Man pages for httk
High-Throughput Toxicokinetics
| add_chemtable | Add a table of chemical information for use in making httk... |
| age_draw_smooth | Draws ages from a smoothed distribution for a given... |
| apply_clint_adjustment | Correct the measured intrinsive hepatic clearance for... |
| apply_fup_adjustment | Correct the measured fraction unbound in plasma for lipid... |
| 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... |
| available_rblood2plasma | Find the best available ratio of the blood to plasma... |
| aylward2014 | Aylward et al. 2014 |
| benchmark_httk | Assess the current performance of httk relative to historical... |
| 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. |
| calc_analytic_css | Calculate the analytic steady state plasma concentration. |
| calc_analytic_css_1comp | Calculate the analytic steady state concentration for the one... |
| calc_analytic_css_3comp | Calculate the analytic steady state concentration for model... |
| calc_analytic_css_3compss | Calculate the analytic steady state concentration for the... |
| calc_analytic_css_pbtk | Calculate the analytic steady state plasma concentration for... |
| calc_css | Find the steady state concentration and the day it is... |
| calc_dow | Calculate the distribution coefficient |
| calc_elimination_rate | Calculate the elimination rate for a one compartment model |
| calc_fbio.oral | Functions for calculating the bioavaialble fractions from... |
| calc_fetal_phys | Calculate maternal-fetal physiological parameters |
| calc_fup_correction | Calculate the correction for lipid binding in plasma binding... |
| 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... |
| calc_ma | Calculate the membrane affinity |
| calc_maternal_bw | Calculate maternal body weight |
| calc_mc_css | Distribution of chemical steady state concentration with... |
| 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... |
| 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... |
| CAS.checksum | Test the check digit of a CAS number to confirm validity |
| check_model | Check for sufficient model parameters |
| 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... |
| ckd_epi_eq | CKD-EPI equation for GFR. |
| concentration_data_Linakis2020 | Concentration data involved in Linakis 2020 vignette... |
| convert_solve_x | convert_solve_x |
| convert_units | convert_units |
| create_mc_samples | Create a table of parameter values for Monte Carlo |
| dawson2021 | Dawson et al. 2021 data |
| 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... |
| example.toxcast | ToxCast Example Data The main page for the ToxCast data is... |
| export_pbtk_jarnac | Export model to jarnac. |
| export_pbtk_sbml | Export model to sbml. |
| fetalpcs | Fetal Partition Coefficients |
| Frank2018invivo | Literature In Vivo Data on Doses Causing Neurological Effects |
| 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_chem_id | Retrieve chemical identity from HTTK package |
| get_cheminfo | Retrieve chemical information available from HTTK package |
| get_clint | Retrieve and parse intrinsic hepatic clearance |
| get_fbio | Retrieve or calculate fraction of chemical absorbed from the... |
| 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... |
| 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... |
| get_rblood2plasma | Get ratio of the blood concentration to the plasma... |
| 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). |
| hct_h | KDE bandwidths for residual variability in hematocrit |
| hematocrit_infants | Predict hematocrit in infants under 1 year old. |
| honda2023.data | Measured Caco-2 Apical-Basal Permeability Data |
| honda2023.qspr | Predicted Caco-2 Apical-Basal Permeabilities |
| honda.ivive | Return the assumptions used in Honda et al. 2019 |
| howgate | Howgate 2006 |
| httk-package | httk: High-Throughput Toxicokinetics |
| 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... |
| httkpop_direct_resample | Generate a virtual population by directly resampling the... |
| 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... |
| httkpop_virtual_indiv | Generate a virtual population by the virtual individuals... |
| hw_H | KDE bandwidth for residual variability in height/weight |
| in.list | Convenience Boolean (yes/no) functions to identify chemical... |
| invitro_mc | Monte Carlo for in vitro toxicokinetic parameters including... |
| is.httk | Convenience Boolean (yes/no) function to identify chemical... |
| is_in_inclusive | Checks whether a value, or all values in a vector, is within... |
| johnson | Johnson 2006 |
| kapraun2019 | Kapraun et al. 2019 data |
| kidney_mass_children | Predict kidney mass for children |
| 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... |
| 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 |
| mcnally_dt | Reference tissue masses and flows from tables in McNally et... |
| mecdt | Pre-processed NHANES data. |
| metabolism_data_Linakis2020 | Metabolism data involved in Linakis 2020 vignette analysis. |
| monte_carlo | Monte Carlo for toxicokinetic model parameters |
| Obach2008 | Published Pharmacokinetic Parameters from Obach et al. 2008 |
| onlyp | NHANES Exposure Data |
| pancreas_mass_children | Predict pancreas mass for children |
| parameterize_1comp | Parameters for a one compartment (empirical) toxicokinetic... |
| parameterize_3comp | Parameters for a three-compartment toxicokinetic model... |
| parameterize_fetal_pbtk | Parameterize_fetal_PBTK |
| parameterize_gas_pbtk | Parameters for a generic gas inhalation physiologically-based... |
| parameterize_pbtk | Parameters for a generic physiologically-based toxicokinetic... |
| parameterize_schmitt | Parameters for Schmitt's (2008) Tissue Partition Coefficient... |
| parameterize_steadystate | Parameters for a three-compartment toxicokinetic model at... |
| pc.data | Partition Coefficient Data |
| pearce2017regression | Pearce et al. 2017 data |
| pharma | DRUGS|NORMAN: Pharmaceutical List with EU, Swiss, US... |
| physiology.data | Species-specific physiology parameters |
| pksim.pcs | Partition Coefficients from PK-Sim |
| pradeep2020 | Pradeep et al. 2020 |
| predict_partitioning_schmitt | Predict partition coefficients using the method from Schmitt... |
| pregnonpregaucs | AUCs for Pregnant and Non-Pregnant Women |
| propagate_invitrouv_1comp | Propagates uncertainty and variability in in vitro HTTK data... |
| propagate_invitrouv_3comp | Propagates uncertainty and variability in in vitro HTTK data... |
| propagate_invitrouv_pbtk | Propagates uncertainty and variability in in vitro HTTK data... |
| 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... |
| rmed0non0u95 | Draw random numbers with LOD median but non-zero upper 95th... |
| scale_dosing | Scale mg/kg body weight doses according to body weight and... |
| scr_h | KDE bandwidths for residual variability in serum creatinine |
| set_httk_precision | set_httk_precision |
| 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... |
| 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... |
| tissue_scale | Allometric scaling. |
| wambaugh2019 | in vitro Toxicokinetic Data from Wambaugh et al. (2019) |
| wambaugh2019.nhanes | NHANES Chemical Intake Rates for chemicals in Wambaugh et al.... |
| wambaugh2019.raw | Raw Bayesian in vitro Toxicokinetic Data Analysis from... |
| wambaugh2019.seem3 | ExpoCast SEEM3 Consensus Exposure Model Predictions for... |
| wambaugh2019.tox21 | Tox21 2015 Active Hit Calls (EPA) |
| wang2018 | Wang et al. 2018 Wang et al. (2018) screened the blood of 75... |
| well_param | Microtiter Plate Well Descriptions for Armitage et al. (2014)... |
| Wetmore2012 | Published toxicokinetic predictions based on in vitro data... |
| wfl | WHO weight-for-length charts |
