R: High-Throughput Toxicokinetics

# High-Throughput Toxicokinetics

## Documentation for package ‘httk’ version 2.7.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E G H I K L M P R S T W

## -- A --

add_chemtable | Add a table of chemical information for use in making httk predictions.
age_draw_smooth | Draws ages from a smoothed distribution for a given gender/race combination
apply_clint_adjustment | Correct the measured intrinsive hepatic clearance for fraction free
apply_fup_adjustment | Correct the measured fraction unbound in plasma for lipid binding
armitage_estimate_sarea | Estimate well surface area
armitage_eval | Armitage In Vitro Distribution Model
augment.table | Add a parameter value to the chem.physical_and_invitro.data table
available_rblood2plasma | Find the best available ratio of the blood to plasma concentration constant.

## -- B --

benchmark_httk | Assess the current performance of httk relative to historical benchmarks
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.

## -- C --

calc_analytic_css | Calculate the analytic steady state plasma concentration.
calc_analytic_css_1comp | Calculate the analytic steady state concentration for the one compartment model.
calc_analytic_css_3comp | Calculate the analytic steady state concentration for model 3compartment
calc_analytic_css_3comp2 | Calculate the analytic steady state concentration for model 3compartment
calc_analytic_css_3compss | Calculate the analytic steady state concentration for the three compartment steady-state model
calc_analytic_css_pbtk | Calculate the analytic steady state plasma concentration for model pbtk.
calc_analytic_css_sumclearances | Calculate the steady state concentration for the sum of clearances steady-state model with exhalation
calc_clearance_frac | Calculate the fractional contributions to total clearance
calc_css | Find the steady state concentration and the day it is reached.
calc_dermal_equiv | Calculate Dermal Equivalent Dose
calc_dow | Calculate the distribution coefficient
calc_elimination_rate | Calculate the elimination rate for a one compartment model
calc_fabs.oral | Functions for calculating the bioavaialble fractions from oral doses
calc_fbio.oral | Functions for calculating the bioavaialble fractions from oral doses
calc_fetal_phys | Calculate maternal-fetal physiological parameters
calc_fgut.oral | Functions for calculating the bioavaialble fractions from oral doses
calc_fup_correction | Calculate the correction for lipid binding in plasma binding assay
calc_half_life | Calculates the half-life for a one compartment model.
calc_hepatic_clearance | Calculate the hepatic clearance (deprecated).
calc_hep_bioavailability | Calculate first pass heaptic metabolism
calc_hep_clearance | Calculate the hepatic clearance.
calc_hep_fu | Calculate the free chemical in the hepaitic clearance assay
calc_ionization | Calculate the ionization.
calc_kair | Calculate air:matrix partition coefficients
calc_kgutabs | Functions for calculating the bioavaialble fractions from oral doses
calc_krbc2pu | Back-calculates the Red Blood Cell to Unbound Plasma Partition Coefficient
calc_ma | Calculate the membrane affinity
calc_maternal_bw | Calculate maternal body weight
calc_mc_css | Distribution of chemical steady state concentration with uncertainty and variability
calc_mc_oral_equiv | Calculate Monte Carlo Oral Equivalent Dose
calc_mc_tk | Conduct multiple TK simulations using Monte Carlo
calc_peff | Functions for calculating the bioavaialble fractions from oral doses
calc_rblood2plasma | Calculate the constant ratio of the blood concentration to the plasma concentration.
calc_stats | Calculate toxicokinetic summary statistics (deprecated).
calc_tkstats | Calculate toxicokinetic summary statistics.
calc_total_clearance | Calculate the total plasma clearance.
calc_vdist | Calculate the volume of distribution for a one compartment model.
CAS.checksum | Test the check digit of a CAS number to confirm validity
cas_id_check | CAS number format check function
check_model | Check for sufficient model parameters
chem.invivo.PK.aggregate.data | Parameter Estimates from Wambaugh et al. (2018)
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
ckd_epi_eq | CKD-EPI equation for GFR.
convert_solve_x | convert_solve_x
convert_units | convert_units
create_mc_samples | Create a table of parameter values for Monte Carlo

## -- D --

Dawson2021 | Dawson et al. 2021 data
dawson2021 | Dawson et al. 2021 data
dawson2023 | Machine Learning PFAS Half-Life Predictions from Dawson et al. 2023
dtxsid_id_check | DTXSID number format check function

