{
  "_id": "6ac0b1fc91601a2ad29976e1",
  "Package": "toxpiR",
  "Type": "Package",
  "Title": "Create ToxPi Prioritization Models",
  "Version": "1.3.2",
  "Authors@R": "c(person(\"Jonathon F\", \"Fleming\",\nrole = c(\"aut\",\"cre\"),\nemail = \"jffleming0129@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2447-3139\")),\nperson(\"Dayne L\", \"Filer\",\nrole = c(\"aut\", \"fnd\"),\nemail = \"dayne.filer@gmail.com\",\ncomment = c(ORCID = \"0000-0002-3443-5315\")),\nperson(\"Dillon T\", \"Lloyd\",\nrole = \"aut\"),\nperson(\"Preethi\", \"Thunga\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-5447-0129\")),\nperson(\"Skylar W\", \"Marvel\",\nrole = \"aut\"),\nperson(\"Alison A\", \"Motsinger-Reif\",\nrole = c(\"fnd\"),\ncomment = c(ORCID = \"0000-0003-1346-2493\")),\nperson(\"David M\", \"Reif\",\nrole = c(\"aut\", \"fnd\"),\nemail = \"reif.david@gmail.com\",\ncomment = c(ORCID = \"0000-0001-7815-6767\")))",
  "Description": "Enables users to build 'ToxPi' prioritization models and\nprovides functionality within the grid framework for plotting\nToxPi graphs. 'toxpiR' allows for more customization than the\n'ToxPi GUI' (<https://toxpi.github.io/>) and integration into\nexisting workflows for greater ease-of-use, reproducibility,\nand transparency. toxpiR package behaves nearly identically to\nthe GUI; the package documentation includes notes about all\ndifferences. The vignettes download example files from\n<https://github.com/ToxPi/ToxPi-example-files>.",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
  "Config/testthat/parallel": "true",
  "VignetteBuilder": "knitr",
  "License": "GPL (>= 3)",
  "URL": "https://github.com/ToxPi/toxpiR, https://toxpi.github.io/toxpiR/",
  "BugReports": "https://github.com/ToxPi/toxpiR/issues",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://toxpi.r-universe.dev",
  "Date/Publication": "2026-05-01 16:12:28 UTC",
  "RemoteUrl": "https://github.com/toxpi/toxpir",
  "RemoteRef": "HEAD",
  "RemoteSha": "4d20bb56377ac83a432c57f32a41f090d2735c9c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-03 07:37:04 UTC",
    "User": "root"
  },
  "Author": "Jonathon F Fleming [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-2447-3139>),\nDayne L Filer [aut, fnd] (ORCID:\n<https://orcid.org/0000-0002-3443-5315>),\nDillon T Lloyd [aut],\nPreethi Thunga [aut] (ORCID: <https://orcid.org/0000-0001-5447-0129>),\nSkylar W Marvel [aut],\nAlison A Motsinger-Reif [fnd] (ORCID:\n<https://orcid.org/0000-0003-1346-2493>),\nDavid M Reif [aut, fnd] (ORCID:\n<https://orcid.org/0000-0001-7815-6767>)",
  "Maintainer": "Jonathon F Fleming <jffleming0129@gmail.com>",
  "_user": "toxpi",
  "_type": "src",
  "_file": "toxpiR_1.3.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/34f88caa1bf87910882e0622ab1a7a5d86844cdbc8c25c336e947e7e22e74dba",
  "_filesize": 12058660,
  "_sha256": "34f88caa1bf87910882e0622ab1a7a5d86844cdbc8c25c336e947e7e22e74dba",
  "_expires": "2027-01-11T07:42:49.000Z",
  "_created": "2026-10-03T07:37:04.000Z",
  "_published": "2026-10-03T07:42:52.271Z",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/toxpi/actions/runs/37106730284",
  "_status": "success",
  "_upstream": "https://github.com/toxpi/toxpir",
  "_commit": {
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    "author": "Jonathon Fleming <jffleming0129@gmail.com>",
    "committer": "Jonathon Fleming <jffleming0129@gmail.com>",
    "message": "removed embedded namespace for txp_example_model and updated package versioning\n",
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  "_maintainer": {
    "name": "Jonathon F Fleming",
    "email": "jffleming0129@gmail.com",
    "login": "flemingjf",
    "orcid": "0000-0003-2447-3139",
    "description": "",
    "uuid": 153934679
  },
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  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
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    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
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    {
      "package": "rmarkdown",
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    },
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  ],
  "_owner": "toxpi",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2025-49",
      "n": 4
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "data-science",
    "modeling",
    "toxicology"
  ],
  "_stars": 11,
  "_contributors": [
    {
      "user": "daynefiler",
      "count": 36,
      "uuid": 10778237
    },
    {
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  ],
  "_userbio": {
    "uuid": 65192026,
    "type": "organization",
    "name": "ToxPi",
    "followers": 3
  },
  "_downloads": {
    "count": 530,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/toxpiR"
