httk: High-Throughput Toxicokinetics

Generic models and chemical-specific data for simulation and statistical analysis of chemical toxicokinetics ("TK") as described by Pearce et al. (2017) <doi:10.18637/jss.v079.i04>. Chemical-specific in vitro data have been obtained from relatively high throughput experiments. Both physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models can be parameterized with the data provided for thousands of chemicals, multiple exposure routes, and various species. The models consist of systems of ordinary differential equations which are solved using compiled (C-based) code for speed. A Monte Carlo sampler is included, which allows for simulating human biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and propagating parameter uncertainty. Calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>). These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (for example, Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

Version: 2.0.4
Depends: R (≥ 2.10)
Imports: deSolve, msm, data.table, survey, mvtnorm, truncnorm, stats, graphics, utils, magrittr, purrr, methods
Suggests: ggplot2, knitr, rmarkdown, R.rsp, GGally, gplots, scales, EnvStats, MASS, RColorBrewer, TeachingDemos, classInt, ks, stringr, reshape, reshape2, gdata, viridis, CensRegMod, gmodels, colorspace, cowplot, ggrepel, dplyr, forcats, smatr, gtools, gridExtra, testthat
Published: 2021-05-10
Author: John Wambaugh ORCID iD [aut, cre], Robert Pearce ORCID iD [aut], Caroline Ring ORCID iD [aut], Greg Honda ORCID iD [aut], Mark Sfeir [aut], Matt Linakis ORCID iD [aut], Sarah Davidson ORCID iD [aut], Miyuki Breen ORCID iD [ctb], Shannon Bell [ctb], Xiaoqing Chang ORCID iD [ctb], Jimena Davis [ctb], James Sluka ORCID iD [ctb], Nisha Sipes ORCID iD [ctb], Barbara Wetmore ORCID iD [ctb], Woodrow Setzer ORCID iD [ctb]
Maintainer: John Wambaugh <wambaugh.john at>
License: GPL-3
Copyright: This package is primarily developed by employees of the U.S. Federal government as part of their official duties and is therefore public domain.
NeedsCompilation: yes
Citation: httk citation info
Materials: NEWS
CRAN checks: httk results


Reference manual: httk.pdf
Vignettes: Frank et al. (2018): Creating IVIVE Figure (Fig. 6)
Honda et al. (2019): Updated Armitage et al. (2014) Model
Linakis et al. (2020): Analysis and Figure Generation
Ring et al. (2017): AER plotting
Wambaugh et al. (2018): Creating All Figures
Wambaugh et al. (2019): Creating Figures for the Manuscript
Package source: httk_2.0.4.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries: r-release: httk_2.0.3.tgz, r-oldrel: not available
Old sources: httk archive


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