# High-Throughput Toxicokinetics

## Documentation for package ‘httk’ version 2.0.1

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

## Help Pages

A B C E F G H I J K L M N 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_dist_smooth | Smoothed age distributions by race and gender.
age_draw_smooth | Draws ages from a smoothed distribution for a given gender/race combination
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)
available_rblood2plasma | Find the best available ratio of the blood to plasma concentration constant.

## -- 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 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 oompartment steady-state model
calc_analytic_css_pbtk | Calculate the analytic steady state concentration for model pbtk.
calc_css | Find the steady state concentration and the day it is reached.
calc_elimination_rate | Calculate the elimination rate 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_krbc2pu | Back-calculates the Red Blood Cell to Unbound Plasma Partition Coefficient
calc_mc_css | Find the monte carlo steady state concentration.
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.
calc_total_clearance | Calculate the total clearance.
calc_vdist | Calculate the volume of distribution for a one compartment model.
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.lists | Chemical membership in different research projects
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
create_mc_samples | Create a data table of draws of parameter values for Monte Carlo

## -- E --

EPA.ref | Reference for EPA Physico-Chemical Data
estimate_gfr | Predict GFR.
estimate_gfr_ped | Predict GFR in children.
estimate_hematocrit | Predict hematocrit using smoothing spline.
export_pbtk_jarnac | Export model to jarnac.
export_pbtk_sbml | Export model to sbml.

## -- F --

Frank2018invivo | Literature In Vivo Data on Doses Causing Neurological Effects

## -- G --

gen_age_height_weight | Generate ages, heights, and weights for a virtual population using the virtual-individuals method.
gen_height_weight | Generate heights and weights for a virtual population.
get_cheminfo | Retrieve chemical information from HTTK package
get_chem_id | Retrieve chemical identity from HTTK package
get_gfr_category | Categorize kidney function by GFR.
get_invitroPK_param | Retrieve 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
get_rblood2plasma | Get ratio of the blood concentration to the plasma concentration.
get_weight_class | Given vectors of age, BMI, recumbent length, weight, and gender, categorizes weight classes using CDC and WHO categories.

## -- H --

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
httkpop_mc | Converts the HTTK-Pop population data table to a table of the parameters needed by HTTK, for a specific chemical.
httkpop_virtual_indiv | Generate a virtual population by the virtual individuals method.

## -- I --

in.list | Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
invitro_mc | Draw in vitro TK 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 --

kidney_mass_children | Predict kidney mass for children

## -- L --

liver_mass_children | Predict liver mass for children
load_sipes2017 | Load data from Sipes et al 2017.
lump_tissues | Lump tissue parameters
lung_mass_children | Predict lung mass for children

## -- M --

mcnally_dt | Reference tissue masses and flows from tables in McNally et al. 2014.
metabolism_data_Linakis2020 | Metabolism data involved in Linakis 2020 vignette analysis.
monte_carlo | Monte Carlo for pharmacokinetic models

## -- N --

nhanes_mec_svy | Pre-processed NHANES data.

## -- 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 | Parameterize_1comp
parameterize_3comp | Parameterize_3comp
parameterize_gas_pbtk | Parameterize_gas_pbtk
parameterize_pbtk | Parameterize_PBTK
parameterize_schmitt | Get the Parameters for Schmitt's Tissue Partition Coefficient Method
parameterize_steadystate | Parameterize_SteadyState
pc.data | Partition Coefficient Data
pharma | DRUGS|NORMAN: Pharmaceutical List with EU, Swiss, US Consumption Data
physiology.data | Species-specific physiology parameters
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
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
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_gas_pbtk | solve_gas_pbtk
solve_model | Solve_model
solve_pbtk | Solve_PBTK
spleen_mass_children | Predict spleen mass for children
spline_heightweight | Smoothing splines for log height vs. age and log body weight vs. age, along with 2-D KDE residuals, by race and gender.
spline_hematocrit | Smoothing splines for log hematocrit vs. age in months, and KDE residuals, by race and gender.
spline_serumcreat | Smoothing splines for log serum creatinine vs. age in months, along with KDE residuals, by race and gender.
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)
well_param | Microtiter Plate Well Descriptions for Armitage et al. (2014) Model
Wetmore.data | Published toxicokinetic predictions based on in vitro data
Wetmore2012 | Published toxicokinetic predictions based on in vitro data from Wetmore et al. 2012.
wfl | WHO weight-for-length charts