{ "_id": "6a1165fbacfb0bcc41cf070c", "Package": "toxEval", "Type": "Package", "Title": "Exploring Biological Relevance of Environmental Chemistry\nObservations", "Version": "1.4.2", "Authors@R": "c(person(\"Laura\", \"DeCicco\", \nrole = c(\"aut\",\"cre\"),\nemail = \"ldecicco@usgs.gov\",\ncomment=c(ORCID=\"0000-0002-3915-9487\")),\nperson(\"Steven\", \"Corsi\",\nrole = c(\"aut\"),\nemail = \"srcorsi@usgs.gov\",\ncomment=c(ORCID=\"0000-0003-0583-5536\")),\nperson(\"Daniel\", \"Villeneuve\",\nrole = c(\"aut\"),\ncomment=c(ORCID=\"0000-0003-2801-0203\")),\nperson(\"Brett\", \"Blackwell\",\nrole = c(\"aut\"),\ncomment=c(ORCID=\"0000-0003-1296-4539\")),\nperson(\"Gerald\", \"Ankley\",\nrole = c(\"aut\"),\ncomment=c(ORCID=\"0000-0002-9937-615X\")),\nperson(\"Alison\", \"Appling\",\nrole = \"rev\",\ncomment = \"Reviewed for USGS\"),\nperson(\"Dalma\", \"Martinovic\",\nrole = \"rev\",\ncomment = \"Reviewed for USGS\"))", "Description": "Data analysis package for estimating potential biological\neffects from chemical concentrations in environmental samples.\nIncluded are a set of functions to analyze, visualize, and\norganize measured concentration data as it relates to\nuser-selected chemical-biological interaction benchmark data\nsuch as water quality criteria. The intent of these analyses is\nto develop a better understanding of the potential biological\nrelevance of environmental chemistry data. Results can be used\nto prioritize which chemicals at which sites may be of greatest\nconcern. These methods are meant to be used as a screening\ntechnique to predict potential for biological influence from\nchemicals that ultimately need to be validated with direct\nbiological assays. A description of the analysis can be found\nin Blackwell (2017) .", "License": "CC0", "Copyright": "This software is in the public domain because it contains\nmaterials that originally came from the United States\nGeological Survey, an agency of the United States Department of\nInterior. For more information, see the official USGS copyright\npolicy at\nhttps://www.usgs.gov/visual-id/credit_usgs.html#copyright", "BugReports": "https://github.com/DOI-USGS/toxEval/issues", "VignetteBuilder": "knitr", "BuildVignettes": "true", "LazyLoad": "yes", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libpng-dev libuv1-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev zlib1g-dev", "Repository": "https://ldecicco-usgs.r-universe.dev", "Date/Publication": "2026-01-23 19:04:52 UTC", "RemoteUrl": "https://code.usgs.gov/water/toxEval", "RemoteRef": "HEAD", "RemoteSha": "e0c311ee36948057494fd8c205fccfea23d986b1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 08:27:48 UTC", "User": "root" }, "Author": "Laura DeCicco [aut, cre] (ORCID:\n),\nSteven Corsi [aut] (ORCID: ),\nDaniel Villeneuve [aut] (ORCID:\n),\nBrett Blackwell [aut] (ORCID: ),\nGerald Ankley [aut] (ORCID: ),\nAlison Appling [rev] (Reviewed for USGS),\nDalma Martinovic [rev] (Reviewed for USGS)", "Maintainer": "Laura DeCicco ", "MD5sum": "325c5332d4ae8548fabfa96650092407", "_user": "ldecicco-usgs", "_type": "src", "_file": "toxEval_1.4.2.tar.gz", "_fileid": "c9e117f56cbf857d8e0b83fc58add80e602795e4904a6c410763dc0765e1ffdb", "_filesize": 3305963, "_sha256": "c9e117f56cbf857d8e0b83fc58add80e602795e4904a6c410763dc0765e1ffdb", "_created": "2026-05-23T08:27:48.000Z", "_published": "2026-05-23T08:31:55.952Z", "_distro": "noble", "_jobs": [ { "job": 77509379570, "time": 211, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175649407" }, { "job": 77509379577, "time": 207, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175648923" }, { "job": 77509379591, "time": 112, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175640013" }, { "job": 77509379585, "time": 104, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175639470" }, { "job": 77509115558, "time": 303, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175630550" }, { "job": 77509379578, "time": 163, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175644586" }, { "job": 77509379586, "time": 145, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7175643077" }, { "job": 77509379584, "time": 152, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7175643913" }, { "job": 77509379596, "time": 152, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175643765" } ], "_buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://code.usgs.gov/water/toxEval", "_commit": { "id": "e0c311ee36948057494fd8c205fccfea23d986b1", "author": "Laura DeCicco ", "committer": "Laura DeCicco ", "message": "do what dR does\n", "time": 1769195092 }, "_maintainer": { "name": "Laura DeCicco", "email": "ldecicco@usgs.gov", "login": "ldecicco-usgs", "mastodon": "@ldecicco@fosstodon.org", "bluesky": "@ldecicco.bsky.social", "description": "", "uuid": 1105215, "orcid": "0000-0002-3915-9487" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "DT", "version": ">= 0.1.24", "role": "Imports" }, { "package": "leaflet", "version": ">= 1.0.