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ThetoxEval R-package includes a set of functions to analyze,visualize, and organize measured concentration data as it relates tohttps://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast orother user-selected chemical-biological interaction benchmark data suchas water quality criteria. The intent of these analyses is to develop abetter understanding of the potential biological relevance ofenvironmental chemistry data. Results can be used to prioritize whichchemicals at which sites may be of greatest concern. These methods aremeant to be used as a screening technique to predict potential forbiological influence from chemicals that ultimately need to be validatedwith direct biological assays.

The functions within this package allow great flexibly for exploring thepotential biological affects of measured chemicals. Also included in thepackage is a browser-based application made from theShiny R-package(the app). The app is based on functions within the R-package andincludes many convenient analyses and visualization options for users tochoose. Use of the functions within the R-package allows for additionalflexibility within the functions beyond what the app offers and providesoptions for the user to interact more directly with the data. Theoverview in this document focuses on the R-package.

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

install.packages("toxEval")

To get cutting-edge changes, install from GitHub using theremotespackages:

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

Installation instructions are below. To quickly get going intoxEval,run:

library(toxEval)#> For more information:#> https://doi-usgs.github.io/toxEval/#> ToxCast database: version 4.1

explore_endpoints()

Then click on the “Load Example Data” in the upper right corner. Thisloads the example data that is found here:

file.path(system.file("extdata",package="toxEval"),"OWC_data_fromSup.xlsx")

Once the data is loaded in the app, sample R code is shown below eachtab. This can be copied into the R console (once the app is stopped…) touse as a base for exploring the package directly in R.

Alternatively, an example workflow is shown here (also using exampledata provided in the package):

library(toxEval)path_to_file<- file.path(system.file("extdata",package="toxEval"),"OWC_data_fromSup.xlsx")tox_list<- create_toxEval(path_to_file)ACClong<- get_ACC(tox_list$chem_info$CAS)ACClong<- remove_flags(ACClong)cleaned_ep<- clean_endPoint_info(end_point_info)filtered_ep<- filter_groups(cleaned_ep,groupCol='intended_target_family',remove_groups= c('Background Measurement','Undefined'))chemicalSummary<- get_chemical_summary(tox_list,ACClong,filtered_ep)######################################chem_class_plot<- plot_tox_boxplots(chemicalSummary,category='Chemical Class')chem_class_plot

######################################plot_stacks<- plot_tox_stacks(chemicalSummary,tox_list$chem_site,category="Chemical Class")plot_stacks

######################################plot_heat<- plot_tox_heatmap(chemicalSummary,tox_list$chem_site,category="Chemical Class",font_size=7)plot_heat

This code opens up the example file, loads it into atoxEval object,grabs the pertinent ToxCast information, and creates a “chemicalSummary”data frame that is used in many of the plot and table functions.

There are 4 vignettes to help introduce and navigate thetoxEvalpackage:

Please consider reporting bugs and asking questions on the Issues page:https://github.com/DOI-USGS/toxEval/issues

We want to encourage a warm, welcoming, and safe environment forcontributing to this project. See thecode ofconduct formore information.

The Water and Environmental Health Mission Areas of the USGS, as well asthe Great Lakes Restoration Initiative (GLRI) has supported thedevelopment of thetoxEval R-package. Further maintenance is expectedto be stable through September 2025. Resources are available primarilyfor maintenance and responding to user questions. Priorities on thedevelopment of new features are determined by thetoxEval developmentteam.

Funding fortoxEval is secured through summer 2025, after which bugfixes & new features will be minimal.

To run the toxEval app:

1. Open RStudio
2. In the Console (lower-left window of RStudio) paste the following:

library(toxEval)explore_endpoints()

citation(package="toxEval")#> To cite package 'toxEval' in publications use:#>#>   DeCicco L, Corsi S, Villeneuve D, Blackwell B, Ankley G (2024).#>   _toxEval: Exploring Biological Relevance of Environmental Chemistry#>   Observations_. R package version 1.4.0.#>#> A BibTeX entry for LaTeX users is#>#>   @Manual{,#>     title = {toxEval: Exploring Biological Relevance of Environmental Chemistry#> Observations},#>     author = {Laura DeCicco and Steven Corsi and Daniel Villeneuve and Brett Blackwell and Gerald Ankley},#>     year = {2024},#>     note = {R package version 1.4.0},#>   }