{ "_id": "6a21b09fcd65a98ecbd3945a", "Package": "phyloatlas", "Type": "Package", "Title": "Access to the 'Phylo-Species Atlas' of Empirical Phylogenies", "Version": "0.1.0", "Authors@R": "person(given = \"Francisco\",\nfamily = \"Richter\",\nemail = \"richtf@usi.ch\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0924-4613\"))", "Description": "Provides convenience functions to fetch standardized\nphylogenetic trees and per-tree provenance metadata from the\n'Phylo-Species Atlas'\n\ndirectly from R. The atlas is a curated collection of empirical\nspecies-level trees covering Bacteria, Archaea, and Eukaryota,\norganized into 62 partitions of life with tip labels normalized\nagainst a shared dictionary of standardized species\nidentifiers. Functions load any of the standardized trees with\nspecies labels resolved from the dictionary, list available\ntrees, and inspect per-tree provenance.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/franciscorichter/phylo-species-atlas,\nhttps://franciscorichter.github.io/phylo-species-atlas/", "BugReports": "https://github.com/franciscorichter/phylo-species-atlas/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 17:04:13 UTC", "User": "root" }, "Author": "Francisco Richter [aut, cre] (ORCID:\n)", "Maintainer": "Francisco Richter ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-06-04 14:12:10 UTC", "RemoteUrl": "https://github.com/cran/phyloatlas", "RemoteRef": "HEAD", "RemoteSha": "7a8673aadb87fe2a2bd7ae26ccbeeb468f37c2f6", "MD5sum": "401d55a12f9424285de5716c670bb9f1", "_user": "cran", "_type": "src", "_file": "phyloatlas_0.1.0.tar.gz", "_fileid": "afe34e094144152f4606f9c49dd3d6aac52f07a935860d210c1978076c675183", "_filesize": 123837, "_sha256": "afe34e094144152f4606f9c49dd3d6aac52f07a935860d210c1978076c675183", "_created": "2026-06-04T17:04:13.000Z", "_published": "2026-06-04T17:06:39.346Z", "_distro": "noble", "_jobs": [ { "job": 79572252303, "time": 116, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7417952977" }, { "job": 79572252324, "time": 101, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7417947249" }, { "job": 79571696406, "time": 171, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7417907317" }, { "job": 79572252418, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7417949652" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26966850800", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/phyloatlas", "_commit": { "id": "7a8673aadb87fe2a2bd7ae26ccbeeb468f37c2f6", "author": "Francisco Richter ", "committer": "cran-robot ", "message": "version 0.1.0\n", "time": 1780582330 }, "_maintainer": { "name": "Francisco Richter", "email": "richtf@usi.ch", "orcid": "0000-0002-0924-4613" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-23", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2026-06-04" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phyloatlas" }, "_devurl": "https://github.com/franciscorichter/phylo-species-atlas", "_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/phyloatlas.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2026-06-04" } ], "_exports": [ "atlas_clear_cache", "atlas_info", "list_trees", "load_atlas_tree" ], "_help": [ { "page": "atlas_clear_cache", "title": "Clear the in-memory cache", "concept": [ "atlas" ], "topics": [ "atlas_clear_cache" ] }, { "page": "atlas_info", "title": "Get metadata for a single tree", "concept": [ "atlas" ], "topics": [ "atlas_info" ] }, { "page": "list_trees", "title": "List trees available in the Phylo-Species Atlas", "concept": [ "atlas" ], "topics": [ "list_trees" ] }, { "page": "load_atlas_tree", "title": "Load a tree from the Phylo-Species Atlas", "concept": [ "atlas" ], "topics": [ "load_atlas_tree" ] } ], "_readme": "https://github.com/cran/phyloatlas/raw/HEAD/README.md", "_rundeps": [ "ape", "digest", "lattice", "nlme", "Rcpp" ], "_vignettes": [ { "source": "phyloatlas.Rmd", "filename": "phyloatlas.html", "title": "Getting started with phyloatlas", "engine": "knitr::rmarkdown", "headings": [ "What this package does", "Loading a tree (offline demo)", "Loading a real atlas tree (requires network)", "Browsing available trees", "Pointing at a fork or local mirror", "Provenance and reproducibility", "Where to learn more" ], "created": "2026-06-04 14:12:10", "modified": "2026-06-04 14:12:10", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": false, "_nocasepkg": "phyloatlas", "_universes": [ "cran", "franciscorichter" ], "_indexurl": "https://franciscorichter.r-universe.dev/phyloatlas", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-06-04T17:06:13.000Z", "distro": "noble", "commit": "7a8673aadb87fe2a2bd7ae26ccbeeb468f37c2f6", "fileid": "7b722cfedf6603742f540e7248fbb20dac8cb1effc5ec762ac0b3e3bb988f046", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26966850800" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-06-04T17:05:59.000Z", "distro": "noble", "commit": "7a8673aadb87fe2a2bd7ae26ccbeeb468f37c2f6", "fileid": "2eab57718d79bd2057204e5442082dcbaa46dfb19fa9209fc9ae56efd9af4696", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26966850800" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-06-04T17:06:15.000Z", "commit": "7a8673aadb87fe2a2bd7ae26ccbeeb468f37c2f6", "fileid": "dd4717072c6c20e2c394ee6cc87ba1b62ab152620f88c95f1a3ae9940b993664", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26966850800" } ] }