High-Throughput Toxicokinetics

Documentation for package ‘httk’ version 2.7.4

Help Pages

-- 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