## -- E --

EPA.ref | Reference for EPA Physico-Chemical Data
estimate_gfr | Predict GFR.
estimate_gfr_ped | Predict GFR in children.
estimate_hematocrit | Generate hematocrit values for a virtual population
example.seem | SEEM Example Data We can grab SEEM daily intake rate predictions already in RData format from https://github.com/HumanExposure/SEEM3RPackage/tree/main/SEEM3/data Download the file Ring2018Preds.RData
example.toxcast | ToxCast Example Data The main page for the ToxCast data is here: https://www.epa.gov/comptox-tools/exploring-toxcast-data Most useful to us is a single file containing all the hits across all chemcials and assays: https://clowder.edap-cluster.com/datasets/6364026ee4b04f6bb1409eda?space=62bb560ee4b07abf29f88fef
export_pbtk_jarnac | Export model to jarnac.
export_pbtk_sbml | Export model to sbml.

## -- G --

gen_age_height_weight | Generate demographic parameters for a virtual population
gen_height_weight | Generate heights and weights for a virtual population.
gen_serum_creatinine | Generate serum creatinine values for a virtual population.
get_2023pfasinfo | Retrieve chemical information on 2023 EPA PFAS Chemicals
get_caco2 | Retrieve in vitro measured Caco-2 membrane permeabilit
get_cheminfo | Retrieve chemical information available from HTTK package
get_chem_id | Retrieve chemical identity from HTTK package
get_clint | Retrieve and parse intrinsic hepatic clearance
get_fbio | Retrieve or calculate fraction of chemical absorbed from the gut
get_fup | Retrieve and parse fraction unbound in plasma
get_gfr_category | Categorize kidney function by GFR.
get_input_param_timeseries | Get timeseries containing the change of each of the input parameters.
get_invitroPK_param | Retrieve species-specific in vitro data from chem.physical_and_invitro.data table
get_lit_cheminfo | Get literature Chemical Information.
get_lit_css | Get literature Css
get_lit_oral_equiv | Get Literature Oral Equivalent Dose
get_physchem_param | Get physico-chemical parameters from chem.physical_and_invitro.data table
get_rblood2plasma | Get ratio of the blood concentration to the plasma concentration.
get_weight_class | Assign weight class (underweight, normal, overweight, obese)
get_wetmore_cheminfo | Get literature Chemical Information. (deprecated).
get_wetmore_css | Get literature Css (deprecated).
get_wetmore_oral_equiv | Get Literature Oral Equivalent Dose (deprecated).

## -- H --

hct_h | KDE bandwidths for residual variability in hematocrit
hematocrit_infants | Predict hematocrit in infants under 1 year old.
honda.ivive | Return the assumptions used in Honda et al. 2019
honda2023.data | Measured Caco-2 Apical-Basal Permeability Data
honda2023.qspr | Predicted Caco-2 Apical-Basal Permeabilities
httk.performance | Historical Performance of R Package httk
httkpop | httkpop: Virtual population generator for HTTK.
httkpop_biotophys_default | Convert HTTK-Pop-generated parameters to HTTK physiological parameters
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'.
httkpop_generate | Generate a virtual population for PBTK
httkpop_mc | httk-pop: Correlated human physiological parameter Monte Carlo
httkpop_virtual_indiv | Generate a virtual population by the virtual individuals method.
httk_chem_subset | HTTK data chemical subsetting function
httk_vignettes | Interact with HTTK vignettes
hw_H | KDE bandwidth for residual variability in height/weight

## -- I --

in.list | Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
invitro.assay.params | ToxCast In Vitro Assay Descriptors
invitro_mc | Monte Carlo for in vitro toxicokinetic parameters including uncertainty and variability.
is.httk | Convenience Boolean (yes/no) function to identify chemical membership and treatment within the httk project.
is.nhanes | Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.pfas | Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.pharma | Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.seem | Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.tox21 | Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.toxcast | 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

## -- K --

Kapraun2019 | Kapraun et al. 2019 data
kapraun2019 | Kapraun et al. 2019 data
kidney_mass_children | Predict kidney mass for children
kramer_eval | Evaluate the Kramer In Vitro Distribution model

## -- L --

list_models | List all available HTTK models
liver_mass_children | Predict liver mass for children
load_dawson2021 | Load CLint and Fup QSPR predictions from Dawson et al. 2021.
load_honda2023 | Load Caco2 pereneability QSPR predictions from Honda et al. 2025
load_honda2025 | Load Caco2 pereneability QSPR predictions from Honda et al. 2025
load_pradeep2020 | Load CLint and Fup QSPR predictions predictions from Pradeep et al. 2020.
load_sipes2017 | Load CLint and Fup QSPR predictions from Sipes et al 2017.
lump_tissues | Lump tissue parameters into model compartments
lung_mass_children | Predict lung mass for children

