toxEval

The toxEval R-package includes a set of functions to analyze, visualize, and organize measured concentration data as it relates to https://www.epa.gov/chemical-research/toxicity-forecasting or other user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays.

The functions within this package allow great flexibly for exploring the potential biological affects of measured chemicals. Also included in the package is a browser-based application made from the Shiny R-package (the app). The app is based on functions within the R-package and includes many convenient analyses and visualization options for users to choose. Use of the functions within the R-package allows for additional flexibility within the functions beyond what the app offers and provides options for the user to interact more directly with the data. The overview in this document focuses on the R-package.

Documentation: https://doi-usgs.github.io/toxEval/

Installation of toxEval

To install the toxEval package, you must be using R 3.0 or greater and run the following command:

install.packages("toxEval")

To get cutting-edge changes, install from GitHub using the remotes packages:

library(remotes)
install_gitlab("water/toxEval",
               host = "code.usgs.gov",
               build_vignettes = TRUE, 
               build_opts = c("--no-resave-data",
                              "--no-manual"))

Citing toxEval

citation(package = "toxEval")
#> 
#> To cite toxEval in publications, please use:
#> 
#>   De Cicco, L.A., Corsi, S.R., Villeneuve D.L, Blackwell, and B.R,
#>   Ankley, G.T., 2023, toxEval: Evaluation of measured concentration
#>   data using the ToxCast high-throughput screening database or a
#>   user-defined set of concentration benchmarks. R package version
#>   1.3.0., https://code.usgs.gov/water/toxEval, doi:10.5066/P906UQ5I
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     author = {Laura A. {De Cicco} and Steven R. Corsi and Daniel L. Villeneuve and Brett R. Blackwell and Gerald T. Ankley},
#>     title = {toxEval: Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks.},
#>     publisher = {U.S. Geological Survey},
#>     version = {1.3.0},
#>     address = {Reston, VA},
#>     institution = {U.S. Geological Survey},
#>     year = {2023},
#>     doi = {10.5066/P906UQ5I},
#>     url = {https://code.usgs.gov/water/toxEval},
#>   }

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.