{ "_id": "6a1047feacfb0bcc41c9f16a", "Package": "JATSdecoder", "Title": "A Metadata and Text Extraction and Manipulation Tool Set", "Date": "2026-04-09", "Version": "1.3.1", "Authors@R": "c(person(\"Ingmar\", \"Böschen\", email = \"ingmar.boeschen@uni-hamburg.de\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1159-3991\")))", "Maintainer": "Ingmar Böschen ", "Description": "Provides a function collection to extract metadata,\nsectioned text and study characteristics from scientific\narticles in 'NISO-JATS' format. Articles in PDF format can be\nconverted to 'NISO-JATS' with the 'Content ExtRactor and MINEr'\n('CERMINE', ). For\nconvenience, two functions bundle the extraction heuristics:\nJATSdecoder() converts 'NISO-JATS'-tagged XML files to a\nstructured list with elements title, author, journal, history,\n'DOI', abstract, sectioned text and reference list.\nstudy.character() extracts multiple study characteristics like\nnumber of included studies, statistical methods used, alpha\nerror, power, statistical results, correction method for\nmultiple testing, software used. The function get.stats()\nextracts all statistical results from text and recomputes\np-values for many standard test statistics. It performs a\nconsistency check of the reported with the recalculated\np-values. An estimation of the involved sample size is\nperformed based on textual reports within the abstract and the\nreported degrees of freedom within statistical results. In\naddition, the package contains some useful functions to process\ntext (text2sentences(), text2num(), ngram(), strsplit2(),\ngrep2()). See Böschen, I. (2021)\n Böschen, I. (2021)\n, Böschen, I. (2023)\n, and Böschen, I. (2024)\n.", "License": "GPL-3", "URL": "https://github.com/ingmarboeschen/JATSdecoder", "BugReports": "https://github.com/ingmarboeschen/JATSdecoder/issues", "Language": "en-US", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "make default-jdk", "Repository": "https://ingmarboeschen.r-universe.dev", "Date/Publication": "2026-04-10 12:11:57 UTC", "RemoteUrl": "https://github.com/ingmarboeschen/jatsdecoder", "RemoteRef": "HEAD", "RemoteSha": "d42fa097c8d7a9a5df70f9597f1c85f2f73d27f2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-10 09:11:08 UTC", "User": "root" }, "Author": "Ingmar Böschen [aut, cre] (ORCID:\n)", "MD5sum": "c2d8fca8e175287f3bb74c2216c8c619", "_user": "ingmarboeschen", "_type": "src", "_file": "JATSdecoder_1.3.1.tar.gz", "_fileid": "7f465fd821f6d2fa4f0f28c095a2986d5a40aaad247aaf3c989945de3c48282e", "_filesize": 685176, "_sha256": "7f465fd821f6d2fa4f0f28c095a2986d5a40aaad247aaf3c989945de3c48282e", "_created": "2026-05-10T09:11:08.000Z", "_published": "2026-05-22T12:11:42.659Z", "_distro": "noble", "_jobs": [ { "job": 77376775819, "time": 163, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6902577066" }, { "job": 77376775661, "time": 127, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6902574287" }, { "job": 77376775793, "time": 184, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6902702749" }, { "job": 77376775662, "time": 127, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6902689610" }, { "job": 77376775123, "time": 174, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902562529" }, { "job": 77376774967, "time": 118, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160158779" }, { "job": 77376775461, "time": 97, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6902571454" }, { "job": 77376776017, "time": 96, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6902571321" }, { "job": 77376776024, "time": 99, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6902571476" } ], "_buildurl": "https://github.com/r-universe/ingmarboeschen/actions/runs/25624822599", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ingmarboeschen/jatsdecoder", "_commit": { "id": "d42fa097c8d7a9a5df70f9597f1c85f2f73d27f2", "author": "Ingmar Böschen <55027155+ingmarboeschen@users.noreply.github.com>", "committer": "GitHub ", "message": "Update DESCRIPTION", "time": 1775823117 }, "_maintainer": { "name": "Ingmar Böschen", "email": "ingmar.boeschen@uni-hamburg.de", "login": "ingmarboeschen", "uuid": 55027155, "orcid": "0000-0003-1159-3991" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.1", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "NLP", "role": "Imports" }, { "package": "openNLP", "role": "Imports" } ], "_owner": "ingmarboeschen", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-25", "n": 1 }, { "week": "2025-31", "n": 12 }, { "week": "2025-38", "n": 1 }, { "week": "2025-41", "n": 1 }, { "week": "2025-45", "n": 1 }, { "week": "2025-49", "n": 1 }, { "week": "2026-02", "n": 5 }, { "week": "2026-04", "n": 1 }, { "week": "2026-13", "n": 2 }, { "week": "2026-14", "n": 4 }, { "week": "2026-15", "n": 4 } ], "_tags": [], "_topics": [ "cermine", "niso-jats", "pubmedcentral", "text-extraction", "text-mining", "xml-files", "openjdk" ], "_stars": 22, "_contributors": [ { "user": "ingmarboeschen", "count": 385, "uuid": 55027155 } ], "_userbio": { "uuid": 55027155, "type": "user", "name": "Ingmar Böschen" }, "_downloads": { "count": 611, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/JATSdecoder" }, "_devurl": "https://github.com/ingmarboeschen/jatsdecoder", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/JATSdecoder.