GeoTox open-source R software package for characterizing
the risk of perturbing molecular targets involved in adverse human
health outcomes based on exposure to spatially-referenced stressor
mixtures via the GeoTox framework - otherwise known as
source-to-outcome-continuum modeling. The package, methods, and
case-studies are described in Messier,
Reif, and Marvel, 2024, medRxiv-Preprint.
The GeoTox framework was first described in Eccles et al. A geospatial modeling approach to quantifying the risk of exposure to environmental chemical mixtures via a common molecular target. Sci Total Environ. 2023 Jan 10;855:158905.
install.packages("GeoTox")The development version can be installed from GitHub.
#install.packages("pak")
pak::pak("NIEHS/GeoTox")Figure 1 below shows the steps in the source-to-outcome-continuum or
GeoTox modeling framework that is capable in the GeoTox
package. blue text nodes represent an
object and green text, rounded nodes
represent a methodology or function required to go from one to the next.
The GeoTox package uses R S3 object-oriented programming to
create the GeoTox object. The GeoTox
object is a list that contains all of the information required to run
the analysis including tracking exposure, assays, dose-response, and
geospatial referencing.
Figure 1: Overview of the steps in the GeoTox framework
Please refer to the introduction
vignette for a detailed description of how to use
GeoTox.
For citation information, please refer to our CITATION file.
To add or edit functionality, open a pull request into the main branch with a detailed description of the proposed changes. Pull requests must pass all status checks, and then will be approved or rejected by the GeoTox maintainers.
Utilize GitHub issues to notify the authors of bugs, questions, or recommendations. Identify each issue with the appropriate label to help ensure a timely response.