{ "_id": "6a3507ba3efcd9bda43d9ab4", "Package": "tcplfit2", "Title": "A Concentration-Response Modeling Utility", "Version": "0.1.9", "Authors@R": "c(person(\"Thomas\", \"Sheffield\", role = c(\"aut\")),\nperson(\"Jason\", \"Brown\", role = \"ctb\", email = \"brown.jason@epa.gov\", comment = c(ORCID = \"0009-0000-2294-641X\")),\nperson(\"Sarah E.\",\"Davidson-Fritz\",role=c(\"ctb\"),email=\"davidsonfritz.sarah@epa.gov\", comment = c(ORCID = \"0000-0002-2891-9380\")),\nperson(\"Madison\",\"Feshuk\",role = c(\"ctb\",\"cre\"),email = \"feshuk.madison@epa.gov\", comment = c(ORCID = \"0000-0002-1390-6405\")),\nperson(\"Lindsay\",\"Knupp\",role=c(\"ctb\"),email = \"knupp.lindsay@epa.gov\"),\nperson(\"Zhihui\",\"Zhao\",role=c(\"ctb\")),\nperson(\"Richard S\", \"Judson\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-2348-9633\")),\nperson(\"Katie\", \"Paul Friedman\", role=c(\"ctb\"), email = \"paul-friedman.katie@epa.gov\", comment = c(ORCID = \"0000-0002-2710-1691\"))\n)", "Description": "The tcplfit2 R package performs basic\nconcentration-response curve fitting. The original tcplFit()\nfunction in the tcpl R package performed basic\nconcentration-response curvefitting to 3 models. With tcplfit2,\nthe core tcpl concentration-response functionality has been\nexpanded to process diverse high-throughput screen (HTS) data\ngenerated at the US Environmental Protection Agency, including\ntargeted ToxCast, high-throughput transcriptomics (HTTr) and\nhigh-throughput phenotypic profiling (HTPP). tcplfit2 can be\nused independently to support analysis for diverse chemical\nscreening efforts.", "URL": "https://github.com/USEPA/CompTox-ToxCast-tcplFit2", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "BugReports": "https://github.com/USEPA/CompTox-ToxCast-tcplFit2/issues", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://usepa.r-universe.dev", "Date/Publication": "2025-07-24 13:02:16 UTC", "RemoteUrl": "https://github.com/usepa/comptox-toxcast-tcplfit2", "RemoteRef": "HEAD", "RemoteSha": "e4c3a0d183184a4584f5c8223a664830c2e46c77", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-19 09:07:40 UTC", "User": "root" }, "Author": "Thomas Sheffield [aut],\nJason Brown [ctb] (ORCID: ),\nSarah E. Davidson-Fritz [ctb] (ORCID:\n),\nMadison Feshuk [ctb, cre] (ORCID:\n),\nLindsay Knupp [ctb],\nZhihui Zhao [ctb],\nRichard S Judson [ctb] (ORCID: ),\nKatie Paul Friedman [ctb] (ORCID:\n)", "Maintainer": "Madison Feshuk ", "MD5sum": "78c2411591ff1e14aad8962b8e382681", "_user": "usepa", "_type": "src", "_file": "tcplfit2_0.1.9.tar.gz", "_fileid": "b29c395638db651c0d4ff3b940f7e38719ba259c470d46e628a481801d2f22ee", "_filesize": 5126370, "_sha256": "b29c395638db651c0d4ff3b940f7e38719ba259c470d46e628a481801d2f22ee", "_created": "2026-06-19T09:07:40.000Z", "_published": "2026-06-19T09:11:22.005Z", "_distro": "noble", "_jobs": [ { "job": 82318941394, "time": 168, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7745957928" }, { "job": 82318941390, "time": 174, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7745959705" }, { "job": 82318941434, "time": 104, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7745937328" }, { "job": 82318941406, "time": 119, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7745942162" }, { "job": 82318246276, "time": 261, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7745902871" }, { "job": 82318941424, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7745942273" }, { "job": 82318941395, "time": 115, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7745941290" }, { "job": 82318941423, "time": 103, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7745937376" }, { "job": 82318941465, "time": 124, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7745943907" } ], "_buildurl": "https://github.com/r-universe/usepa/actions/runs/27816289353", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/usepa/comptox-toxcast-tcplfit2", "_commit": { "id": "e4c3a0d183184a4584f5c8223a664830c2e46c77", "author": "Sarah E. Davidson-Fritz <78621036+sedavid01@users.noreply.github.com>", "committer": "GitHub ", "message": "141 release tcplfit2 019 (#142)\n\n* update README doc with total download from CRAN badge\n\n* update NEWS\n\n* update version number in DESCRIPTION from v0.1.8 to v0.1.9\n\n* update the cran-comment doc for v0.1.9 CRAN release checks\n\n* add