{ "_id": "6a1f3200b401979e73427de0", "Package": "phylogram", "Type": "Package", "Title": "Dendrograms for Evolutionary Analysis", "Version": "2.1.0.9000", "Authors@R": "c(person(\"Shaun\", \"Wilkinson\", role = c(\"aut\", \"cre\"),\nemail = \"shaunpwilkinson@gmail.com\",\ncomment = c(ORCID = '0000-0002-7332-7931')),\nperson(\"Simon\", \"Davy\", role = \"aut\",\nemail = \"simon.davy@vuw.ac.nz\",\ncomment = c(ORCID = '0000-0003-3584-5356'))\n)", "Maintainer": "Shaun Wilkinson ", "Description": "Contains functions for developing phylogenetic trees as\ndeeply-nested lists (\"dendrogram\" objects). Enables\nbi-directional conversion between dendrogram and \"phylo\"\nobjects (see Paradis et al (2004)\n), and features several\ntools for command-line tree manipulation and import/export via\nNewick parenthetic text.", "License": "GPL-3", "URL": "https://docs.ropensci.org/phylogram,\nhttp://github.com/ropensci/phylogram", "BugReports": "http://github.com/ropensci/phylogram/issues", "Encoding": "UTF-8", "RoxygenNote": "6.0.1", "VignetteBuilder": "knitr", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2019-12-09 21:21:51 UTC", "RemoteUrl": "https://github.com/ropensci/phylogram", "RemoteRef": "master", "RemoteSha": "9b7ce7672a048937d702d27205d5d212bf802305", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 08:14:15 UTC", "User": "root" }, "Author": "Shaun Wilkinson [aut, cre] (ORCID:\n),\nSimon Davy [aut] (ORCID: )", "MD5sum": "f279d88942edf78e26002ace7ef58df4", "_user": "ropensci", "_type": "src", "_file": "phylogram_2.1.0.9000.tar.gz", "_fileid": "c1867821885355fba013c0df729f15f6e10b845cfe075ef2969fa4d45528eb60", "_filesize": 1935074, "_sha256": "c1867821885355fba013c0df729f15f6e10b845cfe075ef2969fa4d45528eb60", "_created": "2026-05-15T08:14:15.000Z", "_published": "2026-06-02T19:41:52.781Z", "_distro": "noble", "_jobs": [ { "job": 79156999633, "time": 124, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7012902486" }, { "job": 79157000178, "time": 119, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7012901579" }, { "job": 79157000216, "time": 99, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7012897426" }, { "job": 79156999462, "time": 108, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7012899326" }, { "job": 79156999134, "time": 147, "config": "pkgdown", "r": "4.6.0", "check": "OK", "artifact": "7012873291" }, { "job": 79156999068, "time": 179, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7012879016" }, { "job": 79156998851, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7368037775" }, { "job": 79156999670, "time": 102, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7012898293" }, { "job": 79157000423, "time": 84, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7012894549" }, { "job": 79156999825, "time": 90, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7012896220" } ], "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ropensci/phylogram", "_commit": { "id": "9b7ce7672a048937d702d27205d5d212bf802305", "author": "rOpenSci Bot ", "committer": "rOpenSci Bot ", "message": "Add links to official docs site.\nFor more details: https://ropensci.org/technotes/2019/06/07/ropensci-docs/\n", "time": 1575926511 }, "_maintainer": { "name": "Shaun Wilkinson", "email": "shaunpwilkinson@gmail.com", "login": "shaunpwilkinson", "uuid": 10361217, "orcid": "0000-0002-7332-7931" }, "_registered": true, "_dependencies": [ { "package": "ape", "version": ">= 4.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "dendextend", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "ropensci", "_selfowned": true, "_usedby": 10, "_updates": [], "_tags": [], "_topics": [ "peer-reviewed" ], "_stars": 12, "_contributors": [ { "user": "shaunpwilkinson", "count": 85, "uuid": 10361217 } ], "_userbio": { "uuid": 1200269, "type": "organization", "name": "rOpenSci", "description": "Tools and R Packages for Open Science" }, "_downloads": { "count": 1188, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phylogram" }, "_mentions": 44, "_devurl": "https://github.com/ropensci/phylogram", "_pkgdown": "https://docs.ropensci.org/phylogram", "_searchresults": 259, "_metadata": { "review": { "id": 212, "status": "reviewed", "version": "2.0.1.9000", "organization": "rOpenSci Software Review", "url": "https://github.com/ropensci/software-review/issues/212" }, "ropensci_category": "data-extraction" }, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/phylogram.