Man pages for httk
High-Throughput Toxicokinetics

add_chemtableAdd a table of chemical information for use in making httk...
age_draw_smoothDraws ages from a smoothed distribution for a given...
apply_clint_adjustmentCorrect the measured intrinsive hepatic clearance for...
apply_fup_adjustmentCorrect the measured fraction unbound in plasma for lipid...
armitage_estimate_sareaEstimate well surface area
armitage_evalEvaluate the updated Armitage model
armitage_inputArmitage et al. (2014) Model Inputs from Honda et al. (2019)
augment.tableAdd a parameter value to the chem.physical_and_invitro.data...
available_rblood2plasmaFind the best available ratio of the blood to plasma...
aylward2014Aylward et al. 2014
benchmark_httkAssess the current performance of httk relative to historical...
blood_mass_correctFind average blood masses by age.
blood_weightPredict blood mass.
bmiageCDC BMI-for-age charts
body_surface_areaPredict body surface area.
bone_mass_agePredict bone mass
brain_massPredict brain mass.
calc_analytic_cssCalculate the analytic steady state plasma concentration.
calc_analytic_css_1compCalculate the analytic steady state concentration for the one...
calc_analytic_css_3compCalculate the analytic steady state concentration for model...
calc_analytic_css_3compssCalculate the analytic steady state concentration for the...
calc_analytic_css_pbtkCalculate the analytic steady state plasma concentration for...
calc_cssFind the steady state concentration and the day it is...
calc_dowCalculate the distribution coefficient
calc_elimination_rateCalculate the elimination rate for a one compartment model
calc_fbio.oralFunctions for calculating the bioavaialble fractions from...
calc_fetal_physCalculate maternal-fetal physiological parameters
calc_fup_correctionCalculate the correction for lipid binding in plasma binding...
calc_half_lifeCalculates the half-life for a one compartment model.
calc_hepatic_clearanceCalculate the hepatic clearance (deprecated).
calc_hep_bioavailabilityCalculate first pass heaptic metabolism
calc_hep_clearanceCalculate the hepatic clearance.
calc_hep_fuCalculate the free chemical in the hepaitic clearance assay
calc_ionizationCalculate the ionization.
calc_kairCalculate air:matrix partition coefficients
calc_krbc2puBack-calculates the Red Blood Cell to Unbound Plasma...
calc_maCalculate the membrane affinity
calc_maternal_bwCalculate maternal body weight
calc_mc_cssDistribution of chemical steady state concentration with...
calc_mc_oral_equivCalculate Monte Carlo Oral Equivalent Dose
calc_mc_tkConduct multiple TK simulations using Monte Carlo
calc_rblood2plasmaCalculate the constant ratio of the blood concentration to...
calc_statsCalculate toxicokinetic summary statistics (deprecated).
calc_tkstatsCalculate toxicokinetic summary statistics.
calc_total_clearanceCalculate the total plasma clearance.
calc_vdistCalculate the volume of distribution for a one compartment...
CAS.checksumTest the check digit of a CAS number to confirm validity
check_modelCheck for sufficient model parameters
chem.invivo.PK.aggregate.dataParameter Estimates from Wambaugh et al. (2018)
chem.invivo.PK.dataPublished toxicokinetic time course measurements
chem.invivo.PK.summary.dataSummary of published toxicokinetic time course experiments
chem.physical_and_invitro.dataPhysico-chemical properties and in vitro measurements for...
ckd_epi_eqCKD-EPI equation for GFR.
concentration_data_Linakis2020Concentration data involved in Linakis 2020 vignette...
convert_solve_xconvert_solve_x
convert_unitsconvert_units
create_mc_samplesCreate a table of parameter values for Monte Carlo
dawson2021Dawson et al. 2021 data
EPA.refReference for EPA Physico-Chemical Data
estimate_gfrPredict GFR.
estimate_gfr_pedPredict GFR in children.
estimate_hematocritGenerate hematocrit values for a virtual population
example.seemSEEM Example Data We can grab SEEM daily intake rate...
example.toxcastToxCast Example Data The main page for the ToxCast data is...
export_pbtk_jarnacExport model to jarnac.
export_pbtk_sbmlExport model to sbml.
fetalpcsFetal Partition Coefficients
Frank2018invivoLiterature In Vivo Data on Doses Causing Neurological Effects
gen_age_height_weightGenerate demographic parameters for a virtual population
gen_height_weightGenerate heights and weights for a virtual population.
gen_serum_creatinineGenerate serum creatinine values for a virtual population.
get_caco2Retrieve in vitro measured Caco-2 membrane permeabilit
get_chem_idRetrieve chemical identity from HTTK package
get_cheminfoRetrieve chemical information available from HTTK package
get_clintRetrieve and parse intrinsic hepatic clearance
get_fbioRetrieve or calculate fraction of chemical absorbed from the...
get_fupRetrieve and parse fraction unbound in plasma
get_gfr_categoryCategorize kidney function by GFR.
get_invitroPK_paramRetrieve species-specific in vitro data from...
get_lit_cheminfoGet literature Chemical Information.
get_lit_cssGet literature Css
get_lit_oral_equivGet Literature Oral Equivalent Dose
get_physchem_paramGet physico-chemical parameters from...
get_rblood2plasmaGet ratio of the blood concentration to the plasma...
get_weight_classAssign weight class (underweight, normal, overweight, obese)
get_wetmore_cheminfoGet literature Chemical Information. (deprecated).
get_wetmore_cssGet literature Css (deprecated).
get_wetmore_oral_equivGet Literature Oral Equivalent Dose (deprecated).
hct_hKDE bandwidths for residual variability in hematocrit
hematocrit_infantsPredict hematocrit in infants under 1 year old.
