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httk (version 1.8)

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

733

Version

1.8

License

GPL-3

Maintainer

John Wambaugh

Last Published

January 23rd, 2018

Functions in httk (1.8)

calc_elimination_rate

Calculate the elimination rate for a one compartment model.
calc_rblood2plasma

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

Parameterize_SteadyState
Wetmore.data

Published toxicokinetic predictions based on in vitro data
calc_vdist

Calculate the volume of distribution for a one compartment model.
Obach2008

Published Pharmacokinetic Parameters from Obach et al. 2008
Wetmore2012

Published toxicokinetic predictions based on in vitro data from Wetmore et al. 2012.
get_wetmore_css

Get Wetmore Css
physiology.data

Species-specific physiology parameters
parameterize_pbtk

Parameterize_PBTK
available_rblood2plasma

Find the best available ratio of the blood to plasma concentration constant.
blood_mass_correct

Find average blood masses by age.
calc_total_clearance

Calculate the total clearance.
chem.invivo.PK.aggregate.data

Parameter Estimates from Wambaugh et al. (2018)
body_surface_area

Predict body surface area.
bone_mass_age

Predict bone mass.
blood_weight

Predict blood mass.
bmiage

CDC BMI-for-age charts
calc_css

Find the steady state concentration and the day it is reached.
calc_hepatic_clearance

Calculate the hepatic clearance.
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.
brain_mass

Predict brain mass.
calc_analytic_css

Calculate the analytic steady state concentration.
get_weight_class

Given vectors of age, BMI, recumbent length, weight, and gender, categorizes weight classes using CDC and WHO categories.
get_wetmore_cheminfo

Get Wetmore Chemical Information.
httkpop_generate

Generate a virtual population
httkpop_virtual_indiv

Generate a virtual population by the virtual individuals method.
get_wetmore_oral_equiv

Get Wetmore Oral Equivalent Dose
add_chemtable

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

Calculate the ionization.
calc_mc_css

Find the monte carlo steady state concentration.
chem.invivo.PK.summary.data

Summary of published toxicokinetic time course experiments
chem.physical_and_invitro.data

Physico-chemical properties and in vitro measurements for toxicokinetics
get_httk_params

Converts the HTTK-Pop population data table to a table of the parameters needed by HTTK, for a specific chemical.
ckd_epi_eq

CKD-EPI equation for GFR.
convert_httk

Converts HTTK-Pop virtual population into parameters relevant to an HTTK model.
httk-package

httk httk: High-Throughput Toxicokinetics
httkpop_bio

Convert HTTK-Pop-generated parameters to HTTK physiological parameters
in.list

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

Checks whether a value, or all values in a vector, is within inclusive limits
mcnally_dt

Reference tissue masses and flows from tables in McNally et al. 2014.
monte_carlo

Monte Carlo for pharmacokinetic models
johnson

Johnson 2006
kidney_mass_children

Predict kidney mass for children.
spline_heightweight

Smoothing splines for log height vs. age and log body weight vs. age, along with 2-D KDE residuals, by race and gender.
get_rblood2plasma

Get ratio of the blood concentration to the plasma concentration.
hematocrit_infants

Predict hematocrit in infants under 1 year old.
howgate

Howgate 2006
parameterize_3comp

Parameterize_3comp
pc.data

Partition Coefficient Data
predict_partitioning_schmitt

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

Smoothing splines for log serum creatinine vs. age in months, along with KDE residuals, by race and gender.
lump_tissues

Lump tissue parameters
lung_mass_children

Predict lung mass for children.
sipes.data

Sipes et al. 2017 data
skeletal_muscle_mass

Predict skeletal muscle mass.
tc.dt

Toxcast Data
chem.lists

Chemical membership in different research projects
chem.invivo.PK.data

Published toxicokinetic time course measurements
get_cheminfo

Retrieve chemical information from HTTK package
get_gfr_category

Categorize kidney function by GFR.
nhanes_mec_svy

Pre-processed NHANES data.
onlyp

NHANES Exposure Data
r_left_censored_norm

Returns draws from a normal distribution with a lower censoring limit of lod (limit of detection)
rfun

Randomly draws from a one-dimensional KDE
spline_hematocrit

Smoothing splines for log hematocrit vs. age in months, and KDE residuals, by race and gender.
skeletal_muscle_mass_children

Predict skeletal muscle mass for children.
skin_mass_bosgra

Predict skin mass.
parameterize_schmitt

Parameterize Schmitt's method.
solve_1comp

Solve one compartment TK model
solve_3comp

Solve_3comp
tissue.data

Tissue composition and species-specific physiology parameters
tissue_masses_flows

Given a data.table describing a virtual population by the NHANES quantities, generates HTTK physiological parameters for each individual.
age_dist_smooth

Smoothed age distributions by race and gender.
calc_mc_oral_equiv

Calculate Monte Carlo Oral Equivalent Dose
calc_stats

Calculate the statistics.
draw_fup_clint

Draw Funbound.plasma and Clint from censored or non-censored distributions.
estimate_gfr

Predict GFR.
gen_age_height_weight

Generate ages, heights, and weights for a virtual population using the virtual-individuals method.
gen_height_weight

Generate heights and weights for a virtual population.
httkpop_direct_resample

Generate a virtual population by directly resampling the NHANES data.
httkpop_direct_resample_inner

Inner loop function called by httkpop_direct_resample.
age_draw_smooth

Draws ages from a smoothed distribution for a given gender/race combination
liver_mass_children

Predict liver mass for children.
load_sipes2017

Load data from Sipes et al 2017.
pancreas_mass_children

Predict pancreas mass for children.
parameterize_1comp

Parameterize_1comp
solve_pbtk

Solve_PBTK
spleen_mass_children

Predict spleen mass for children.
tissue_scale

Allometric scaling.
wfl

WHO weight-for-length charts