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: 2.0.3
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
Published: 2020-09-25
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], 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 epa.gov>
BugReports: https://github.com/USEPA/CompTox-ExpoCast-httk
License: GPL-3
URL: https://www.epa.gov/chemical-research/rapid-chemical-exposure-and-dose-research
NeedsCompilation: yes
Citation: httk citation info
Materials: NEWS
CRAN checks: httk results

Downloads:

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
Pearce et al. (2017): Creating Partition Coefficient Evaluation Plots
Ring et al. (2017): Generating subpopulations
Ring et al. (2017): Evaluating HTTK models for subpopulations
Ring et al. (2017): Generating Figure 2
Ring et al. (2017): Generating Figure 3
Ring et al. (2017): Plotting Howgate/Johnson data
Ring et al. (2017): AER plotting
Ring et al. (2017): Virtual study populations
Wambaugh et al. (2018): Creating All Figures
Wambaugh et al. (2019): Creating Figures for the Manuscript
Package source: httk_2.0.3.tar.gz
Windows binaries: r-devel: httk_2.0.3.zip, r-release: httk_2.0.3.zip, r-oldrel: httk_2.0.3.zip
macOS binaries: r-release: httk_2.0.3.tgz, r-oldrel: httk_2.0.3.tgz
Old sources: httk archive

Reverse dependencies:

Reverse imports: plethem

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