# High-Throughput Toxicokinetics

## Documentation for package ‘httk’ version 2.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

httk-package | High-Throughput Toxicokinetics
httkpop-package | httkpop: Virtual population generator for HTTK.

## -- 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 --

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_fetal_phys | Calculate maternal-fetal physiological parameters
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 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/chemical-research/exploring-toxcast-data-downloadable-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_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_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
howgate | Howgate 2006
httk | High-Throughput Toxicokinetics
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 data from Dawson et al. 2021.
load_pradeep2020 | Load data from Pradeep et al. 2020.
load_sipes2017 | Load data from Sipes et al 2017.
lump_tissues | Lump tissue parameters into model compartments This function takes the tissue:plasma partition coefficients from 'predict_partitioning_schmitt' along with the tissue-specific volumes and flows and aggregates (or "lumps") them according to the needed scheme of toxicokinetic model tissue comparments.
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). #' This function implements the method from Schmitt (2008) for predicting the tissue to unbound plasma partition coefficients for the tissues contained in the 'tissue.data' table. The method has been modifed by Pearce et al. (2017) based on an evalaution using in vivo measured partition coefficients.
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
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