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: 1.10.1
Depends: R (≥ 2.10)
Imports: deSolve, msm, data.table, survey, mvtnorm, truncnorm, stats, graphics, utils, magrittr
Suggests: ggplot2, knitr, rmarkdown, R.rsp, GGally, gplots, scales, EnvStats, MASS, RColorBrewer, TeachingDemos, classInt, ks, stringr, reshape, reshape2, gdata, viridis, CensRegMod, gmodels, colorspace
Published: 2019-09-10
Author: John Wambaugh [aut, cre], Robert Pearce [aut], Caroline Ring [aut], Greg Honda [aut], Mark Sfeir [aut], Jimena Davis [ctb], James Sluka [ctb], Nisha Sipes [ctb], Barbara Wetmore [ctb], Woodrow Setzer [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
Materials: NEWS
CRAN checks: httk results

Downloads:

Reference manual: httk.pdf
Vignettes: Honda et al. (2019): Updated Armitage et al. (2014) Model
Pearce et al. (2017) Creating Partition Coefficient Evaluation Plots
Ring et al. (2017) Age distributions
Ring et al. (2017) Global sensitivity analysis
Ring et al. (2017) Global sensitivity analysis plotting
Ring et al. (2017) Height and weight spline fits and residuals
Ring et al. (2017) Hematocrit spline fits and residuals
Ring et al. (2017) Plotting Css95
Ring et al. (2017) Serum creatinine spline fits and residuals
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. (submitted): Creating Figures for the Manuscript
Package source: httk_1.10.1.tar.gz
Windows binaries: r-devel: httk_1.10.1.zip, r-release: httk_1.10.1.zip, r-oldrel: httk_1.10.1.zip
OS X binaries: r-release: httk_1.10.1.tgz, r-oldrel: httk_1.10.1.tgz
Old sources: httk archive

Reverse dependencies:

Reverse imports: plethem

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