{ "_id": "6a571582ff0138dec5d6d837", "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": "2026-07-15 05:01:15 UTC", "User": "root" }, "Author": "Helen Sepman [aut, cre] (ORCID:\n)", "Maintainer": "Helen Sepman ", "_user": "rickhelmus", "_type": "src", "_file": "MS2Quant_1.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/37a6c73ead0d7dcb17ae96400b4107c3498a9ae30cbea261e96ec5b64900abbb", "_filesize": 38430811, "_sha256": "37a6c73ead0d7dcb17ae96400b4107c3498a9ae30cbea261e96ec5b64900abbb", "_expires": "2026-10-23T05:07:10.000Z", "_created": "2026-07-15T05:01:15.000Z", "_published": "2026-07-15T05:07:14.644Z", "_jobs": [ { "job": 87272373968, "time": 278, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8333082099" }, { "job": 87272373953, "time": 195, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8333054092" }, { "job": 87272373951, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8333041857" }, { "job": 87272373961, "time": 121, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8333034719" }, { "job": 87271793667, "time": 269, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8333001008" }, { "job": 87272373931, "time": 161, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8333045037" }, { "job": 87272374034, "time": 146, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8333041432" }, { "job": 87272373975, "time": 143, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8333041251" }, { "job": 87272373970, "time": 202, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8333055800" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841", "_status": "success", "_upstream": "https://github.com/kruvelab/MS2Quant", "_commit": { "id": "d01f631a9c434a1eb2548ac53e38374f905355b8", "author": "helensepman <48623628+helensepman@users.noreply.github.com>", "committer": "GitHub ", "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" }, "_distro": "resolute", "_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", "followers": 24 }, "_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": "4.6.1", "_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-25-jre-headless", "headers": "openjdk-25-jre-headless", "source": "openjdk", "version": "25.0.3+9-2~26.04.2", "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": "2026-07-15T05:05:46.000Z", "distro": "resolute", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/c6d60e245221f0030b6d1313711fe5c555388c119f1b8e9bdc08b16784d51734", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-07-15T05:04:02.000Z", "distro": "resolute", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/98bb527a525d511b98d40543ec3ab74e3b3e2f694f479ccfe9413dd54bfb0f31", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-07-15T05:03:28.000Z", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/aff49244bb239f0915bb4239b2dec13378d46cfeae5e2965f1066cfad51bcf66", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-07-15T05:03:10.000Z", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/f284421fd3a3cc4cf65de5a7d19f1eb18bf87db63d1c771f9589e0b30b564637", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-07-15T05:04:25.000Z", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/e782960f0f438f13e65e60b0843ff59f1ecf4b958a9bec6252f457104c97c77b", "status": "success", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-07-15T05:02:50.000Z", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/e3d79d07f69549693be244c7b07359cea48452cb29bf2225ccce0e2074535876", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-07-15T05:02:58.000Z", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/bb9242029c2a4716565da271070adb56dd71ca2c02efaf838e20cfcbc0bf809e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-07-15T05:03:48.000Z", "commit": "d01f631a9c434a1eb2548ac53e38374f905355b8", "fileid": "https://r2.ropensci.org/5f70cb57dbd97f73bda37a915142938c3eb7131e0a2b7b3aa1567d2be5faa534", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/29390202841" } ] }