{ "_id": "6a293479732311cd875a7a80", "Package": "NBLDA", "Type": "Package", "Title": "Negative Binomial Linear Discriminant Analysis", "Version": "1.0.1.9000", "Date": "2022-02-21", "Authors@R": "c(person(\"Dincer\", \"Goksuluk\", role = c(\"aut\", \"cre\"), email = \"dincergoksuluk@erciyes.edu.tr\"),\nperson(\"Gokmen\", \"Zararsiz\", role = c(\"aut\")),\nperson(\"Selcuk\", \"Korkmaz\", role = c(\"aut\")),\nperson(c(\"Ahmet\", \"Ergun\"), \"Karaagaoglu\", role = c(\"ths\")))", "Description": "We proposed a package for the classification task which\nuses Negative Binomial distribution within Linear Discriminant\nAnalysis (NBLDA). It is an extension of the 'PoiClaClu' package\nto Negative Binomial distribution. The classification\nalgorithms are based on the papers Dong et al. (2016, ISSN:\n1471-2105) and Witten, DM (2011, ISSN: 1932-6157) for NBLDA and\nPLDA, respectively. Although PLDA is a sparse algorithm and can\nbe used for variable selection, the algorithm proposed by Dong\net al. is not sparse. Therefore, it uses all variables in the\nclassifier. Here, we extend Dong et al.'s algorithm to the\nsparse case by shrinking overdispersion towards 0 (Yu et al.,\n2013, ISSN: 1367-4803) and offset parameter towards 1 (as\nproposed by Witten DM, 2011). We support only the\nclassification task with this version.", "License": "GPL(>=2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.2", "Collate": "'FindBestTransform.R' 'all_classes.R' 'all_generics.R'\n'control.R' 'copiedFromOtherPackages.R' 'generateCountData.R'\n'getShrinkedDispersions.R' 'helper_functions.R'\n'normalize_counts.R' 'package_and_supplementary.R'\n'plot.nblda.R' 'predict.nblda.R' 'trainNBLDA.R' 'zzz_methods.R'", "Repository": "https://dncr.r-universe.dev", "Date/Publication": "2022-02-21 19:09:33 UTC", "RemoteUrl": "https://github.com/dncr/nblda", "RemoteRef": "HEAD", "RemoteSha": "3b098934a8797dc9546483eb244960ae4f9ca084", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-10 09:51:02 UTC", "User": "root" }, "Author": "Dincer Goksuluk [aut, cre],\nGokmen Zararsiz [aut],\nSelcuk Korkmaz [aut],\nAhmet Ergun Karaagaoglu [ths]", "Maintainer": "Dincer Goksuluk ", "MD5sum": "53d99c6bf9d656433e448bb90894532a", "_user": "dncr", "_type": "src", "_file": "NBLDA_1.0.1.9000.tar.gz", "_fileid": "d900b47fd06d431ce1297fd6fee027254cf9621bf2441578a44a1f574c5d9284", "_filesize": 266756, "_sha256": "d900b47fd06d431ce1297fd6fee027254cf9621bf2441578a44a1f574c5d9284", "_created": "2026-06-10T09:51:02.000Z", "_published": "2026-06-10T09:55:05.217Z", "_distro": "noble", "_jobs": [ { "job": 80530174433, "time": 118, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7532345939" }, { "job": 80530174499, "time": 117, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7532345607" }, { "job": 80530174447, "time": 204, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7532362112" }, { "job": 80530174434, "time": 153, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7532347623" }, { "job": 80529680776, "time": 154, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7532300446" }, { "job": 80530174420, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7532337751" }, { "job": 80530174489, "time": 91, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7532335736" }, { "job": 80530174753, "time": 94, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7532337691" }, { "job": 80530174451, "time": 95, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7532337836" } ], "_buildurl": "https://github.com/r-universe/dncr/actions/runs/27267915290", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/dncr/nblda", "_commit": { "id": "3b098934a8797dc9546483eb244960ae4f9ca084", "author": "Dinçer GÖKSÜLÜK ", "committer": "GitHub ", "message": "Update DESCRIPTION\n\nVersion changed to 1.0.1.9000 for developement.", "time": 1645470573 }, "_maintainer": { "name": "Dincer Goksuluk", "email": "dincergoksuluk@erciyes.edu.tr" }, "_registered": true, "_dependencies": [ { "package": "ggplot2", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "PoiClaClu", "role": "Suggests" }, { "package": "sSeq", "role": "Suggests" } ], "_owner": "dncr", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "dncr", "count": 40, "uuid": 7161226 } ], "_userbio": { "uuid": 7161226, "type": "user", "name": "Dincer GOKSULUK", "description": "Assoc. Prof. at Department of Biostatistics, Erciyes University, Turkey. R developer and Data Scientist." }, "_downloads": { "count": 765, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/NBLDA" }, "_mentions": 7, "_devurl": "https://github.com/dncr/nblda", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NBLDA.