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.0.0", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "shinydashboard", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "readxl", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "shinyAce", "role": "Imports" }, { "package": "shinycssloaders", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "here", "role": "Suggests" }, { "package": "tcpl", "role": "Suggests" }, { "package": "openxlsx", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "code-water", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-40", "n": 1 }, { "week": "2026-04", "n": 5 } ], "_tags": [ { "name": "v1.4.2", "date": "2026-01-23" } ], "_userbio": { "uuid": 1105215, "type": "user", "name": "Laura DeCicco" }, "_downloads": { "count": 278, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/toxEval" }, "_mentions": 1, "_devurl": "https://github.com/doi-usgs/toxeval", "_searchresults": 98, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/toxEval.html", "manual.pdf" ], "_homeurl": "https://github.com/doi-usgs/toxeval", "_realowner": "doi-usgs", "_cranurl": false, "_releases": [ { "version": "1.0.3", "date": "2019-03-08" }, { "version": "1.0.4", "date": "2019-04-08" }, { "version": "1.1.0", "date": "2019-11-26" }, { "version": "1.2.0", "date": "2020-10-09" }, { "version": "1.3.0", "date": "2023-04-14" }, { "version": "1.3.1", "date": "2024-01-30" }, { "version": "1.3.2", "date": "2024-02-08" }, { "version": "1.4.0", "date": "2024-11-22" }, { "version": "1.4.1", "date": "2025-10-03" }, { "version": "1.4.2", "date": "2026-01-23" } ], "_exports": [ "as.toxEval", "clean_endPoint_info", "create_toxEval", "createLink", "end_point_info", "endpoint_hits", "endpoint_hits_DT", "explore_endpoints", "filter_groups", "flags", "get_ACC", "get_chemical_summary", "get_concentration_summary", "graph_chem_data", "hits_by_groupings", "hits_by_groupings_DT", "hits_summary", "hits_summary_DT", "make_tox_map", "map_tox_data", "plot_chemical_boxplots", "plot_tox_boxplots", "plot_tox_endpoints", "plot_tox_endpoints2", "plot_tox_heatmap", "plot_tox_stacks", "rank_sites", "rank_sites_DT", "remove_flags", "side_by_side_data", "tox_boxplot_data", "tox_chemicals", "ToxCast_ACC" ], "_help": [ { "page": "helperToxEval", "title": "toxEval helper functions", "topics": [ "as.toxEval" ] }, { "page": "clean_endPoint_info", "title": "clean_endPoint_info", "topics": [ "clean_endPoint_info" ] }, { "page": "create_toxEval", "title": "Load and check toxEval data", "topics": [ "create_toxEval" ] }, { "page": "end_point_info", "title": "Endpoint information from ToxCast", "topics": [ "end_point_info" ] }, { "page": "endpoint_hits_DT", "title": "Rank endpoints by category", "topics": [ "endpoint_hits", "endpoint_hits_DT" ] }, { "page": "explore_endpoints", "title": "Explore data in the Shiny Application", "topics": [ "explore_endpoints" ] }, { "page": "filter_groups", "title": "Filter endPoints based on groups and assays.", "topics": [ "filter_groups" ] }, { "page": "flags", "title": "ToxCast Chemical Information", "topics": [ "flags" ] }, { "page": "get_ACC", "title": "Get the ACC values for a selection of chemicals", "topics": [ "get_ACC" ] }, { "page": "get_chemical_summary", "title": "Compute EAR values", "topics": [ "get_chemical_summary" ] }, { "page": "get_concentration_summary", "title": "Create concentration summary", "topics": [ "get_concentration_summary" ] }, { "page": "graph_data_prep", "title": "Prepare boxplot data", "topics": [ "graph_chem_data", "side_by_side_data", "tox_boxplot_data" ] }, { "page": "hits_by_groupings_DT", "title": "Biological hits per category", "topics": [ "hits_by_groupings", "hits_by_groupings_DT" ] }, { "page": "hits_summary_DT", "title": "Summary of hits per site/category", "topics": [ "hits_summary", "hits_summary_DT" ] }, { "page": "make_tox_map", "title": "Create an interactive map of the data", "topics": [ "make_tox_map", "map_tox_data" ] }, { "page": "plot_tox_boxplots", "title": "Grouped Boxplots", "topics": [ "plot_chemical_boxplots", "plot_tox_boxplots" ] }, { "page": "plot_tox_endpoints", "title": "EndPoint boxplots", "topics": [ "plot_tox_endpoints" ] }, { "page": "plot_tox_endpoints2", "title": "EndPoint boxplots with faceting option", "topics": [ "plot_tox_endpoints2" ] }, { "page": "plot_tox_heatmap", "title": "Plot EAR heat maps", "topics": [ "plot_tox_heatmap" ] }, { "page": "plot_tox_stacks", "title": "Plot stacked bar charts", "topics": [ "plot_tox_stacks" ] }, { "page": "rank_sites_DT", "title": "Rank sites by EAR", "topics": [ "rank_sites", "rank_sites_DT" ] }, { "page": "remove_flags", "title": "Remove endpoints with specific data quality flags from data", "topics": [ "remove_flags" ] }, { "page": "summary.toxEval", "title": "Summary of tox_list", "topics": [ "summary.toxEval" ] }, { "page": "tox_chemicals", "title": "ToxCast Chemical Information", "topics": [ "tox_chemicals" ] }, { "page": "ToxCast_ACC", "title": "ACC values included with toxEval. See 'vignette(\"Setting up toxEval package data\", package = \"toxEval\")' for more information on how the data was aggregated.", "topics": [ "ToxCast_ACC" ] } ], "_pkglogo": "https://code.usgs.gov/water/toxEval/raw/HEAD/man/figures/logo.png", "_readme": "https://code.usgs.gov/water/toxEval/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cellranger", "class", "classInt", "cli", "commonmark", "cpp11", "crayon", "crosstalk", "DBI", "digest", "dplyr", "DT", "e1071", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "leaflet", "leaflet.providers", "lifecycle", "magrittr", "MASS", "memoise", "mime", "otel", "pillar", "pkgconfig", "png", "prettyunits", "progress", "promises", "proxy", "purrr", "R6", "rappdirs", "raster", "RColorBrewer", "Rcpp", "readxl", "rematch", "rlang", "rmarkdown", "s2", "S7", "sass", "scales", "sf", "shiny", "shinyAce", "shinycssloaders", "shinydashboard", "sourcetools", "sp", "stringi", "stringr", "terra", "tibble", "tidyr", "tidyselect", "tinytex", "units", "utf8", "vctrs", "viridisLite", "withr", "wk", "xfun", "xtable", "yaml" ], "_vignettes": [ { "source": "Chemical_names.Rmd", "filename": "Chemical_names.html", "title": "Chemical Names", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-01-29 16:59:39", "modified": "2024-10-02 18:29:12", "commits": 2 }, { "source": "Introduction.Rmd", "filename": "Introduction.html", "title": "Introduction to toxEval", "engine": "knitr::rmarkdown", "headings": [ "What is ToxCast?", "Exposure-Activity Ratio", "What is an \"endPoint\"?", "What is a \"group\"?", "Summarizing the data", "Reporting bugs", "Citing toxEval" ], "created": "2018-04-03 19:48:53", "modified": "2024-10-02 18:29:12", "commits": 24 }, { "source": "PrepareData.Rmd", "filename": "PrepareData.html", "title": "Preparing toxEval Data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Preparing the data", "Data", "Chemicals", "Sites", "Exclude", "Benchmarks", "Summary" ], "created": "2018-04-03 19:48:53", "modified": "2024-12-13 19:40:21", "commits": 20 } ], "_score": 4.468347330412158, "_indexed": false, "_nocasepkg": "toxeval", "_universes": [ "ldecicco-usgs" ], "_indexurl": "https://doi-usgs.r-universe.dev/toxEval", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.2", "date": "2026-05-23T08:30:39.000Z", "distro": "noble", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "d9ab13a0130ee7f5cf30460750d8882eef09fc30fbd28e6b31e42cfc9c5ad3ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" }, { "r": "4.6.0", "os": "linux", "version": "1.4.2", "date": "2026-05-23T08:30:39.000Z", "distro": "noble", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "914a067c88564996b53ee67e23579632698720e33e28a098b3130415a99dd2f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" }, { "r": "4.5.3", "os": "mac", "version": "1.4.2", "date": "2026-05-23T08:29:21.000Z", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "9452017a05c7a59110b2822f3c4f213c947d784c595b465b47b2fabe5e3a3c7a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" }, { "r": "4.6.0", "os": "mac", "version": "1.4.2", "date": "2026-05-23T08:29:17.000Z", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "d12b32ee4aacb02c1fa6b3e41490866c6d4a615b5ce2627228f971d92a02b5d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.2", "date": "2026-05-23T08:30:48.000Z", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "55756596fc089d3def42cc992aed820f7cc58d643cbbf4f8a197e1c14ea05417", "status": "success", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" }, { "r": "4.7.0", "os": "win", "version": "1.4.2", "date": "2026-05-23T08:29:18.000Z", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "be44480302397daba96baff1729ed5cea10ed2ecd3227647fed694a4d9057944", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" }, { "r": "4.5.3", "os": "win", "version": "1.4.2", "date": "2026-05-23T08:29:41.000Z", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "461d9d5b2e0b46d34d9a15942e0c04e228bbe3d21af062299c9273c688829717", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" }, { "r": "4.6.0", "os": "win", "version": "1.4.2", "date": "2026-05-23T08:29:19.000Z", "commit": "e0c311ee36948057494fd8c205fccfea23d986b1", "fileid": "a02a90c53ac5c14e79bb4b6413b1285c43738fac88339814e89f129b28aae5b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ldecicco-usgs/actions/runs/26328003092" } ] }