High-Throughput Toxicokinetics


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Documentation for package ‘httk’ version 1.7

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

httk-package High-Throughput Toxicokinetics httk: High-Throughput Toxicokinetics

-- 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
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_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.
calc_ionization Calculate the ionization.
calc_mc_css Find the monte carlo steady state concentration.
calc_mc_oral_equiv Calculate Monte Carlo Oral Equivalent Dose
calc_rblood2plasma Calculate the constant ratio of the blood concentration to the plasma concentration.
calc_stats Calculate the statistics.
calc_total_clearance Calculate the total clearance.
calc_vdist Calculate the volume of distribution for a one compartment model.
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.
convert_httk Converts HTTK-Pop virtual population into parameters relevant to an HTTK model.

-- D --

draw_fup_clint Draw Funbound.plasma and Clint from censored or non-censored distributions.

-- E --

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.

-- 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_gfr_category Categorize kidney function by GFR.
get_httk_params Converts the HTTK-Pop population data table to a table of the parameters needed by HTTK, for a specific chemical.
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.
get_wetmore_cheminfo Get Wetmore Chemical Information.
get_wetmore_css Get Wetmore Css
get_wetmore_oral_equiv Get Wetmore Oral Equivalent Dose

-- H --

hematocrit_infants Predict hematocrit in infants under 1 year old.
howgate Howgate 2006
httk High-Throughput Toxicokinetics httk: High-Throughput Toxicokinetics
httkpop_bio 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_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.
is.expocast Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
is.httk Convenience Boolean (yes/no) functions to identify chemical membership in several key lists.
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.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.
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.
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_pbtk Parameterize_PBTK
parameterize_schmitt Parameterize Schmitt's method.
parameterize_steadystate Parameterize_SteadyState
pc.data Partition Coefficient Data
physiology.data Species-specific physiology parameters
predict_partitioning_schmitt Predict partition coefficients using the method from Schmitt (2008).

-- R --

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 --

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_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.

-- T --

tc.dt Toxcast Data
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 --

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