd
inst/doc/vignette02_evalmodelsubpop.html
inst/doc/supplemental_vignette_serumcreat_splines_kde.Rmd
inst/doc/vignette01_subpopulations.html
inst/doc/vignette05b_plothowgatejohnson.R
inst/doc/supplemental_vignette_globalsensitivityplot.Rmd
inst/doc/vignette04_paper_fig3.Rmd
inst/doc/supplemental_vignette_globalsensitivityanalysis.R
inst/doc/vignette05b_plothowgatejohnson.Rmd
inst/doc/supplemental_vignette_globalsensitivityplot.R
inst/doc/vignette03_paper_fig2.Rmd
inst/doc/supplemental_vignette_age_dist.R
tests
tests/cheminfo_test.R
tests/cheminfo_test.Rout.save
tests/other_tests.R
tests/other_tests.Rout.save
src
src/vLiverPBPK.c
src/3compPBPKmodel.c
src/pbtk1comp.c
src/R_init_httk.c
NAMESPACE
NEWS
data
data/vignettes.RData
data/httkpop.RData
data/datalist
data/Tables.RData
R
R/tissue_mass_functions.R R/ionization_functions.R R/gen_age_height_weight.R R/utils.R R/get_chem_id.R R/get_weight_class.R R/calc_analytic_css.R R/get_rblood2plasma.R R/get_Wetmore_Oral_Equiv.R R/Parameterize_3comp.r R/estimate_gfr_ped.R R/lump_tissues.R R/parameterize_1comp.R R/solve_1comp.R R/httkpop_virtual_indiv.R R/3compPBPKmodel_inits.R R/solve_pbtk.R R/gen_height_weight.R R/r_left_censored_norm.R R/tissue_scale.R R/monte_carlo.R R/tissue_masses_flows.R R/httkpop_direct_resample_inner.R R/get_Wetmore_cheminfo.R R/data.R R/get_cheminfo.R R/Calc_Hepatic_Clearance.r R/httkpop_direct_resample.R R/Calc_ratioblood2plasma.R R/calc_mc_oral_equiv.R R/parameterize_schmitt.R R/solve_3comp.R R/Export_PBTK_Jarnac.R R/ckd_epi_eq.R R/Get_invitroPK_param.r R/get_param.r R/add_chemtable.R R/calc_fu_hep.R R/Parameterize_PBTK.r R/Calc_elimination_rate.R R/calc_chem_stats.R R/httkpop_generate.R R/Calc_volume_of_distribution.R R/get_Wetmore_Css.R R/httkpop.R R/Predict_partitioning_Schmitt.R R/Calc_timecourse_peak.r R/age_draw_smooth.R R/get_gfr_category.R R/Calc_total_clearance.R R/pbtk1comp_inits.R R/estimate_hematocrit.R R/in.list.R R/Parameterize_SteadyState.R R/calc_mc_css.R R/httkpop_bio.R R/Export_PBTK_SBML.R R/draw_fup_clint.R R/estimate_gfr.R R/calc_stats.R R/convert_httk.R R/vLiverPBPK_inits.R R/get_httk_params.R R/Get_physchem_param.r R/hematocrit_infants.R R/calc_css.R
vignettes
vignettes/vignette_05a_virtualstudypops.Rmd
vignettes/supplemental_vignette_age_dist.Rmd
vignettes/supplemental_vignette_globalsensitivityanalysis.Rmd
vignettes/httk.pdf.asis
vignettes/vignette01_subpopulations.Rmd
vignettes/supplemental_vignette_hematocrit_splines.Rmd
vignettes/vignette02_evalmodelsubpop.Rmd
vignettes/supplemental_vignette_plot_css95.Rmd
vignettes/supplemental_vignette_heightweight_splines_kde.Rmd
vignettes/vignette06_aerplotting.Rmd
vignettes/supplemental_vignette_serumcreat_splines_kde.Rmd
vignettes/supplemental_vignette_globalsensitivityplot.Rmd
vignettes/vignette04_paper_fig3.Rmd
vignettes/vignette05b_plothowgatejohnson.Rmd
vignettes/vignette03_paper_fig2.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/body_surface_area.Rd man/httkpop_direct_resample_inner.Rd man/johnson.Rd man/estimate_hematocrit.Rd man/get_gfr_category.Rd man/gen_age_height_weight.Rd man/Calc_elimination_rate.Rd man/chem_physical_and_invitro_data.Rd man/get_cheminfo.Rd man/convert_httk.Rd man/get_httk_params.Rd man/skeletal_muscle_mass_children.Rd man/lump_tissues.Rd man/add_chemtable.Rd man/lung_mass_children.Rd man/tissue_masses_flows.Rd man/age_draw_smooth.Rd man/is_in_inclusive.Rd man/calc_stats.Rd man/blood_mass_correct.Rd man/blood_weight.Rd man/Parameterize_PBTK.Rd man/parameterize_schmitt.Rd man/Wetmore_Oral_Equiv.Rd man/bmiage.Rd man/httkpop_bio.Rd man/calc_total_clearance.Rd man/chem.lists.Rd man/monte_carlo.Rd man/draw_fup_clint.Rd man/tissue_data.Rd man/Wetmore.data.Rd man/kidney_mass_children.Rd man/get_rblood2plasma.Rd man/export_pbtk_jarnac.Rd man/calc_mc_css.Rd man/Wetmore2012.Rd man/get_wetmore_cheminfo.Rd man/tissue_scale.Rd man/estimate_gfr_ped.Rd man/calc_ionization.Rd man/get_weight_class.Rd man/httkpop.Rd man/spline_serumcreat.Rd man/httkpop_generate.Rd man/chem_invivo_PK_summary_data.Rd man/parameterize_3comp.Rd man/mcnally_dt.Rd man/httkpop_virtual_indiv.Rd man/in_list.Rd man/skeletal_muscle_mass.Rd man/ckd_epi_eq.Rd man/gen_height_weight.Rd man/calc_css.Rd man/howgate.Rd man/spline_hematocrit.Rd man/wfl.Rd man/bone_mass_age.Rd man/Obach2008.Rd man/pancreas_mass_children.Rd man/calc_hepatic_clearance.Rd man/spleen_mass_children.Rd man/PK_physiology_data.Rd man/Calc_volume_of_distriution.Rd man/httkpop_direct_resample.Rd man/tc.dt.Rd man/Wetmore_Css.Rd man/calc_analytic_css.Rd man/export_pbtk_sbml.Rd man/brain_mass.Rd man/estimate_gfr.Rd man/hematocrit_infants.Rd man/onlyp.Rd man/chem_invivo_PK_data.Rd man/parameterize_1comp.Rd man/Calc_ratioblood2plasma.Rd man/solve_1comp_pk.Rd man/age_dist_smooth.Rd man/predict_partitioning_schmitt.Rd man/Parameterize_SteadyState.Rd man/solve_3comp_pbpk.Rd man/r_left_censored_norm.Rd man/spline_heightweight.Rd man/rfun.Rd man/solve_pbtk.Rd man/skin_mass_bosgra.Rd man/nhanes_mec_svy.Rd man/calc_mc_oral_equiv.Rd man/liver_mass_children.Rd

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