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/dncr/nblda", "_realowner": "dncr", "_cranurl": true, "_releases": [ { "version": "0.99.0", "date": "2018-07-01" }, { "version": "1.0.0", "date": "2020-05-28" }, { "version": "1.0.1", "date": "2022-02-21" } ], "_exports": [ "control", "FindBestTransform", "generateCountData", "getShrinkedDispersions", "inputs", "nbldaControl", "nbldaTrained", "normalization", "NullModel", "NullModelTest", "plot", "predict", "selectedFeatures", "show", "trainNBLDA" ], "_datasets": [ { "name": "cervical", "title": "Cervical cancer data", "object": "cervical", "class": [ "data.frame" ], "fields": [ "N1", "N2", "N3", "N4", "N5", "N6", "N7", "N8", "N9", "N10", "N11", "N12", "N13", "N14", "N15", "N16", "N17", "N18", "N19", "N20", "N21", "N22", "N23", "N24", "N25", "N26", "N27", "N28", "N29", "T1", "T2", "T3", "T4", "T5", "T6", "T7", "T8", "T9", "T10", "T11", "T12", "T13", "T14", "T15", "T16", "T17", "T18", "T19", "T20", "T21", "T22", "T23", "T24", "T25", "T26", "T27", "T28", "T29" ], "rows": 714, "table": true, "tojson": true } ], "_help": [ { "page": "NBLDA-package", "title": "Classifying count data using Poisson/Negative Binomial linear discriminant analysis", "topics": [ "NBLDA-package" ] }, { "page": "cervical", "title": "Cervical cancer data", "topics": [ "cervical" ] }, { "page": "control", "title": "Accessors for the 'control' slot.", "topics": [ "control", "control,nblda-method", "control,nblda_trained-method" ] }, { "page": "FindBestTransform", "title": "Find the Power Transformation Parameter.", "topics": [ "FindBestTransform" ] }, { "page": "generateCountData", "title": "Generate Count Data", "topics": [ "generateCountData" ] }, { "page": "getShrinkedDispersions", "title": "Estimate Shrinked Overdispersions", "topics": [ "getShrinkedDispersions" ] }, { "page": "inputs", "title": "Accessors for the 'input' slot.", "topics": [ "inputs", "inputs,nblda-method" ] }, { "page": "nblda_input-class", "title": "'nblda_input' object", "topics": [ "nblda_input-class" ] }, { "page": "nblda_trained-class", "title": "'nblda_trained' object", "topics": [ "nblda_trained-class" ] }, { "page": "nblda-class", "title": "'nblda' object", "topics": [ "nblda-class" ] }, { "page": "nbldaControl", "title": "Control parameters for trained NBLDA model.", "topics": [ "nbldaControl" ] }, { "page": "nbldaTrained", "title": "Accessors for the 'crossValidated' slot.", "topics": [ "nbldaTrained", "nbldaTrained,nblda-method", "nbldaTrained,nblda_trained-method" ] }, { "page": "normalization", "title": "Accessors for the 'type' slot.", "topics": [ "normalization", "normalization,nblda-method", "normalization,nblda_trained-method" ] }, { "page": "NullModel", "title": "Calculate the Normalized Counts and Related Training Parameters.", "topics": [ "NullModel", "NullModelTest" ] }, { "page": "plot", "title": "Plot Method for the 'nblda' and 'nblda_trained' Classes", "topics": [ "plot", "plot,nblda-method", "plot,nblda_trained-method", "plot.nblda", "plot.nblda_trained" ] }, { "page": "predict", "title": "Extract predictions from NBLDA model", "topics": [ "predict", "predict,nblda-method", "predict.nblda" ] }, { "page": "selectedFeatures", "title": "Accessors for the 'selectedFeatures' slot.", "topics": [ "selectedFeatures", "selectedFeatures,nblda-method", "selectedFeatures,nblda_trained-method" ] }, { "page": "show", "title": "Show Method for the S4 classes in NBLDA Package", "topics": [ "show", "show,nblda-method", "show,nblda_input-method", "show,nblda_trained-method", "show.nblda", "show.nblda_input", 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