{ "_id": "6a1eeb5bb401979e734122a1", "Package": "zoolog", "Title": "Zooarchaeological Analysis with Log-Ratios", "Version": "1.1.1.001", "Date": "2022-9-5", "Authors@R": "c(\nperson(c(\"Jose\",\"M\"), \"Pozo\",\nrole = c(\"aut\", \"cre\"),\nemail = \"josmpozo@gmail.com\",\ncomment = c(ORCID = \"0000-0002-0759-3510\")),\nperson(\"Angela\", \"Trentacoste\",\nrole = c(\"aut\"),\nemail = \"angela.trentacoste@arch.ox.ac.uk\",\ncomment = c(ORCID = \"0000-0001-7096-5252\")),\nperson(\"Ariadna\", \"Nieto-Espinet\",\nrole = c(\"aut\"),\nemail = \"arinietoespinet@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2567-1735\")),\nperson(\"Silvia\", \"Guimarães Chiarelli\",\nrole = c(\"aut\"),\nemail = \"biguimaraes@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-3778-3315\")),\nperson(\"Silvia\", \"Valenzuela-Lamas\",\nrole = c(\"aut\"),\nemail = \"svalenzuela@imf.csic.es\",\ncomment = c(ORCID = \"0000-0001-9886-0372\")))", "Description": "Includes functions and reference data to generate and\nmanipulate log-ratios (also known as log size index (LSI)\nvalues) from measurements obtained on zooarchaeological\nmaterial. Log ratios are used to compare the relative (rather\nthan the absolute) dimensions of animals from archaeological\ncontexts (Meadow 1999, ISBN: 9783896463883). zoolog is also\nable to seamlessly integrate data and references with\nheterogeneous nomenclature, which is internally managed by a\nzoolog thesaurus. A preliminary version of the zoolog methods\nwas first used by Trentacoste, Nieto-Espinet, and\nValenzuela-Lamas (2018) .", "License": "GPL-3", "Encoding": "UTF-8", "Language": "en-GB", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.1", "Config/testthat/edition": "3", "RdMacros": "Rdpack", "VignetteBuilder": "knitr", "URL": "https://josempozo.github.io/zoolog/", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://josempozo.r-universe.dev", "Date/Publication": "2022-09-07 07:10:19 UTC", "RemoteUrl": "https://github.com/josempozo/zoolog", "RemoteRef": "HEAD", "RemoteSha": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-19 09:49:13 UTC", "User": "root" }, "Author": "Jose M Pozo [aut, cre] (ORCID: ),\nAngela Trentacoste [aut] (ORCID:\n),\nAriadna Nieto-Espinet [aut] (ORCID:\n),\nSilvia Guimarães Chiarelli [aut] (ORCID:\n),\nSilvia Valenzuela-Lamas [aut] (ORCID:\n)", "Maintainer": "Jose M Pozo ", "MD5sum": "a2d24f054589e7bef89cf2d56a65fbf2", "_user": "josempozo", "_type": "src", "_file": "zoolog_1.1.1.001.tar.gz", "_fileid": "42d7896e98c1675f5bf1f2d060ca807022a20ead059c226347322c9613721d86", "_filesize": 1208672, "_sha256": "42d7896e98c1675f5bf1f2d060ca807022a20ead059c226347322c9613721d86", "_created": "2026-05-19T09:49:13.000Z", "_published": "2026-06-02T14:40:27.533Z", "_distro": "noble", "_jobs": [ { "job": 79097393753, "time": 136, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7080227967" }, { "job": 79097393115, "time": 141, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7080229824" }, { "job": 79097392967, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7080221879" }, { "job": 79097393459, "time": 153, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7080224017" }, { "job": 79097392130, "time": 207, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7080179717" }, { "job": 79097391829, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7360930376" }, { "job": 79097392768, "time": 124, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7080214918" }, { "job": 79097393139, "time": 87, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7080210850" }, { "job": 79097392960, "time": 84, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7080209834" } ], "_buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/josempozo/zoolog", "_commit": { "id": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "author": "Jose M Pozo <72624361+josempozo@users.noreply.github.com>", "committer": "Jose M Pozo <72624361+josempozo@users.noreply.github.com>", "message": "BUG: In AddToThesaurus, removing repeated names with sensitiveness\n\nPreviously using base::unique, now changed by using\nzoolog::RemoveRepeatedNames.