Package: GeoTox 1.0.0

Skylar Marvel

GeoTox: Spatiotemporal Mixture Risk Assessment

Connecting spatiotemporal exposure to individual and population-level risk via source-to-outcome continuum modeling. The package, methods, and case-studies are described in Messier, Reif, and Marvel (2025) <doi:10.1186/s40246-024-00711-8> and Eccles et al. (2023) <doi:10.1016/j.scitotenv.2022.158905>.

Authors:Skylar Marvel [aut, cre], David Reif [aut], Kyle Messier [aut], Spatiotemporal Exposures and Toxicology Group [cph]

GeoTox_1.0.0.tar.gz
GeoTox_1.0.0.zip(r-4.7)GeoTox_1.0.0.zip(r-4.6)GeoTox_1.0.0.zip(r-4.5)
GeoTox_1.0.0.tgz(r-4.6-any)GeoTox_1.0.0.tgz(r-4.5-any)
GeoTox_1.0.0.tar.gz(r-4.7-any)GeoTox_1.0.0.tar.gz(r-4.6-any)
GeoTox_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeoTox/json (API)

# Install 'GeoTox' in R:

install.packages('GeoTox', repos = c('https://niehs.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/niehs/geotox/issues

Pkgdown/docs site:https://niehs.github.io

Datasets:

geo_tox_data - GeoTox Data

On CRAN:

quarto

5.62 score 7 stars 4 scripts 582 downloads 30 exports 31 dependencies

Last updated from:6fef1cac9d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	270
source / vignettes	OK	218
linux-release-x86_64	OK	256
macos-release-arm64	OK	293
macos-oldrel-arm64	OK	297
windows-devel	OK	285
windows-release	OK	271
windows-oldrel	OK	287
wasm-release	OK	163

Exports:add_age add_exposure add_exposure_rate_params add_hill_params add_obesity calc_internal_dose calc_invitro_concentration calc_response calc_risk calc_sensitivity fit_hill GeoTox get_assay_table get_boundary get_con get_concentration_mean get_risk_quantiles get_risk_sensitivity get_risk_values sample_simulated_css sensitivity_analysis set_boundary set_fixed_css set_sample set_simulated_css simulate_age simulate_exposure simulate_exposure_rate simulate_obesity simulate_population

Dependencies:blob cachem cli collections cpp11 DBI dbplyr dplyr duckdb duckplyr fastmap generics glue jsonlite lifecycle magrittr memoise pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect truncnorm utf8 vctrs withr

GeoTox Package Data

Rendered frompackage_data.qmdusingquarto::html

Last update: 2026-05-19
Started: 2026-05-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add age simulation data	add_age
Add exposure simulation data	add_exposure
Add exposure rate simulation data	add_exposure_rate_params
Add Hill model parameters	add_hill_params
Add obesity simulation data	add_obesity
Calculate internal dose	calc_internal_dose
Calculate in vitro concentration	calc_invitro_concentration
Calculate concentrations and risks	calc_response
Calculate risk scores	calc_risk
Calculate risk sensitivity to a single variable	calc_sensitivity
Fit 2- or 3-parameter Hill model	fit_hill
GeoTox Data	geo_tox_data
GeoTox S3 object	GeoTox get_con
Get risk metric results	get_assay_table get_risk_quantiles get_risk_sensitivity get_risk_values
Get concentration mean values	get_concentration_mean
Sample from pre-simulated steady-state plasma concentrations	sample_simulated_css
Perform sensitivity analysis	sensitivity_analysis
Store and retrieve boundary geometries	get_boundary set_boundary
Prepare steady-state plasma concentrations for sensitivity analysis	set_fixed_css
Set sample data	set_sample
Set pre-simulated steady-state plasma concentrations	set_simulated_css
Simulate age values	simulate_age
Simulate exposure concentrations	simulate_exposure
Simulate exposure rates	simulate_exposure_rate
Simulate obesity values	simulate_obesity
Simulate population characteristics and exposures	simulate_population