ggplot2 version requirement\n\n---------\n\nCo-authored-by: Sarah Davidson-Fritz \nCo-authored-by: Feshuk ", "time": 1753362136 }, "_maintainer": { "name": "Madison Feshuk", "email": "feshuk.madison@epa.gov", "login": "madison-feshuk", "linkedin": "in/madison-feshuk", "orcid": "0000-0002-1390-6405", "description": "Biologist at the @USEPA", "uuid": 117102339 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "numDeriv", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { 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concentration-response data set from invitrodb", "topics": [ "mc3" ] }, { "page": "nestselect", "title": "Nest Select", "topics": [ "nestselect" ] }, { "page": "plot_allcurves", "title": "Plot All Curves Fit with tcplfit2_core - ggplot2", "topics": [ "plot_allcurves" ] }, { "page": "poly1", "title": "Polynomial 1 Model", "topics": [ "poly1" ] }, { "page": "poly2", "title": "Polynomial 2 Model", "topics": [ "poly2" ] }, { "page": "poly2bmds", "title": "Polynomial 2 Model (BMDS)", "topics": [ "poly2bmds" ] }, { "page": "post_hit_AUC", "title": "Calculate Area Under the Curve After Hit-calling", "topics": [ "post_hit_AUC" ] }, { "page": "pow", "title": "Power Model", "topics": [ "pow" ] }, { "page": "signatures", "title": "Sample concentration-response data set from HTTR", "topics": [ "signatures" ] }, { "page": "tcplfit2_core", "title": "Concentration-response curve fitting", "topics": [ "tcplfit2_core" ] }, { "page": "tcplhit2_core", "title": "Hitcalling Function", "topics": [ "tcplhit2_core" ] }, { "page": "tcplObj", "title": "Concentration Response Objective Function", "topics": [ "tcplObj" ] }, { "page": "toplikelihood", "title": "Top Likelihood", "topics": [ "toplikelihood" ] } ], "_readme": "https://github.com/usepa/comptox-toxcast-tcplfit2/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "numDeriv", "plyr", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "tcplfit2-vignette.Rmd", "filename": "tcplfit2-vignette.html", "title": "tcplfit2: A Concentration-Response Modeling Utility", "author": "US EPA's Center for Computational Toxicology and Exposure ccte@epa.gov", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Suggested packages for use with this vignette", "Concentration-Response Modeling", "Concentration-Response Modeling for a Single Series with concRespCore", "Concentration-Response Modeling for Multiple Series with tcplfit2_core and tcplhit2_core", "Concentration-Response Modeling for tcpl-like data without a database connection", "- Source Data Formatting", "- Adjustments", "- Normalization", "- Dose-Response Curve Fitting", "Hitcalling", "- $p_1$: AIC Weight", "- $p_2$: Responses Outside Cutoff", "- $p_3$: Top Likelihood Ratio", "Visual Representation of Proportional Weights", "Consideration: Continuous Hitcalls to Activity Calls", "Bounding the Benchmark Dose (BMD)", "Imposing Lower BMD Bounds", "Imposing Upper BMD Bounds", "Bounding BMDs with tcplhit2_core", "Impacts if BMD is between the BMD Lower Bound and Lowest Dose Tested", "Plotting", "Plotting All Models with concRespCore and concRespPlot", "Plotting All Models with tcplfit2_core Output", "Plotting the Winning Model with concRespPlot2", "Customizing concRespPlot2 Plots", "- Adding a Plot Title, Shade Cutoff Band, and Potency Estimates", "- Label All Potency Estimates", "- Add Additional Curves", "Area Under the Curve (AUC)", "Area Under the Curve (AUC) with concRespCore", "Area Under the Curve (AUC) with tcplfit2_core and tcplhit2_core", "- Positive Responses", "- Negative Responses", "- Bi-phasic Responses", "Model Details", "Polynomial 1 (poly1)", "Polynomial 2 (poly2)", "Power (pow)", "Hill", "Gain-Loss (gnls)", "Exponential 2 (Exp2)", "Exponential 3 (Exp3)", "Exponential 4 (Exp4)", "Exponential 5 (Exp5)", "Table of All Model Details", "Glossary" ], "created": "2020-01-07 22:18:40", "modified": "2025-04-09 18:36:49", "commits": 20 } ], "_score": 6.905256048748451, "_indexed": true, "_nocasepkg": "tcplfit2", "_universes": [ "usepa", "madison-feshuk" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.9", "date": "2026-06-19T09:10:17.000Z", "distro": "noble", "commit": "e4c3a0d183184a4584f5c8223a664830c2e46c77", "fileid": "810bc883f5e0275d41a6f72866d127f12c5816abc6e9bec4b7c260436e72989f", "status": "success", "check": "OK", 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