\n", "time": 1662534619 }, "_maintainer": { "name": "Jose M Pozo", "email": "josmpozo@gmail.com", "login": "josempozo", "description": "", "uuid": 72624361, "orcid": "0000-0002-0759-3510" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "Rdpack", "version": ">= 0.7", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "stats", "role": "Suggests" } ], "_owner": "josempozo", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 6, "_contributors": [ { "user": "josempozo", "count": 289, "uuid": 72624361 }, { "user": "svalenzl", "count": 28, "uuid": 68766447 } ], "_userbio": { "uuid": 72624361, "type": "user", "name": "Jose M Pozo" }, "_downloads": { "count": 188, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/zoolog" }, "_devurl": "https://github.com/josempozo/zoolog", "_pkgdown": "https://josempozo.github.io/zoolog/", "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "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/zoolog.html", "manual.pdf" ], "_homeurl": "https://github.com/josempozo/zoolog", "_realowner": "josempozo", "_cranurl": true, "_releases": [ { "version": "0.2.1", "date": "2021-02-17" }, { "version": "0.3.0", "date": "2021-04-07" }, { "version": "0.3.1", "date": "2021-05-04" }, { "version": "0.4.0", "date": "2021-08-02" }, { "version": "0.4.1", "date": "2021-09-02" }, { "version": "1.0.0", "date": "2022-05-02" }, { "version": "1.0.1", "date": "2022-05-03" }, { "version": "1.1.0", "date": "2022-08-26" } ], "_exports": [ "AddToThesaurus", "AssembleReference", "CondenseLogs", "GetSpeciesIn", "InCategory", "LogRatios", "NewThesaurus", "ReadThesaurus", "ReadThesaurusSet", "RemoveNACases", "RemoveRepeatedNames", "StandardizeDataSet", "StandardizeNomenclature", "Subtaxonomy", "SubtaxonomySet", "ThesaurusAmbiguity", "WriteThesaurus", "WriteThesaurusSet" ], "_datasets": [ { "name": "reference", "title": "References", "object": "reference", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "referencesDatabase", "title": "References", "object": "referencesDatabase", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "referenceSets", "title": "References", "object": "referenceSets", "class": [ "data.frame" ], "fields": [ "Bos taurus", "Bos primigenius", "Ovis aries", "Ovis orientalis", "Capra hircus", "Capra aegagrus", "Sus domesticus", "Sus scrofa", "Cervus elaphus", "Dama mesopotamica", "Gazella gazella", "Equus asinus", "Equus caballus", "Oryctolagus cuniculus", "Canis lupus" ], "rows": 4, "table": true, "tojson": true }, { "name": "zoologTaxonomy", "title": "Taxonomy hierarchy for 'zoolog'", "object": "zoologTaxonomy", "class": [ "data.frame" ], "fields": [ "Species", "Genus", "Tribe", "Subfamily", "Family" ], "rows": 16, "table": true, "tojson": true }, { "name": "zoologThesaurus", "title": "Thesaurus Set for 'zoolog'", "object": "zoologThesaurus", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "AssembleReference", "title": "Assemble Reference", "topics": [ "AssembleReference" ] }, { "page": "CondenseLogs", "title": "Condense Measure Log-Ratios", "topics": [ "CondenseLogs" ] }, { "page": "dataValenzuelaLamas2008", "title": "Example dataset", "topics": [ "dataValenzuelaLamas2008" ] }, { "page": "InCategory", "title": "Value Matching by Thesaurus Category", "topics": [ "InCategory" ] }, { "page": "LogRatios", "title": "Log Ratios of Measurements", "topics": [ "LogRatios" ] }, { "page": "referencesDatabase", "title": "References", "topics": [ "reference", "referencesDatabase", "referenceSets" ] }, { "page": "RemoveNACases", "title": "Remove Cases Missing All Measurements", "topics": [ "RemoveNACases" ] }, { "page": "StandardizeNomenclature", "title": "Standardize Nomenclature", "topics": [ "StandardizeDataSet", "StandardizeNomenclature" ] }, { "page": "Subtaxonomy", "title": "Subtaxonomy under taxonomical category", "topics": [ "GetSpeciesIn", "Subtaxonomy", "SubtaxonomySet" ] }, { "page": "ThesaurusManagement", "title": "Thesaurus