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ingmarboeschen/jatsdecoder", "_realowner": "ingmarboeschen", "_cranurl": true, "_releases": [ { "version": "1.1", "date": "2022-09-30" }, { "version": "1.1.1", "date": "2022-10-21" }, { "version": "1.1.2", "date": "2023-02-27" }, { "version": "1.2.0", "date": "2023-10-12" }, { "version": "1.2.1", "date": "2025-08-01" }, { "version": "1.2.2", "date": "2026-01-08" }, { "version": "1.3.0", "date": "2026-02-16" }, { "version": "1.3.1", "date": "2026-04-09" } ], "_exports": [ "allStats", "est.ss", "get.abstract", "get.aff", "get.alpha.error", "get.assumptions", "get.author", "get.category", "get.contrib", "get.country", "get.doi", "get.editor", "get.history", "get.journal", "get.keywords", "get.method", "get.multi.comparison", "get.n.studies", "get.outlier.def", "get.power", "get.R.package", "get.references", "get.sentence.with.pattern", "get.sig.adjectives", "get.software", "get.stats", "get.subject", "get.tables", "get.test.direction", "get.text", "get.title", "get.type", "get.vol", "grep2", "has.interaction", "JATSdecoder", "letter.convert", "ngram", "pCheck", "preCheck", "standardStats", "strsplit2", "study.character", "text2num", "text2sentences", "vectorize.text", "which.term" ], "_help": [ { "page": "allStats", "title": "allStats", "topics": [ "allStats" ] }, { "page": "est.ss", "title": "est.ss", "topics": [ "est.ss" ] }, { "page": "get.abstract", "title": "get.abstract", "topics": [ "get.abstract" ] }, { "page": "get.aff", "title": "get.aff", "topics": [ "get.aff" ] }, { "page": "get.alpha.error", "title": "get.alpha.error", "topics": [ "get.alpha.error" ] }, { "page": "get.assumptions", "title": "get.assumptions", "topics": [ "get.assumptions" ] }, { "page": "get.author", "title": "get.author", "topics": [ "get.author" ] }, { "page": "get.category", "title": "get.category", "topics": [ "get.category" ] }, { "page": "get.country", "title": "get.country", "topics": [ "get.country" ] }, { "page": "get.doi", "title": "get.doi", "topics": [ "get.doi" ] }, { "page": "get.editor", "title": "get.editor", "topics": [ "get.editor" ] }, { "page": "get.history", "title": "get.history", "topics": [ "get.history" ] }, { "page": "get.journal", "title": "get.journal", "topics": [ "get.journal" ] }, { "page": "get.keywords", "title": "get.keywords", "topics": [ "get.keywords" ] }, { "page": "get.method", "title": "get.method", "topics": [ "get.method" ] }, { "page": "get.multi.comparison", "title": "get.multi.comparison", "topics": [ "get.multi.comparison" ] }, { "page": "get.n.studies", "title": "get.n.studies", "topics": [ "get.n.studies" ] }, { "page": "get.outlier.def", "title": "get.outlier.def", "topics": [ "get.outlier.def" ] }, { "page": "get.power", "title": "get.power", "topics": [ "get.power" ] }, { "page": "get.R.package", "title": "get.R.package", "topics": [ "get.R.package" ] }, { "page": "get.references", "title": "get.references", "topics": [ "get.references" ] }, { "page": "get.sig.adjectives", "title": "get.sig.adjectives", "topics": [ "get.sig.adjectives" ] }, { "page": "get.software", "title": "get.software", "topics": [ "get.software" ] }, { "page": "get.stats", "title": "get.stats", "topics": [ "get.stats" ] }, { "page": "get.subject", "title": "get.subject", "topics": [ "get.subject" ] }, { "page": "get.tables", "title": "get.tables", "topics": [ "get.tables" ] }, { "page": "get.test.direction", "title": "get.test.direction", "topics": [ "get.test.direction" ] }, { "page": "get.text", "title": "get.text", "topics": [ "get.text" ] }, { "page": "get.title", "title": "get.title", "topics": [ "get.title" ] }, { "page": "get.type", "title": "get.type", "topics": [ "get.type" ] }, { "page": "get.vol", "title": "get.vol", "topics": [ "get.vol" ] }, { "page": "grep2", "title": "grep2", "topics": [ "grep2" ] }, { "page": "has.interaction", "title": "has.interaction", "topics": [ "has.interaction" ] }, { "page": "JATSdecoder", "title": "JATSdecoder", "topics": [ "JATSdecoder" ] }, { "page": "letter.convert", "title": "letter.convert", "topics": [ "letter.convert" ] }, { "page": "ngram", "title": "ngram", "topics": [ "ngram" ] }, { "page": "pCheck", "title": "pCheck", "topics": [ "pCheck" ] }, { "page": "standardStats", "title": "standardStats", "topics": [ "standardStats" ] }, { "page": "strsplit2", "title": "strsplit2", "topics": [ "strsplit2" ] }, { "page": "study.character", "title": "study.character", "topics": [ "study.character" ] }, { "page": "text2num", "title": "text2num", "topics": [ "text2num" ] }, { "page": "text2sentences", "title": "text2sentences", "topics": [ "text2sentences" ] }, { "page": "vectorize.text", "title": "vectorize.text", "topics": [ "vectorize.text" ] }, { "page": "which.term", "title": "which.term", "topics": [ "which.term" ] } 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