{
  "_id": "6a16951aacfb0bcc41d7abca",
  "Package": "MS2Quant",
  "Title": "Ionization efficiency prediction and quantification of\nunidentified chemicals",
  "Version": "1.1.0",
  "Authors@R": "person(\"Helen\", \"Sepman\", , \"helen.sepman@aces.su.se\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8222-9962\"))",
  "Description": "MS2Quant harvests pre-trained xgbTree algorithm-based\nionization efficiency prediction model. Using strucutral\ninformation (SMILES) or predicted fingerprints calculated with\nSIRIUS+CSI_FingerID software, ionization efficiency can be\npredicted. If calibrants have been measured together with\nsuspects subject to quantification, predicted ionization\nefficiencies can be converted into measurement-specific\nresponse factors and concentration of unknown chemcals can be\nestimated.",
  "License": "`use_mit_license()`, `use_gpl3_license()` or friends to pick a\nlicense",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "make default-jdk libicu-dev libpng-dev libxml2-dev\nlibx11-dev",
  "Repository": "https://rickhelmus.r-universe.dev",
  "Date/Publication": "2026-02-26 08:45:42 UTC",
  "RemoteUrl": "https://github.com/kruvelab/MS2Quant",
  "RemoteRef": "main",
  "RemoteSha": "d01f631a9c434a1eb2548ac53e38374f905355b8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 06:49:47 UTC",
    "User": "root"
  },
  "Author": "Helen Sepman [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8222-9962>)",
  "Maintainer": "Helen Sepman <helen.sepman@aces.su.se>",
  "MD5sum": "abcf6c09efd48e9d6b5802accd356268",
  "_user": "rickhelmus",
  "_type": "src",
  "_file": "MS2Quant_1.1.0.tar.gz",
  "_fileid": "5f86c8fa94e9ac2c0db6cf3657e832c42635ce29f6cf9c906a23f323305b2d18",
  "_filesize": 38427957,
  "_sha256": "5f86c8fa94e9ac2c0db6cf3657e832c42635ce29f6cf9c906a23f323305b2d18",
  "_created": "2026-05-27T06:49:47.000Z",
  "_published": "2026-05-27T06:54:18.229Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78023155908,
      "time": 197,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7233797806"
    },
    {
      "job": 78023155946,
      "time": 208,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7233800251"
    },
    {
      "job": 78023155901,
      "time": 146,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7233793543"
    },
    {
      "job": 78023155934,
      "time": 121,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7233803547"
    },
    {
      "job": 78022691779,
      "time": 212,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233744790"
    },
    {
      "job": 78023155903,
      "time": 148,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233784624"
    },
    {
      "job": 78023155906,
      "time": 146,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7233784080"
    },
    {
      "job": 78023155967,
      "time": 144,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7233783708"
    },
    {
      "job": 78023155995,
      "time": 146,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7233784374"
    }
  ],
  "_buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/kruvelab/MS2Quant",
  "_commit": {
    "id": "d01f631a9c434a1eb2548ac53e38374f905355b8",
    "author": "helensepman <48623628+helensepman@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #8 from rickhelmus/main\n\nAdd compatibility to recent xgboost versions",
    "time": 1772095542
  },
  "_maintainer": {
    "name": "Helen Sepman",
    "email": "helen.sepman@aces.su.se",
    "orcid": "0000-0002-8222-9962"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "caret",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "enviPat",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "rcdk",
      "role": "Imports"
    },
    {
      "package": "rcdklibs",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rJava",
      "role": "Imports"
    },
    {
      "package": "rlist",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "xfun",
      "role": "Imports"
    },
    {
      "package": "xgboost",
      "role": "Imports"
    }
  ],
  "_owner": "kruvelab",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-09",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 5,
  "_contributors": [
    {
      "user": "helensepman",
      "count": 50,
      "uuid": 48623628
    },
    {
      "user": "w-cwang",
      "count": 12,
      "uuid": 112269706
    },
    {
      "user": "rickhelmus",
      "count": 8,
      "uuid": 37015911
    },
    {
      "user": "drewszabo",
      "count": 3,
      "uuid": 103048720
    }
  ],
  "_userbio": {
    "uuid": 37015911,
    "type": "user",
    "name": "rickhelmus"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MS2Quant"
  },
  "_devurl": "https://github.com/kruvelab/ms2quant",
  "_searchresults": 6,
  "_topics": [
    "openjdk"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MS2Quant.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "add_mobile_phase_composition",
    "Fingerprint_calc",
    "FingerPrintTable",
    "FpTableForPredictions",
    "isotopedistribution",
    "linear_regression",
    "MS2Quant_predict_IE",
    "MS2Quant_quantify",
    "organicpercentage",
    "polarityindex",
    "read_in_fingerprints",
    "SiriusScoreRank1",
    "summarized_SIRIUS_identification_results",
    "surfacetension",
    "viscosity"
  ],
  "_help": [
    {
      "page": "isotopedistribution",
      "title": "Isotope distribution",
      "topics": [
        "isotopedistribution"
      ]
    },
    {
      "page": "linear_regression",
      "title": "Linear regression",
      "topics": [
        "linear_regression"
      ]
    }
  ],
  "_readme": "https://github.com/kruvelab/MS2Quant/raw/main/README.md",
  "_rundeps": [
    "bit",
    "bit64",
    "caret",
    "class",
    "cli",
    "clipr",
    "clock",
    "codetools",
    "cpp11",
    "crayon",
    "data.table",
    "diagram",
    "digest",
    "dplyr",
    "e1071",
    "enviPat",
    "farver",
    "fingerprint",
    "foreach",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "hms",
    "ipred",
    "isoband",
    "iterators",
    "itertools",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "listenv",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "ModelMetrics",
    "nlme",
    "nnet",
    "numDeriv",
    "parallelly",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "pROC",
    "prodlim",
    "progress",
    "progressr",
    "proxy",
    "purrr",
    "R6",
    "rcdk",
    "rcdklibs",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "recipes",
    "reshape2",
    "rJava",
    "rlang",
    "rlist",
    "rpart",
    "S7",
    "scales",
    "shape",
    "sparsevctrs",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xgboost",
    "XML",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-21-jre-headless",
      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.10+7-1~24.04",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_score": 3.1760912590556813,
  "_indexed": false,
  "_nocasepkg": "ms2quant",
  "_universes": [
    "rickhelmus"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T06:52:35.000Z",
      "distro": "noble",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "a3efb10c6181aa92611837b1ddeaf13b58363619b8ca60a0dcdd9c5d0b27dea6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T06:52:41.000Z",
      "distro": "noble",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "eb6587bd7420027b0ee7b8192c8ef004eccad4dd1d9f0457d18b9f3a30577397",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T06:52:40.000Z",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "42b25ed44682c497b5cc6124493eb44d157e168838241a6d0c13925303ce6fb2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T06:53:17.000Z",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "037f6773d7c12a0c6cf1b7bd403d832819fd9a996df778707b8c63f403aa00b6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-05-27T06:52:47.000Z",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "ae0b879833a3f6b28102d612e928739dbbf2db2cbc566b0713cb88a9f45ac1b2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T06:51:25.000Z",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "13de751a550b5e4092672e85fcd5cfdc00f7f81c253acbb47542bb46fa51217f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T06:51:29.000Z",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "b6a11cb8bf0fab2941c7dd844154b71f2f11e99399e33d9feebeb97dd57e0651",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T06:51:37.000Z",
      "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8",
      "fileid": "c463598e0e9d2aededbb7122194f49460e98720b071fd40818e4f9602fe01904",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/26495505067"
    }
  ]
}