Management", "topics": [ "AddToThesaurus", "NewThesaurus", "RemoveRepeatedNames", "ThesaurusAmbiguity", "ThesaurusManagement" ] }, { "page": "ThesaurusReaderWriter", "title": "Thesaurus Readers and Writers", "topics": [ "ReadThesaurus", "ReadThesaurusSet", "ThesaurusReaderWriter", "WriteThesaurus", "WriteThesaurusSet" ] }, { "page": "zoologTaxonomy", "title": "Taxonomy hierarchy for 'zoolog'", "topics": [ "zoologTaxonomy" ] }, { "page": "zoologThesaurus", "title": "Thesaurus Set for 'zoolog'", "topics": [ "zoologThesaurus" ] } ], "_readme": "https://github.com/josempozo/zoolog/raw/HEAD/README.md", "_rundeps": [ "rbibutils", "Rdpack", "stringi" ], "_vignettes": [ { "source": "index.Rmd", "filename": "index.html", "title": "zoolog: Zooarchaeological Analysis with Log-Ratios", "author": "Jose M Pozo, Angela Trentacoste, Ariadna Nieto-Espinet, Silvia Guimarães Chiarelli, and Silvia Valenzuela-Lamas", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Acknowledgements", "Installation", "Reference standards", "Thesaurus", "Taxonomy", "Functions", "Examples", "Reading data and calculating log ratios", "A note on the warnings of LogRatios", "Dealing with lazy datasets", "Using the same ovis reference for all caprines", "Pruning the data from cases with no available measure", "Condensing log values", "Standardizing the dataset nomenclature", "Selecting only caprines", "Different plots for data visualisation", "Horizontal Boxplot with dots grouped by site", "Histograms grouped by site", "Vertical boxplot with dots grouped by taxon and site", "Histograms grouped by taxon and site", "Statistical test", "How to cite the package zoolog", "Bibliography" ], "created": "2021-01-19 11:58:32", "modified": "2022-08-22 17:50:20", "commits": 30 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "zoolog", "_universes": [ "josempozo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1.001", "date": "2026-05-19T09:51:25.000Z", "distro": "noble", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "f0acbd1e8e00af6bfaf29eafa0858bf2eb8d81af98260f71f727ece905bccaaa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" }, { "r": "4.6.0", "os": "linux", "version": "1.1.1.001", "date": "2026-05-19T09:51:25.000Z", "distro": "noble", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "1b03b2e78c5556c0755245e5f0611b5e6029241d23484eabc7c775cf6611ae35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1.001", "date": "2026-05-19T09:51:12.000Z", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "2e0a117bb069df9e310d5c3d8929cb8ac02037b5cfa7ec60b1b861099f14f0d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" }, { "r": "4.6.0", "os": "mac", "version": "1.1.1.001", "date": "2026-05-19T09:51:15.000Z", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "2682950227d7e9e730afe09c1a2108660b373eb4f1ed4332d3403cc6f51904ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" }, { "r": "4.7.0", "os": "win", "version": "1.1.1.001", "date": "2026-05-19T09:50:36.000Z", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "04581f586af245d0c45bd2904ad167570d1d50ae010c7b77a242e84d81909b61", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" }, { "r": "4.5.3", "os": "win", "version": "1.1.1.001", "date": "2026-05-19T09:50:32.000Z", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "8c5c4890ae5ee77c1edffead26b20ff01bb9d3a589460c3d92ea13a63a12bb0d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" }, { "r": "4.6.0", "os": "win", "version": "1.1.1.001", "date": "2026-05-19T09:50:25.000Z", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "dd577bdac364944fb8110260771e41aab2080085215bd4e9acc36a136b446f58", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1.001", "date": "2026-06-02T14:40:02.000Z", "commit": "a7a340a4bfedbf88d86afa85dfbf343e6d752470", "fileid": "39123311dfb99390cbab036c9f208a15b2139676b3e251b488e814a983b6797a", "status": "success", "buildurl": "https://github.com/r-universe/josempozo/actions/runs/26089392832" } ] }