honda2023.dataMeasured Caco-2 Apical-Basal Permeability Data
honda2023.qsprPredicted Caco-2 Apical-Basal Permeabilities
honda.iviveReturn the assumptions used in Honda et al. 2019
howgateHowgate 2006
httk-packagehttk: High-Throughput Toxicokinetics
httk.performanceHistorical Performance of R Package httk
httkpophttkpop: Virtual population generator for HTTK.
httkpop_biotophys_defaultConvert HTTK-Pop-generated parameters to HTTK physiological...
httkpop_direct_resampleGenerate a virtual population by directly resampling the...
httkpop_direct_resample_innerInner loop function called by 'httkpop_direct_resample'.
httkpop_generateGenerate a virtual population for PBTK
httkpop_mchttk-pop: Correlated human physiological parameter Monte...
httkpop_virtual_indivGenerate a virtual population by the virtual individuals...
hw_HKDE bandwidth for residual variability in height/weight
in.listConvenience Boolean (yes/no) functions to identify chemical...
invitro_mcMonte Carlo for in vitro toxicokinetic parameters including...
is.httkConvenience Boolean (yes/no) function to identify chemical...
is_in_inclusiveChecks whether a value, or all values in a vector, is within...
johnsonJohnson 2006
kapraun2019Kapraun et al. 2019 data
kidney_mass_childrenPredict kidney mass for children
liver_mass_childrenPredict liver mass for children
load_dawson2021Load CLint and Fup QSPR predictions from Dawson et al. 2021.
load_honda2023Load Caco2 QSPR predictions from Honda et al. 2023
load_pradeep2020Load CLint and Fup QSPR predictions predictions from Pradeep...
load_sipes2017Load CLint and Fup QSPR predictions from Sipes et al 2017.
lump_tissuesLump tissue parameters into model compartments
lung_mass_childrenPredict lung mass for children
mcnally_dtReference tissue masses and flows from tables in McNally et...
mecdtPre-processed NHANES data.
metabolism_data_Linakis2020Metabolism data involved in Linakis 2020 vignette analysis.
monte_carloMonte Carlo for toxicokinetic model parameters
Obach2008Published Pharmacokinetic Parameters from Obach et al. 2008
onlypNHANES Exposure Data
pancreas_mass_childrenPredict pancreas mass for children
parameterize_1compParameters for a one compartment (empirical) toxicokinetic...
parameterize_3compParameters for a three-compartment toxicokinetic model...
parameterize_fetal_pbtkParameterize_fetal_PBTK
parameterize_gas_pbtkParameters for a generic gas inhalation physiologically-based...
parameterize_pbtkParameters for a generic physiologically-based toxicokinetic...
parameterize_schmittParameters for Schmitt's (2008) Tissue Partition Coefficient...
parameterize_steadystateParameters for a three-compartment toxicokinetic model at...
pc.dataPartition Coefficient Data
pearce2017regressionPearce et al. 2017 data
pharmaDRUGS|NORMAN: Pharmaceutical List with EU, Swiss, US...
physiology.dataSpecies-specific physiology parameters
pksim.pcsPartition Coefficients from PK-Sim
pradeep2020Pradeep et al. 2020
predict_partitioning_schmittPredict partition coefficients using the method from Schmitt...
pregnonpregaucsAUCs for Pregnant and Non-Pregnant Women
propagate_invitrouv_1compPropagates uncertainty and variability in in vitro HTTK data...
propagate_invitrouv_3compPropagates uncertainty and variability in in vitro HTTK data...
propagate_invitrouv_pbtkPropagates uncertainty and variability in in vitro HTTK data...
reset_httkReset HTTK to Default Data Tables
rfunRandomly draws from a one-dimensional KDE
r_left_censored_normReturns draws from a normal distribution with a lower...
rmed0non0u95Draw random numbers with LOD median but non-zero upper 95th...
scale_dosingScale mg/kg body weight doses according to body weight and...
scr_hKDE bandwidths for residual variability in serum creatinine
set_httk_precisionset_httk_precision
sipes2017Sipes et al. 2017 data
skeletal_muscle_massPredict skeletal muscle mass
skeletal_muscle_mass_childrenPredict skeletal muscle mass for children
skin_mass_bosgraPredict skin mass
solve_1compSolve one compartment TK model
solve_3compSolve_3comp
solve_fetal_pbtkSolve_fetal_PBTK
solve_gas_pbtksolve_gas_pbtk
solve_modelSolve_model
solve_pbtkSolve_PBTK
spleen_mass_childrenPredict spleen mass for children
supptab1_Linakis2020Supplementary output from Linakis 2020 vignette analysis.
supptab2_Linakis2020More supplementary output from Linakis 2020 vignette...
Tables.Rdata.stampA timestamp of table creation
tissue.dataTissue composition and species-specific physiology parameters
tissue_masses_flowsGiven a data.table describing a virtual population by the...
tissue_scaleAllometric scaling.
wambaugh2019in vitro Toxicokinetic Data from Wambaugh et al. (2019)
wambaugh2019.nhanesNHANES Chemical Intake Rates for chemicals in Wambaugh et al....
wambaugh2019.rawRaw Bayesian in vitro Toxicokinetic Data Analysis from...
wambaugh2019.seem3ExpoCast SEEM3 Consensus Exposure Model Predictions for...
wambaugh2019.tox21Tox21 2015 Active Hit Calls (EPA)
wang2018Wang et al. 2018 Wang et al. (2018) screened the blood of 75...
well_paramMicrotiter Plate Well Descriptions for Armitage et al. (2014)...
Wetmore2012Published toxicokinetic predictions based on in vitro data...
wflWHO weight-for-length charts
httk documentation built on Sept. 11, 2024, 9:32 p.m.