  },
  "_devurl": "https://github.com/toxpi/toxpir",
  "_pkgdown": "https://toxpi.github.io/toxpiR/",
  "_searchresults": 26,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/toxpiR.html"
  ],
  "_homeurl": "https://github.com/toxpi/toxpir",
  "_realowner": "toxpi",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.2",
      "date": "2022-02-07"
    },
    {
      "version": "1.0.3",
      "date": "2022-02-19"
    },
    {
      "version": "1.2.1",
      "date": "2022-07-20"
    },
    {
      "version": "1.3.0",
      "date": "2024-09-12"
    },
    {
      "version": "1.3.1",
      "date": "2025-12-16"
    },
    {
      "version": "1.3.2",
      "date": "2026-05-01"
    }
  ],
  "_exports": [
    "as.data.frame",
    "as.TxpModelList",
    "as.TxpResultList",
    "as.TxpSliceList",
    "as.TxpTransFuncList",
    "duplicated",
    "grid.pieGridGrob",
    "grid.pieGrob",
    "merge",
    "pieGridGrob",
    "pieGrob",
    "plot",
    "sort",
    "txpCalculateScores",
    "txpExportGui",
    "txpIDs",
    "txpIDs<-",
    "txpImportGui",
    "txpMissing",
    "txpModel",
    "TxpModel",
    "TxpModelList",
    "txpRanks",
    "TxpResultList",
    "txpResultParam",
    "txpScores",
    "TxpSlice",
    "TxpSliceList",
    "txpSlices",
    "txpSlices<-",
    "txpSliceScores",
    "TxpTransFunc",
    "TxpTransFuncList",
    "txpTransFuncs",
    "txpTransFuncs<-",
    "txpValueNames",
    "txpValueNames<-",
    "txpWeights",
    "txpWeights<-"
  ],
  "_datasets": [
    {
      "name": "txp_example_input",
      "title": "toxpiR data objects",
      "object": "txp_example_input",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "metric1",
        "metric2",
        "metric3",
        "metric4",
        "metric5",
        "metric6",
        "metric7",
        "metric8"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "txp_example_model",
      "title": "toxpiR data objects",
      "object": "txp_example_model",
      "class": [
        "TxpModel"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "boxLegendGrob",
      "title": "Create a filled-box legend",
      "topics": [
        "boxLegendGrob"
      ]
    },
    {
      "page": "pieGridGrob",
      "title": "Make grid of pieGrobs",
      "topics": [
        "grid.pieGridGrob",
        "pieGridGrob"
      ]
    },
    {
      "page": "pieGrob",
      "title": "Create a pie grob",
      "topics": [
        "grid.pieGrob",
        "pieGrob"
      ]
    },
    {
      "page": "toxpiR-datasets",
      "title": "toxpiR data objects",
      "topics": [
        "toxpiR-datasets",
        "txp_example_input",
        "txp_example_model"
      ]
    },
    {
      "page": "txpCalculateScores",
      "title": "Calculate ToxPi Scores for the given model and input data",
      "topics": [
        "txpCalculateScores",
        "txpCalculateScores,list,data.frame-method",
        "txpCalculateScores,TxpModel,data.frame-method",
        "txpCalculateScores,TxpModelList,data.frame-method"
      ]
    },
    {
      "page": "txpExportGui",
      "title": "Export comma-separated file intended for ToxPi GUI",
      "topics": [
        "txpExportGui"
      ]
    },
    {
      "page": "txpGenerics",
      "title": "toxpiR package generics",
      "topics": [
        "txpGenerics",
        "txpIDs",
        "txpIDs<-",
        "txpMissing",
        "txpModel",
        "txpRanks",
        "txpResultParam",
        "txpScores",
        "txpSlices",
        "txpSlices<-",
        "txpSliceScores",
        "txpTransFuncs",
        "txpTransFuncs<-",
        "txpValueNames",
        "txpValueNames<-",
        "txpWeights",
        "txpWeights<-"
      ]
    },
    {
      "page": "txpImportGui",
      "title": "Import data file generated by ToxPi GUI",
      "topics": [
        "txpImportGui"
      ]
    },
    {
      "page": "TxpModel-class",
      "title": "ToxPi Model",
      "topics": [
        "length,TxpModel-method",
        "merge,TxpModel,TxpModel-method",
        "names,TxpModel-method",
        "names<-,TxpModel-method",
        "TxpModel",
        "TxpModel-class",
        "TxpModel-txpSlices",
        "txpSlices,TxpModel-method",
        "txpSlices<-,TxpModel-method",
        "txpTransFuncs,TxpModel-method",
        "txpTransFuncs<-,TxpModel-method",
        "txpValueNames,TxpModel-method",
        "txpWeights,TxpModel-method",
        "txpWeights<-,TxpModel-method"
      ]
    },
    {
      "page": "TxpModelList-class",
      "title": "List of TxpModel objects",
      "topics": [
        "as.TxpModelList",
        "duplicated,TxpModelList-method",
        "TxpModelList",
        "TxpModelList-class"
      ]
    },
    {
      "page": "TxpResult-class",
      "title": "ToxPi Result",
      "topics": [
        "as.data.frame,TxpResult-method",
