High-Throughput Toxicokinetics
Find the best available ratio of the blood to plasma concentration con...
Aylward et al. 2014
Assess the current performance of httk relative to historical benchmar...
Find average blood masses by age.
Predict blood mass.
CDC BMI-for-age charts
Predict body surface area.
Predict bone mass
Predict brain mass.
Calculate the analytic steady state concentration for the one compartm...
Calculate the analytic steady state concentration for model 3compartme...
Calculate the analytic steady state concentration for model 3compartme...
Calculate the analytic steady state concentration for the three compar...
Calculate the analytic steady state plasma concentration for model pbt...
Calculate the steady state concentration for the sum of clearances ste...
Calculate the analytic steady state plasma concentration.
Calculate the fractional contributions to total clearance
Find the steady state concentration and the day it is reached.
Back-calculates the Red Blood Cell to Unbound Plasma Partition Coeffic...
Calculate the membrane affinity
Calculate maternal body weight
Distribution of chemical steady state concentration with uncertainty a...
Calculate Monte Carlo Oral Equivalent Dose
Conduct multiple TK simulations using Monte Carlo
Test the check digit of a CAS number to confirm validity
Create a table of parameter values for Monte Carlo
Dawson et al. 2021 data
Machine Learning PFAS Half-Life Predictions from Dawson et al. 2023
Dimitrijevic et al. (2022)In Vitro Cellular and Nominal Concentration
DTXSID number format check function
Reference for EPA Physico-Chemical Data
Predict GFR in children.
Predict GFR.
Literature In Vivo Data on Doses Causing Neurological Effects
Retrieve chemical identity from HTTK package
Retrieve chemical information available from HTTK package
Retrieve and parse intrinsic hepatic clearance
Parameterize Armitage In Vitro Distribution Model
Parameterizea generic PBTK model with dermal exposure
Parameterize_fetal_PBTK
Parameters for a generic gas inhalation physiologically-based toxicoki...
Partition Coefficient Data
Pearce et al. 2017 data
Interspecies In vivo Clearance Data for PFAS
DRUGS|NORMAN: Pharmaceutical List with EU, Swiss, US Consumption Data
solve_gas_pbtk
Solve_model
Solve the pbtk_lifestage model, which has time-dependent parameters
Solve_PBTK
Predict spleen mass for children
Supplementary output from Linakis 2020 vignette analysis.
More supplementary output from Linakis 2020 vignette analysis.
A timestamp of table creation
ToxCast thyroid-related bioactivity data
Add a table of chemical information for use in making httk predictions...
Draws ages from a smoothed distribution for a given gender/race combin...
Solve one compartment TK model
Solve_1tri_PBTK
Solve the 3comp_lifestage model, which has time-dependent parameters
Solve_3comp
Solve_3comp2
Solve_dermal_PBTK
Solve_fetal_PBTK
Solve_full_pregnancy
Calculate air:matrix partition coefficients
Predict kidney mass for children
Evaluate the Kramer In Vitro Distribution model
List all available HTTK models
Predict liver mass for children
Load CLint and Fup QSPR predictions from Dawson et al. 2021.
Tox21 2015 Active Hit Calls (EPA)
Wang et al. 2018 Wang et al. (2018) screened the blood of 75 pregnant ...
Published toxicokinetic predictions based on in vitro data from Wetmor...
WHO weight-for-length charts
Parameters for a three-compartment model at steady-state with exhalati...
Propagates uncertainty and variability in in vitro HTTK data into PBPK...
Returns draws from a normal distribution with a lower censoring limit ...
Reset HTTK to Default Data Tables
Correct the measured intrinsive hepatic clearance for fraction free
Correct the measured fraction unbound in plasma for lipid binding
Estimate well surface area
Armitage In Vitro Distribution Model
Add a parameter value to the chem.physical_and_invitro.data table
Randomly draws from a one-dimensional KDE
Calculate Dermal Equivalent Dose
Calculate the distribution coefficient
Calculate the elimination rate for a one compartment model
Functions for calculating the bioavaialble fractions from oral doses
Calculate maternal-fetal physiological parameters
Calculate the correction for lipid binding in plasma binding assay
Calculates the half-life for a one compartment model.
Calculate first pass heaptic metabolism
Calculate the hepatic clearance.
Calculate the free chemical in the hepaitic clearance assay
Calculate the hepatic clearance (deprecated).
Calculate the ionization.
Calculate the constant ratio of the blood concentration to the plasma ...
Calculate toxicokinetic summary statistics (deprecated).
Calculate toxicokinetic summary statistics.
Calculate the total plasma clearance.
Calculate the volume of distribution for a one compartment model.
CAS number format check function
Check for sufficient model parameters
Parameter Estimates from Wambaugh et al. (2018)
Summary of published toxicokinetic time course experiments
Physico-chemical properties and in vitro measurements for toxicokineti...
CKD-EPI equation for GFR.
Concentration data involved in Linakis 2020 vignette analysis.
convert_solve_x
convert_units
Generate hematocrit values for a virtual population
SEEM Example Data We can grab SEEM daily intake rate predictions alrea...
ToxCast Example Data The main page for the ToxCast data is here: https...
Export model to jarnac.
Export model to sbml.
Fetal Partition Coefficients
Generate demographic parameters for a virtual population
Generate heights and weights for a virtual population.
Generate serum creatinine values for a virtual population.
