{
"_id": "6a226a3fcd65a98ecbd462fb",
"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' () 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.",
"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": "2026-06-05 06:14:16 UTC",
"User": "root"
},
"Author": "Jonathon F Fleming [aut, cre] (ORCID:\n),\nDayne L Filer [aut, fnd] (ORCID:\n),\nDillon T Lloyd [aut],\nPreethi Thunga [aut] (ORCID: ),\nSkylar W Marvel [aut],\nAlison A Motsinger-Reif [fnd] (ORCID:\n),\nDavid M Reif [aut, fnd] (ORCID:\n)",
"Maintainer": "Jonathon F Fleming ",
"MD5sum": "bd2d23a4be9b105fc6486598d995b0c1",
"_user": "toxpi",
"_type": "src",
"_file": "toxpiR_1.3.2.tar.gz",
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"_created": "2026-06-05T06:14:16.000Z",
"_published": "2026-06-05T06:18:39.398Z",
"_distro": "noble",
"_jobs": [
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"_status": "success",
"_host": "GitHub-Actions",
"_upstream": "https://github.com/toxpi/toxpir",
"_commit": {
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"author": "Jonathon Fleming ",
"committer": "Jonathon Fleming ",
"message": "removed embedded namespace for txp_example_model and updated package versioning\n",
"time": 1777651948
},
"_maintainer": {
"name": "Jonathon F Fleming",
"email": "jffleming0129@gmail.com",
"login": "flemingjf",
"orcid": "0000-0003-2447-3139",
"description": "",
"uuid": 153934679
},
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{
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"version": ">= 4.0",
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{
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},
{
"package": "methods",
"role": "Imports"
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{
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"role": "Imports"
},
{
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},
{
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"role": "Imports"
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{
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{
"package": "BiocGenerics",
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{
"package": "tidyr",
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},
{
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{
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},
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"package": "DBI",
"role": "Suggests"
}
],
"_owner": "toxpi",
"_selfowned": true,
"_usedby": 0,
"_updates": [
{
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"n": 1
},
{
"week": "2025-49",
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},
{
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},
{
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}
],
"_tags": [],
"_topics": [
"data-science",
"modeling",
"toxicology"
],
"_stars": 11,
"_contributors": [
{
"user": "daynefiler",
"count": 36,
"uuid": 10778237
},
{
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},
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},
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}
],
"_userbio": {
"uuid": 65192026,
"type": "organization",
"name": "ToxPi"
},
"_downloads": {
"count": 555,
"source": "https://cranlogs.r-pkg.org/downloads/total/last-month/toxpiR"
},
"_devurl": "https://github.com/toxpi/toxpir",
"_pkgdown": "https://toxpi.github.io/toxpiR/",
"_searchresults": 20,
"_rbuild": "4.6.0",
"_assets": [
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"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/toxpiR.html",
"manual.pdf"
],
"_homeurl": "https://github.com/toxpi/toxpir",
"_realowner": "toxpi",
"_cranurl": true,
"_releases": [
{
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"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",
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"cli",
"cpp11",
"dplyr",
"farver",
"generics",
"ggplot2",
"glue",
"gtable",
"isoband",
"labeling",
"lifecycle",
"magrittr",
"pillar",
"pkgconfig",
"purrr",
"R6",
"RColorBrewer",
"rlang",
"S4Vectors",
"S7",
"scales",
"stringi",
"stringr",
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"tidyselect",
"utf8",
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"filename": "exportToGui.html",
"title": "Export ToxPi GUI Files",
"engine": "knitr::rmarkdown",
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"Slice weights",
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"Metrics in multiple slices",
"Example use",
"Compare the data files",
"Compare results"
],
"created": "2022-07-20 20:07:17",
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},
{
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"filename": "importFromGui.html",
"title": "Import ToxPi GUI Files",
"engine": "knitr::rmarkdown",
"headings": [],
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"modified": "2025-12-16 14:48:46",
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},
{
"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"
],
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