        "length,TxpResult-method",
        "names,TxpResult-method",
        "names<-,TxpResult-method",
        "sort,TxpResult-method",
        "txpIDs,TxpResult-method",
        "txpIDs<-,TxpResult-method",
        "txpMissing,TxpResult-method",
        "txpModel,TxpResult-method",
        "txpRanks,TxpResult-method",
        "TxpResult",
        "TxpResult-class",
        "txpResultParam,TxpResult-method",
        "txpScores,TxpResult-method",
        "txpSlices,TxpResult-method",
        "txpSliceScores,TxpResult-method",
        "txpTransFuncs,TxpResult-method",
        "txpValueNames,TxpResult-method",
        "txpWeights,TxpResult-method",
        "[,TxpResult,character,missing-method",
        "[,TxpResult,integer,missing-method",
        "[,TxpResult,logical,missing-method",
        "[,TxpResult,numeric,missing-method"
      ]
    },
    {
      "page": "TxpResult-plot",
      "title": "Plot TxpResult objects",
      "topics": [
        "plot",
        "plot,TxpResult,missing-method",
        "plot,TxpResult,numeric-method",
        "TxpResult-plot"
      ]
    },
    {
      "page": "TxpResultList-class",
      "title": "List of TxpResult objects",
      "topics": [
        "as.TxpResultList",
        "duplicated,TxpResultList-method",
        "TxpResultList",
        "TxpResultList-class"
      ]
    },
    {
      "page": "TxpResultParam-class",
      "title": "ToxPi Result Parameters",
      "topics": [
        "TxpResultParam",
        "TxpResultParam-class"
      ]
    },
    {
      "page": "TxpSlice-class",
      "title": "ToxPi Slice",
      "topics": [
        "length,TxpSlice-method",
        "merge,TxpSlice,TxpSlice-method",
        "TxpSlice",
        "TxpSlice-class",
        "txpTransFuncs,TxpSlice-method",
        "txpTransFuncs<-,TxpSlice-method",
        "txpValueNames,TxpSlice-method",
        "txpValueNames<-,TxpSlice-method"
      ]
    },
    {
      "page": "TxpSliceList-class",
      "title": "List of TxpSlice objects",
      "topics": [
        "as.TxpSliceList",
        "duplicated,TxpSliceList-method",
        "TxpSliceList",
        "TxpSliceList-class",
        "txpTransFuncs,TxpSliceList-method",
        "txpValueNames,TxpSliceList-method"
      ]
    },
    {
      "page": "TxpTransFunc-class",
      "title": "Numeric transformation function",
      "topics": [
        "TxpTransFunc",
        "TxpTransFunc-class"
      ]
    },
    {
      "page": "TxpTransFuncList-class",
      "title": "List of TxpTransFunc objects",
      "topics": [
        "as.TxpTransFuncList",
        "TxpTransFuncList",
        "TxpTransFuncList-class"
      ]
    }
  ],
  "_readme": "https://github.com/toxpi/toxpir/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rlang",
    "S4Vectors",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "exportToGui.rmd",
      "filename": "exportToGui.html",
      "title": "Export ToxPi GUI Files",
      "engine": "knitr::rmarkdown",
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        "Slice weights",
        "Transformation/scaling functions",
        "Metrics in multiple slices",
        "Example use",
        "Compare the data files",
        "Compare results"
      ],
      "created": "2022-07-20 20:07:17",
      "modified": "2025-12-16 14:48:46",
      "commits": 2
    },
    {
      "source": "importFromGui.Rmd",
      "filename": "importFromGui.html",
      "title": "Import ToxPi GUI Files",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2022-02-02 21:00:31",
      "modified": "2025-12-16 14:48:46",
      "commits": 4
    },
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "toxpiR Introduction",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "What is ToxPi?",
        "Outline",
        "Installation",
        "Standard installation",
        "Installation from GitHub",
        "Launching package in R",
        "Flowchart",
        "Example usage",
        "Load the dataset",
        "Specify slice information",
        "TxpSlice(txpValueNames, txpTransFuncs)",
        "TxpSliceList()",
        "Create ToxPi model",
        "TxpModel()",
        "Calculate ToxPi scores",
        "txpCalculateScores()",
        "Visualization",
        "ggplot Method",
        "Default plot",
        "Coloration Options",
        "Binary Options",
        "Format/Theme Options",
        "pieGrob Method",
        "ggplot vs grid Comparison",
        "Citation"
      ],
      "created": "2022-02-02 21:00:31",
      "modified": "2025-12-16 14:48:46",
      "commits": 8
    }
  ],
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  "_indexed": true,
  "_nocasepkg": "toxpir",
  "_universes": [
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    "flemingjf"
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