Retrieve chemical information on 2023 EPA PFAS Chemicals
Retrieve in vitro measured Caco-2 membrane permeabilit
Retrieve or calculate fraction of chemical absorbed from the gut
Retrieve and parse fraction unbound in plasma
Categorize kidney function by GFR.
Get timeseries containing the change of each of the input parameters.
Retrieve species-specific in vitro data from chem.physical_and_invitro...
Get literature Chemical Information.
Predict skeletal muscle mass for children
Get literature Css
Get Literature Oral Equivalent Dose
Get physico-chemical parameters from chem.physical_and_invitro.data ta...
Get ratio of the blood concentration to the plasma concentration.
Assign weight class (underweight, normal, overweight, obese)
Get literature Chemical Information. (deprecated).
Get literature Css (deprecated).
Get Literature Oral Equivalent Dose (deprecated).
KDE bandwidths for residual variability in hematocrit
Predict hematocrit in infants under 1 year old.
Return the assumptions used in Honda et al. 2019
Measured Caco-2 Apical-Basal Permeability Data
Predicted Caco-2 Apical-Basal Permeabilities
Howgate 2006
HTTK data chemical subsetting function
httk: High-Throughput Toxicokinetics
Historical Performance of R Package httk
Convert HTTK-Pop-generated parameters to HTTK physiological parameters
Inner loop function called by httkpop_direct_resample.
Generate a virtual population by directly resampling the NHANES data.
Generate a virtual population for PBTK
httk-pop: Correlated human physiological parameter Monte Carlo
Generate a virtual population by the virtual individuals method.
KDE bandwidth for residual variability in height/weight
Convenience Boolean (yes/no) functions to identify chemical membership...
Monte Carlo for in vitro toxicokinetic parameters including uncertaint...
Checks whether a value, or all values in a vector, is within inclusive...
Convenience Boolean (yes/no) function to identify chemical membership ...
Johnson 2006
Kapraun et al. 2019 data
Load Caco2 pereneability QSPR predictions from Honda et al. 2025
Load CLint and Fup QSPR predictions predictions from Pradeep et al. 20...
Load CLint and Fup QSPR predictions from Sipes et al 2017.
Lump tissue parameters into model compartments
Predict lung mass for children
Reference tissue masses and flows from tables in McNally et al. 2014.
Predict skeletal muscle mass
Pre-processed NHANES data.
Metabolism data involved in Linakis 2020 vignette analysis.
Monte Carlo for toxicokinetic model parameters
Published Pharmacokinetic Parameters from Obach et al. 2008
NHANES Exposure Data
Predict pancreas mass for children
Parameters for a one compartment (empirical) toxicokinetic model
Parameterize_1tri_PBTK
Parameters for a three-compartment toxicokinetic model (dynamic)
Parameters for a three-compartment toxicokinetic model (dynamic)
Predict skin mass
Solve 1comp_lifestage model, which has time-dependent parameters
Parameterize In Vitro Distribution Models
Parameterize Kramer IVD Model
Parameters for a generic physiologically-based toxicokinetic model
Parameters for a one compartment (empirical) toxicokinetic model for P...
Parameters for Schmitt's (2008) Tissue Partition Coefficient Method
Parameters for a three-compartment toxicokinetic model at steady-state
Parameters for a three-compartment model at steady-state with exhalati...
Species-specific physiology parameters
Partition Coefficients from PK-Sim
Pradeep et al. 2020
Predict partition coefficients using the method from Schmitt (2008).
AUCs for Pregnant and Non-Pregnant Women
Propagates uncertainty and variability in in vitro HTTK data into one ...
Propagates uncertainty and variability in in vitro HTTK data into thre...
Draw random numbers with LOD median but non-zero upper 95th percentile
Scale mg/kg body weight doses according to body weight and units
Literature Measurements of In Vitro Cellular and Nominal Concentration
KDE bandwidths for residual variability in serum creatinine
set_httk_precision
Sipes et al. 2017 data
Given a data.table describing a virtual population by the NHANES quant...
Allometric scaling.
Tissue composition and species-specific physiology parameters
SEEM3 Example Data for Truong et al. 2025
NHANES Chemical Intake Rates for chemicals in Wambaugh et al. (2019)
Raw Bayesian in vitro Toxicokinetic Data Analysis from Wambaugh et al....
ExpoCast SEEM3 Consensus Exposure Model Predictions for Chemical Intak...
Pre-made models that can be rapidly tailored to various chemicals and species using chemical-specific in vitro data and physiological information. These tools allow incorporation of chemical toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE") into bioinformatics, as described by Pearce et al. (2017) (<doi:10.18637/jss.v079.i04>). Chemical-specific in vitro data characterizing toxicokinetics have been obtained from relatively high-throughput experiments. The chemical-independent ("generic") physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models included here can be parameterized with in vitro data or in silico predictions which are provided for thousands of chemicals, multiple exposure routes, and various species. High throughput toxicokinetics ("HTTK") is the combination of in vitro data and generic models. We establish the expected accuracy of HTTK for chemicals without in vivo data through statistical evaluation of HTTK predictions for chemicals where in vivo data do exist. The models are systems of ordinary differential equations that are developed in MCSim and solved using compiled (C-based) code for speed. A Monte Carlo sampler is included for simulating human biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and propagating parameter uncertainty (Wambaugh et al., 2019 <doi:10.1093/toxsci/kfz205>). Empirically calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>). These functions and data provide a set of tools for using IVIVE to convert concentrations from high-throughput screening experiments (for example, Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Useful links