httk: High-Throughput Toxicokinetics

Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") as in 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 (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability (Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>) and measurement limitations. 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 (e.g., Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

Version: 2.0.1
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: 2020-03-02
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 [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. (Submitted): 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_2.0.1.tar.gz
Windows binaries: r-devel: httk_2.0.1.zip, r-devel-gcc8: httk_2.0.1.zip, r-release: httk_2.0.1.zip, r-oldrel: httk_2.0.1.zip
OS X binaries: r-release: httk_2.0.1.tgz, r-oldrel: httk_2.0.1.tgz
Old sources: httk archive

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