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ropensci/phylogram", "_realowner": "ropensci", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2017-06-12" }, { "version": "1.0.1", "date": "2017-06-14" }, { "version": "2.0.0", "date": "2018-04-10" }, { "version": "2.0.1", "date": "2018-04-13" }, { "version": "2.1.0", "date": "2018-06-25" } ], "_exports": [ "as.cladogram", "as.dendrogram", "as.dendrogram.phylo", "as.phylo", "as.phylo.dendrogram", "ladder", "prune", "read.dendrogram", "remidpoint", "reposition", "write.dendrogram" ], "_help": [ { "page": "as.cladogram", "title": "Apply unweighted branch lengths.", "topics": [ "as.cladogram" ] }, { "page": "as.dendrogram.phylo", "title": "Convert a \"phylo\" object to a dendrogram.", "topics": [ "as.dendrogram.phylo" ] }, { "page": "as.phylo.dendrogram", "title": "Convert a dendrogram to a \"phylo\" object.", "topics": [ "as.phylo.dendrogram" ] }, { "page": "ladder", "title": "Reorder tree branches in ladderized pattern.", "topics": [ "ladder" ] }, { "page": "phylogram", "title": "Dendrograms for evolutionary analysis.", "topics": [ "phylogram-package", "phylogram" ] }, { "page": "prune", "title": "Remove tree nodes by regular expression pattern matching.", "topics": [ "prune" ] }, { "page": "read.dendrogram", "title": "Read a dendrogram from parenthetic text.", "topics": [ "read.dendrogram" ] }, { "page": "remidpoint", "title": "Set dendrogram attributes for a nested list.", "topics": [ "remidpoint" ] }, { "page": "reposition", "title": "Reset dendrogram height attributes.", "topics": [ "reposition" ] }, { "page": "write.dendrogram", "title": "Write a dendrogram object to parenthetic text.", "topics": [ "write.dendrogram" ] } ], "_readme": "https://github.com/ropensci/phylogram/raw/master/README.md", "_rundeps": [ "ape", "digest", "lattice", "nlme", "Rcpp" ], "_vignettes": [ { "source": "phylogram-vignette.Rmd", "filename": "phylogram-vignette.html", "title": "phylogram: an R package for phylogenetic analysis with dendrograms", "author": "Shaun P. Wilkinson ^1,2^ and Simon K. Davy ^1^", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Introduction", "The phylogram package", "Importing and exporting trees", "Example 1: Import and export a tree from a Newick string", "Converting tree objects", "Example 2: Convert a \"phylo\" object to a dendrogram", "Tree editing/manipulation", "Example 3: Building and manipulating dendrograms", "Tree visualization", "Summary", "Acknowledgements", "Author Contributions", "References" ], "created": "2017-01-18 03:18:28", "modified": "2018-06-26 05:06:12", "commits": 28 } ], "_score": 8.743388709829734, "_indexed": true, "_nocasepkg": "phylogram", "_universes": [ "ropensci", "shaunpwilkinson" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.0.9000", "date": "2026-05-15T08:16:18.000Z", "distro": "noble", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "fe710a0196c18b43b90029a2140b06c428836dd8c1ba968d0d43df6830f64216", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" }, { "r": "4.6.0", "os": "linux", "version": "2.1.0.9000", "date": "2026-05-15T08:16:15.000Z", "distro": "noble", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "d2462559d8c1ecf815b840701880559d348baeff8f3e86cdc516857a747a1743", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" }, { "r": "4.5.3", "os": "mac", "version": "2.1.0.9000", "date": "2026-05-15T08:15:55.000Z", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "e8068558c3ecc5e78d228ae7347df864f9c4cd7fc46d777f3cab5c6e5b1171ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" }, { "r": "4.6.0", "os": "mac", "version": "2.1.0.9000", "date": "2026-05-15T08:16:05.000Z", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "0611a5ff87bfa34261b192057367353a5619c9c2aa8c76b41d7926522d58ef9b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" }, { "r": "4.7.0", "os": "win", "version": "2.1.0.9000", "date": "2026-05-15T08:15:54.000Z", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "e952c114634f4f011fc80a29a32d91f46213a72497bd3780437cf16e48d7d54d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" }, { "r": "4.5.3", "os": "win", "version": "2.1.0.9000", "date": "2026-05-15T08:15:33.000Z", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "e539a741f388fd47595b9fdd4abce95f9e002ee387a443e84e3e06f61b10bdde", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" }, { "r": "4.6.0", "os": "win", "version": "2.1.0.9000", "date": "2026-05-15T08:15:39.000Z", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "437ec0ce3f359f0c359e836551b5e6ebb6d3c625202869a1415bb204f617c065", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.0.9000", "date": "2026-06-02T19:41:24.000Z", "commit": "9b7ce7672a048937d702d27205d5d212bf802305", "fileid": "aab5d724f1eff21975a191bccef02f2174589164bfca283dbc34b30f2ff26675", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25907506426" } ] }