Other packages > Find by keyword >

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", "2.5.0")



Attach the package and use:
library("httk")
Maintained by
John Wambaugh
[Scholar Profile | Author Map]
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 2.5.0, https://cran.r-project.org/web/packages/httk. Accessed 02 Apr. 2025.
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), 2.3.1 (2024-03-27 01:00), 2.4.0 (2024-09-06 00:40)
Other packages that cited httk R package
View httk citation profile
Other R packages that httk depends, imports, suggests or enhances
Complete documentation for httk
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
Downloads during the last 30 days
03/0303/0403/0503/0603/0703/0803/0903/1003/1103/1203/1303/1403/1503/1603/1703/1803/1903/2003/2103/2203/2303/2403/2503/2603/2703/2803/2903/3003/3104/01Downloads for httk0102030405060708090TrendBars

Today's Hot Picks in Authors and Packages

CodeDepends  
Analysis of R Code for Reproducible Research and Code Comprehension
Tools for analyzing R expressions or blocks of code and determining the dependencies between them. ...
Download / Learn more Package Citations See dependency  
binom  
Binomial Confidence Intervals for Several Parameterizations
Constructs confidence intervals on the probability of success in a binomial experiment via several ...
Download / Learn more Package Citations See dependency  
CTShiny  
Interactive Document for Working with Classification Tree Analysis
An interactive document on the topic of classification tree analysis using 'rmarkdown' and 'shiny' ...
Download / Learn more Package Citations See dependency  
pirate  
Generated Effect Modifier
An implementation of the generated effect modifier (GEM) method. This method constructs composite va ...
Download / Learn more Package Citations See dependency  
Maintainer: Zhe Su (view profile)
munfold  
Metric Unfolding
Multidimensional unfolding using Schoenemann's algorithm for metric and Procrustes rotation of unfo ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  

23,990

R Packages

207,311

Dependencies

64,809

Author Associations

23,991

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA