R: High-Throughput Toxicokinetics Examples

# High-Throughput Toxicokinetics Examples

## Documentation for package ‘httkexamples’ version 0.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

Abraham2024 | Abraham et al. 2024 Abraham et al. (2024) (doi:10.1016/j.envint.2024.109047 <https://doi.org/10.1016/j.envint.2024.109047>) determined the half-lives of 15 per- and polyfluoroalkyl substances in a single male volunteer.
abraham2024 | Abraham et al. 2024 Abraham et al. (2024) (doi:10.1016/j.envint.2024.109047 <https://doi.org/10.1016/j.envint.2024.109047>) determined the half-lives of 15 per- and polyfluoroalkyl substances in a single male volunteer.
Armitage_input | Parameters for in vitro distribution analysis in Honda et al. (2019) Honda et al. (2019) (doi:10.1371/journal.pone.0217564 <https://doi.org/10.1371/journal.pone.0217564>) used the Armitage et al. (2014) (doi:10.1021/es501955g <https://doi.org/10.1021/es501955g>) mass-balance model to predict the impact of in vitro partitioning on free chemical concentrations.
armitage_input | Parameters for in vitro distribution analysis in Honda et al. (2019) Honda et al. (2019) (doi:10.1371/journal.pone.0217564 <https://doi.org/10.1371/journal.pone.0217564>) used the Armitage et al. (2014) (doi:10.1021/es501955g <https://doi.org/10.1021/es501955g>) mass-balance model to predict the impact of in vitro partitioning on free chemical concentrations.
Aylward2014 | Aylward et al. 2014
aylward2014 | Aylward et al. 2014
concentration_data_Linakis2020 | Concentration data involved in Linakis 2020 vignette analysis.
dermal.nonvolatilechems | Non-volatile chemicals with ToxCast data Meade et al. (submitted) performed in vitro-in vivo extrapolation for dermal exposures assuming 8 hours of exposure via hands submerged in a liquid with 1 ppm of chemical. These were the chemicals analyzed.
dermal.toxcast | Chemicals with ToxCast data for Meade et al. (submitted) chemicals Meade et al. (submitted) performed in vitro-in vivo extrapolation for dermal exposures assuming 8 hours of exposure via hands submerged in a liquid with 1 ppm of chemical. These are the ToxCast in vitro screening data for those chemicals.
dermalCvT2025 | Toxicokinetic concentration vs. time (CvT) data for Meade et al. (submitted) chemicals Meade et al. (submitted) evaluated a generic PBTK model for dermal exposure using in vivo CvT data curated from the literature. These data will eventually be incorporated in the the CvTdb (Sayre et al., 2020, doi:10.1038/s41597-020-0455-1 <https://doi.org/10.1038/s41597-020-0455-1>).
Dimitrijevic.IVD | Dimitrijevic et al. (2022)In Vitro Cellular and Nominal Concentration
fetalPCs | Fetal Partition Coefficients
fetalpcs | Fetal Partition Coefficients
Frank2018invivo | Literature In Vivo Data on Doses Causing Neurological Effects
howgate | Howgate et al. (2006)
Huh2011 | Huh et al. 2011 Huh et al. (2011) (doi:10.3109/00498254.2011.598582 <https://doi.org/10.3109/00498254.2011.598582>) provided interspecies allometric scaling parameters for whole body clearance for a a variety of pharmaceuticals.
huh2011 | Huh et al. 2011 Huh et al. (2011) (doi:10.3109/00498254.2011.598582 <https://doi.org/10.3109/00498254.2011.598582>) provided interspecies allometric scaling parameters for whole body clearance for a a variety of pharmaceuticals.
johnson | Johnson et al. (2006)
Meade2025 | Simulation outputs from Meade et al. (submitted) Meade et al. (submitted) performed generic PBTK simulations for dermal exposure under a variety of assumptions. Although the code to recreate these simulations is provided, it is time-intensive. The 2025 outputs from the simulations are stored in this list of data.frames.
meade2025 | Simulation outputs from Meade et al. (submitted) Meade et al. (submitted) performed generic PBTK simulations for dermal exposure under a variety of assumptions. Although the code to recreate these simulations is provided, it is time-intensive. The 2025 outputs from the simulations are stored in this list of data.frames.
metabolism_data_Linakis2020 | Metabolism data involved in Linakis et al. 2020 (doi:10.1038/s41370-020-0238-y <https://doi.org/10.1038/s41370-020-0238-y>) vignette analysis.
Obach2008 | Published Pharmacokinetic Parameters from Obach et al. 2008
onlyp | NHANES Exposure Data
pc.data | Partition Coefficient Data
pharma | DRUGS|NORMAN: Pharmaceutical List with EU, Swiss, US Consumption Data
pksim.pcs | Partition Coefficients from PK-Sim
pregnonpregaucs | AUCs for Pregnant and Non-Pregnant Women
Scherer2025.IVD | Literature Measurements of In Vitro Cellular and Nominal Concentration
supptab1_Linakis2020 | Supplementary output from Linakis 2020 vignette analysis.
supptab2_Linakis2020 | More supplementary output from Linakis 2020 vignette analysis.
thyroid.ac50s | ToxCast thyroid-related bioactivity data
truong25.seem3 | SEEM3 Example Data for Truong et al. 2025
Wallis2023 | Wallis et al. 2023 Wallis et al. (2023) (doi:10.1021/acs.est.2c08241 <https://doi.org/10.1021/acs.est.2c08241>) estimated the human toxicokinetic half-lives for a range of per- and poly-fluorinated alkyl substances (PFAS).
wallis2023 | Wallis et al. 2023 Wallis et al. (2023) (doi:10.1021/acs.est.2c08241 <https://doi.org/10.1021/acs.est.2c08241>) estimated the human toxicokinetic half-lives for a range of per- and poly-fluorinated alkyl substances (PFAS).
wambaugh2019 | in vitro Toxicokinetic Data from Wambaugh et al. (2019)
wambaugh2019.nhanes | NHANES Chemical Intake Rates for chemicals in Wambaugh et al. (2019)
wambaugh2019.raw | Raw Bayesian in vitro Toxicokinetic Data Analysis from Wambaugh et al. (2019)
wambaugh2019.seem3 | ExpoCast SEEM3 Consensus Exposure Model Predictions for Chemical Intake Rates
wambaugh2019.tox21 | Tox21 2015 Active Hit Calls (EPA)
Wang2018 | Wang et al. 2018 Wang et al. (2018) screened the blood of 75 pregnant women for the presence of environmental organic acids (EOAs) and identified mass spectral features corresponding to 453 chemical formulae of which 48 could be mapped to likely structures. Of the 48 with tentative structures the identity of six were confirmed with available chemical standards.
wang2018 | Wang et al. 2018 Wang et al. (2018) screened the blood of 75 pregnant women for the presence of environmental organic acids (EOAs) and identified mass spectral features corresponding to 453 chemical formulae of which 48 could be mapped to likely structures. Of the 48 with tentative structures the identity of six were confirmed with available chemical standards.
Wetmore2012 | Published toxicokinetic predictions based on in vitro data from Wetmore et al. 2012.