## -- M --

mcnally_dt | Reference tissue masses and flows from tables in McNally et al. (2014)
mecdt | Pre-processed NHANES data.
monte_carlo | Monte Carlo for toxicokinetic model parameters

## -- P --

pancreas_mass_children | Predict pancreas mass for children
parameterize_1comp | Parameters for a one compartment (empirical) toxicokinetic model
parameterize_1tri_pbtk | Parameterize_1tri_PBTK
parameterize_3comp | Parameters for a three-compartment toxicokinetic model (dynamic)
parameterize_3comp2 | Parameters for a three-compartment toxicokinetic model (dynamic)
parameterize_armitage | Parameterize Armitage In Vitro Distribution Model
parameterize_dermal_pbtk | Parameterizea generic PBTK model with dermal exposure
parameterize_fetal_pbtk | Parameterize_fetal_PBTK
parameterize_gas_pbtk | Parameters for a generic gas inhalation physiologically-based toxicokinetic model
parameterize_IVD | Parameterize In Vitro Distribution Models
parameterize_kramer | Parameterize Kramer IVD Model
parameterize_pbtk | Parameters for a generic physiologically-based toxicokinetic model
parameterize_pfas1comp | Parameters for a one compartment (empirical) toxicokinetic model for PFAS
parameterize_schmitt | Parameters for Schmitt's (2008) Tissue Partition Coefficient Method
parameterize_steadystate | Parameters for a three-compartment toxicokinetic model at steady-state
parameterize_sumclearances | Parameters for a three-compartment model at steady-state with exhalation
parameterize_sumclearancespfas | Parameters for a three-compartment model at steady-state with exhalation and resorption
Pearce2017Regression | Pearce et al. 2017 data
pearce2017regression | Pearce et al. 2017 data
pfas.clearance | Interspecies In vivo Clearance Data for PFAS
physiology.data | Species-specific physiology parameters
Pradeep2020 | Pradeep et al. 2020
pradeep2020 | Pradeep et al. 2020
predict_partitioning_schmitt | Predict partition coefficients using the method from Schmitt (2008).
propagate_invitrouv_1comp | Propagates uncertainty and variability in in vitro HTTK data into one compartment model parameters
propagate_invitrouv_3comp | Propagates uncertainty and variability in in vitro HTTK data into three compartment model parameters
propagate_invitrouv_pbtk | Propagates uncertainty and variability in in vitro HTTK data into PBPK model parameters

## -- R --

reset_httk | Reset HTTK to Default Data Tables
rfun | Randomly draws from a one-dimensional KDE
rmed0non0u95 | Draw random numbers with LOD median but non-zero upper 95th percentile
r_left_censored_norm | Returns draws from a normal distribution with a lower censoring limit of lod (limit of detection)

## -- S --

scale_dosing | Scale mg/kg body weight doses according to body weight and units
scr_h | KDE bandwidths for residual variability in serum creatinine
set_httk_precision | set_httk_precision
Sipes2017 | Sipes et al. 2017 data
sipes2017 | Sipes et al. 2017 data
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 | Solve one compartment TK model
solve_1comp_lifestage | Solve '1comp_lifestage' model, which has time-dependent parameters
solve_1tri_pbtk | Solve_1tri_PBTK
solve_3comp | Solve_3comp
solve_3comp2 | Solve_3comp2
solve_3comp_lifestage | Solve the '3comp_lifestage' model, which has time-dependent parameters
solve_dermal_pbtk | Solve_dermal_PBTK
solve_fetal_pbtk | Solve_fetal_PBTK
solve_full_pregnancy | Solve_full_pregnancy
solve_gas_pbtk | solve_gas_pbtk
solve_model | Solve_model
solve_pbtk | Solve_PBTK
solve_pbtk_lifestage | Solve the 'pbtk_lifestage' model, which has time-dependent parameters
spleen_mass_children | Predict spleen mass for children

## -- T --

Tables.Rdata.stamp | A timestamp of table creation
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.
tissue_scale | Allometric scaling.

## -- W --

well_param | Microtiter Plate Well Descriptions for Armitage et al. (2014) Model
wfl | WHO weight-for-length charts