High-Throughput Toxicokinetics

Documentation for package ‘httk’ version 2.3.1

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	Evaluate the updated Armitage model
armitage_input	Armitage et al. (2014) Model Inputs from Honda et al. (2019)
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.
Aylward2014	Aylward et al. 2014
aylward2014	Aylward et al. 2014

-- 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 3comp
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_css	Find the steady state concentration and the day it is reached.
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_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_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
chem.invivo.PK.aggregate.data	Parameter Estimates from Wambaugh et al. (2018)
chem.invivo.PK.data	Published toxicokinetic time course measurements
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.
concentration_data_Linakis2020	Concentration data involved in Linakis 2020 vignette analysis.
convert_httkpop_1comp	Converts HTTK-Pop physiology into parameters relevant to the one compartment model
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

-- 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.

-- F --

fetalPCs	Fetal Partition Coefficients
fetalpcs	Fetal Partition Coefficients
Frank2018invivo	Literature In Vivo Data on Doses Causing Neurological Effects

-- 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_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_fabsgut	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_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
howgate	Howgate 2006
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.
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_mc	Monte Carlo for in vitro toxicokinetic parameters including uncertainty and variability.
is.expocast	Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
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.nhanes.blood.analyte	Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.nhanes.blood.parent	Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.nhanes.serum.analyte	Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.nhanes.serum.parent	Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.nhanes.urine.analyte	Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.nhanes.urine.parent	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.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

-- J --

johnson

Johnson 2006

-- K --

Kapraun2019	Kapraun et al. 2019 data
kapraun2019	Kapraun et al. 2019 data
kidney_mass_children	Predict kidney mass for children

-- L --

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 QSPR predictions from Honda et al. 2023
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.
metabolism_data_Linakis2020	Metabolism data involved in Linakis 2020 vignette analysis.
monte_carlo	Monte Carlo for toxicokinetic model parameters

-- O --

Obach2008	Published Pharmacokinetic Parameters from Obach et al. 2008
onlyp	NHANES Exposure Data

-- P --

pancreas_mass_children	Predict pancreas mass for children
parameterize_1comp	Parameters for a one compartment (empirical) toxicokinetic model
parameterize_3comp	Parameters for a three-compartment toxicokinetic model (dynamic)
parameterize_fetal_pbtk	Parameterize_fetal_PBTK
parameterize_gas_pbtk	Parameters for a generic gas inhalation physiologically-based toxicokinetic model
parameterize_pbtk	Parameters for a generic physiologically-based toxicokinetic model
parameterize_schmitt	Parameters for Schmitt's (2008) Tissue Partition Coefficient Method
parameterize_steadystate	Parameters for a three-compartment toxicokinetic model at steady-state
pc.data	Partition Coefficient Data
Pearce2017Regression	Pearce et al. 2017 data
pearce2017regression	Pearce et al. 2017 data
pharma	DRUGS\|NORMAN: Pharmaceutical List with EU, Swiss, US Consumption Data
physiology.data	Species-specific physiology parameters
pksim.pcs	Partition Coefficients from PK-Sim
Pradeep2020	Pradeep et al. 2020
pradeep2020	Pradeep et al. 2020
predict_partitioning_schmitt	Predict partition coefficients using the method from Schmitt (2008).
pregnonpregaucs	AUCs for Pregnant and Non-Pregnant Women
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_3comp	Solve_3comp
solve_fetal_pbtk	Solve_fetal_PBTK
solve_gas_pbtk	solve_gas_pbtk
solve_model	Solve_model
solve_pbtk	Solve_PBTK
spleen_mass_children	Predict spleen mass for children
supptab1_Linakis2020	Supplementary output from Linakis 2020 vignette analysis.
supptab2_Linakis2020	More supplementary output from Linakis 2020 vignette analysis.

-- 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 --

wambaugh2019	in vitro Toxicokinetic Data from Wambaugh et al. (2019)
wambaugh2019.nhanes	NHANES Chemical Intake Rates for chemicals in Wambaugh et al. (2019)
wambaugh2019.raw	Raw Bayesian in vitro Toxicokinetic Data Analysis from Wambaugh et al. (2019)
wambaugh2019.seem3	ExpoCast SEEM3 Consensus Exposure Model Predictions for Chemical Intake Rates
wambaugh2019.tox21	Tox21 2015 Active Hit Calls (EPA)
Wang2018	Wang et al. 2018 Wang et al. (2018) screened the blood of 75 pregnant women for the presence of environmental organic acids (EOAs) and identified mass spectral features corresponding to 453 chemical formulae of which 48 could be mapped to likely structures. Of the 48 with tentative structures the identity of six were confirmed with available chemical standards.
wang2018	Wang et al. 2018 Wang et al. (2018) screened the blood of 75 pregnant women for the presence of environmental organic acids (EOAs) and identified mass spectral features corresponding to 453 chemical formulae of which 48 could be mapped to likely structures. Of the 48 with tentative structures the identity of six were confirmed with available chemical standards.
well_param	Microtiter Plate Well Descriptions for Armitage et al. (2014) Model
Wetmore2012	Published toxicokinetic predictions based on in vitro data from Wetmore et al. 2012.
wfl	WHO weight-for-length charts