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httk  

High-Throughput Toxicokinetics
View on CRAN: Click here


Download and install httk package within the R console
Install from CRAN:
install.packages("httk")

Install from Github:
library("remotes")
install_github("cran/httk")

Install by package version:
library("remotes")
install_version("httk", "2.3.1")



Attach the package and use:
library("httk")
Maintained by
John Wambaugh
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-03-06
Latest Update: 2023-12-08
Description:
Pre-made models that can be rapidly tailored to various chemicals and species using chemical-specific in vitro data and physiological information. These tools allow incorporation of chemical toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE") into bioinformatics, as described by Pearce et al. (2017) (). Chemical-specific in vitro data characterizing toxicokinetics have been obtained from relatively high-throughput experiments. The chemical-independent ("generic") physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models included here can be parameterized with in vitro data or in silico predictions which are provided for thousands of chemicals, multiple exposure routes, and various species. High throughput toxicokinetics ("HTTK") is the combination of in vitro data and generic models. We establish the expected accuracy of HTTK for chemicals without in vivo data through statistical evaluation of HTTK predictions for chemicals where in vivo data do exist. The models are systems of ordinary differential equations that are developed in MCSim and solved using compiled (C-based) code for speed. A Monte Carlo sampler is included for simulating human biological variability (Ring et al., 2017 ) and propagating parameter uncertainty (Wambaugh et al., 2019 ). Empirically calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 ). These functions and data provide a set of tools for using IVIVE to convert concentrations from high-throughput screening experiments (for example, Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 ).
How to cite:
John Wambaugh (2015). httk: High-Throughput Toxicokinetics. R package version 2.3.1, https://cran.r-project.org/web/packages/httk
Previous versions and publish date:
1.1 (2015-03-06 17:47), 1.2 (2015-05-11 16:53), 1.3 (2015-10-14 09:53), 1.4 (2016-02-03 01:14), 1.5 (2017-03-03 18:16), 1.6 (2017-06-08 18:55), 1.7 (2017-07-15 08:28), 1.8 (2018-01-23 22:54), 1.9.1 (2019-04-17 21:00), 1.9.2 (2019-04-25 18:10), 1.9 (2019-02-04 21:33), 1.10.0 (2019-07-12 00:21), 1.10.1 (2019-09-10 06:30), 2.0.0 (2020-02-17 07:10), 2.0.1 (2020-03-02 07:00), 2.0.2 (2020-07-19 15:50), 2.0.3 (2020-09-25 13:00), 2.0.4 (2021-05-10 09:50), 2.1.0 (2022-03-26 02:20), 2.2.0 (2022-09-08 23:32), 2.2.1 (2022-09-24 07:40), 2.2.2 (2023-02-20 23:40), 2.3.0 (2023-12-08 19:50)
Other packages that cited httk R package
View httk citation profile
Other R packages that httk depends, imports, suggests or enhances
Functions, R codes and Examples using the httk R package
Some associated functions: CAS.checksum . EPA.ref . Frank2018invivo . Obach2008 . Tables.Rdata.stamp . Wetmore2012 . add_chemtable . age_draw_smooth . apply_clint_adjustment . apply_fup_adjustment . armitage_estimate_sarea . armitage_eval . armitage_input . augment.table . available_rblood2plasma . aylward2014 . benchmark_httk . blood_mass_correct . blood_weight . bmiage . body_surface_area . bone_mass_age . brain_mass . calc_analytic_css . calc_analytic_css_1comp . calc_analytic_css_3comp . calc_analytic_css_3compss . calc_analytic_css_pbtk . calc_css . calc_dow . calc_elimination_rate . calc_fbio.oral . calc_fetal_phys . calc_fup_correction . calc_half_life . calc_hep_bioavailability . calc_hep_clearance . calc_hep_fu . calc_hepatic_clearance . calc_ionization . calc_kair . calc_krbc2pu . calc_ma . calc_maternal_bw . calc_mc_css . calc_mc_oral_equiv . calc_mc_tk . calc_rblood2plasma . calc_stats . calc_tkstats . calc_total_clearance . calc_vdist . chem.invivo.PK.aggregate.data . chem.invivo.PK.data . chem.invivo.PK.summary.data . chem.physical_and_invitro.data . ckd_epi_eq . concentration_data_Linakis2020 . convert_httkpop_1comp . convert_solve_x . convert_units . create_mc_samples . dawson2021 . estimate_gfr . estimate_gfr_ped . estimate_hematocrit . example.seem . example.toxcast . export_pbtk_jarnac . export_pbtk_sbml . fetalpcs . gen_age_height_weight . gen_height_weight . gen_serum_creatinine . get_caco2 . get_chem_id . get_cheminfo . get_clint . get_fabsgut . get_fup . get_gfr_category . get_invitroPK_param . get_lit_cheminfo . get_lit_css . get_lit_oral_equiv . get_physchem_param . get_rblood2plasma . get_weight_class . get_wetmore_cheminfo . get_wetmore_css . get_wetmore_oral_equiv . hct_h . hematocrit_infants . honda.ivive . honda2023.data . honda2023.qspr . howgate . httk-package . httk.performance . httkpop . httkpop_biotophys_default . httkpop_direct_resample . httkpop_direct_resample_inner . httkpop_generate . httkpop_mc . httkpop_virtual_indiv . hw_H . in.list . invitro_mc . is.httk . is_in_inclusive . johnson . kapraun2019 . kidney_mass_children . liver_mass_children . load_dawson2021 . load_honda2023 . load_pradeep2020 . load_sipes2017 . lump_tissues . lung_mass_children . mcnally_dt . mecdt . metabolism_data_Linakis2020 . monte_carlo . onlyp . pancreas_mass_children . parameterize_1comp . parameterize_3comp . parameterize_fetal_pbtk . parameterize_gas_pbtk . parameterize_pbtk . parameterize_schmitt . parameterize_steadystate . pc.data . pearce2017regression . pharma . physiology.data . pksim.pcs . pradeep2020 . predict_partitioning_schmitt . pregnonpregaucs . propagate_invitrouv_1comp . propagate_invitrouv_3comp . propagate_invitrouv_pbtk . r_left_censored_norm . reset_httk . rfun . rmed0non0u95 . scale_dosing . scr_h . set_httk_precision . sipes2017 . skeletal_muscle_mass . skeletal_muscle_mass_children . skin_mass_bosgra . solve_1comp . solve_3comp . solve_fetal_pbtk . solve_gas_pbtk . solve_model . solve_pbtk . spleen_mass_children . supptab1_Linakis2020 . supptab2_Linakis2020 . tissue.data . tissue_masses_flows . tissue_scale . wambaugh2019.nhanes . wambaugh2019 . wambaugh2019.raw . wambaugh2019.seem3 . wambaugh2019.tox21 . wang2018 . well_param . wfl . 
Some associated R codes: add_chemtable.R . age_draw_smooth.R . apply_clint_adjustment.R . apply_fup_adjustment.R . armitage.R . available_rblood2plasma.R . benchmark_httk.R . calc_analytic_css.R . calc_analytic_css_1comp.R . calc_analytic_css_3comp.R . calc_analytic_css_3compss.R . calc_analytic_css_pbtk.R . calc_css.R . calc_elimination_rate.R . calc_fetal_phys.R . calc_fup_correction.R . calc_half_life.R . calc_hep_bioavailability.R . calc_hep_clearance.R . calc_hep_fu.R . calc_kair.R . calc_krbc2pu.R . calc_ma.R . calc_maternal_bw.R . calc_mc_css.R . calc_mc_oral_equiv.R . calc_mc_tk.R . calc_oral_bioavailability.R . calc_rblood2plasma.R . calc_timecourse_peak.R . calc_tkstats.R . calc_total_clearance.R . calc_volume_of_distribution.R . ckd_epi_eq.R . convert_httkpop_1comp.R . convert_solve_x.R . convert_units.R . create_mc_samples.R . data.R . do_initial_dose_pbtk.R . estimate_gfr.R . estimate_gfr_ped.R . estimate_hematocrit.R . export_pbtk_jarnac.R . export_pbtk_sbml.R . gen_age_height_weight.R . gen_height_weight.R . gen_serum_creatinine.R . get_caco2.R . get_chem_id.R . get_cheminfo.R . get_clint.R . get_fabsgut.R . get_fup.R . get_gfr_category.R . get_invitroPK_param.R . get_lit_cheminfo.R . get_lit_css.R . get_lit_oral_equiv.R . get_physchem_param.R . get_rblood2plasma.R . get_weight_class.R . globals.R . hematocrit_infants.R . honda.ivive.R . httk-package.R . httkpop_biotophys_default.R . httkpop_direct_resample.R . httkpop_direct_resample_inner.R . httkpop_generate.R . httkpop_mc.R . httkpop_virtual_indiv.R . in.list.R . inhalation_inits.R . invitro_mc.R . ionization_functions.R . load_dawson2021.R . load_honda2023.R . load_pradeep2020.R . load_sipes2017.R . lump_tissues.R . modelinfo_1comp.R . modelinfo_3comp.R . modelinfo_3compss.R . modelinfo_fetal_pbtk.R . modelinfo_gas_pbtk.R . modelinfo_pbtk.R . modelinfo_schmitt.R . monte_carlo.R . parameterize_1comp.R . parameterize_3comp.R . parameterize_fetal_pbtk.R . parameterize_gas_pbtk.R . parameterize_pbtk.R . parameterize_schmitt.R . parameterize_steadystate.R . predict_partitioning_schmitt.R . propagate_invitrouv_1comp.R . propagate_invitrouv_3comp.R . propagate_invitrouv_pbtk.R . r_left_censored_norm.R . reset_httk.R . rmed0non0u95.R . scale_dosing.R . set_httk_precision.R . solve_1comp.R . solve_3comp.R . solve_fetal_pbtk.R . solve_gas_pbtk.R . solve_model.R . solve_pbtk.R . tissue_mass_functions.R . tissue_masses_flows.R . tissue_scale.R . utils.R . zzz.R .  Full httk package functions and examples
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