{ "_id": "6a454d486ff6f23575528f85", "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", "Repository": "https://franciscorichter.r-universe.dev", "Date/Publication": "2026-07-01 17:05:50 UTC", "RemoteUrl": "https://github.com/franciscorichter/phylo-species-atlas", "RemoteRef": "HEAD", "RemoteSha": "b239881edbcec018dc1b8353623ea94a657b931f", "RemoteSubdir": "phyloatlas", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 17:21:08 UTC", "User": "root" }, "Author": "Francisco Richter [aut, cre] (ORCID:\n)", "Maintainer": "Francisco Richter ", "MD5sum": "847a2ef7502e0a206a819a538101dd9f", "_user": "franciscorichter", "_type": "src", "_file": "phyloatlas_0.1.0.tar.gz", "_fileid": "35fd4cbe5a2fd5e9644c6d6d2c02ec9bc633b62ab081805481dbb8d9fb1635ea", "_filesize": 123168, "_sha256": "35fd4cbe5a2fd5e9644c6d6d2c02ec9bc633b62ab081805481dbb8d9fb1635ea", "_created": "2026-07-01T17:21:08.000Z", "_published": "2026-07-01T17:24:24.149Z", "_distro": "resolute", "_jobs": [ { "job": 84595261131, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8017674120" }, { "job": 84595261147, "time": 164, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8017672199" }, { "job": 84595261187, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8017649188" }, { "job": 84595261104, "time": 96, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8017646624" }, { "job": 84594720857, "time": 168, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8017608701" }, { "job": 84595261074, "time": 138, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8017661836" }, { "job": 84595261122, "time": 59, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8017632487" }, { "job": 84595261111, "time": 78, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8017639576" }, { "job": 84595261127, "time": 128, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8017659116" } ], "_buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/franciscorichter/phylo-species-atlas", "_commit": { "id": "b239881edbcec018dc1b8353623ea94a657b931f", "author": "franciscorichter ", "committer": "franciscorichter ", "message": "Neutralize LLM-workflow phrasing in curation notes (code + Table S7)\n", "time": 1782925550 }, "_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": "franciscorichter", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-15", "n": 5 }, { "week": "2026-19", "n": 1 }, { "week": "2026-20", "n": 36 }, { "week": "2026-21", "n": 49 }, { "week": "2026-22", "n": 6 }, { "week": "2026-24", "n": 4 }, { "week": "2026-26", "n": 1 }, { "week": "2026-27", "n": 5 } ], "_tags": [ { "name": "v1.0.0", "date": "2026-05-11" }, { "name": "v1.0.1", "date": "2026-05-11" }, { "name": "v1.0.2", "date": "2026-05-11" }, { "name": "v1.0.3", "date": "2026-05-12" }, { "name": "v1.0.4", "date": "2026-05-31" }, { "name": "v1.0.5", "date": "2026-06-13" }, { "name": "v1.0.6", "date": "2026-06-29" }, { "name": "v1.0.7", "date": "2026-07-01" } ], "_stars": 0, "_contributors": [ { "user": "franciscorichter", "count": 106, "uuid": 6370020 } ], "_userbio": { "uuid": 6370020, "type": "user", "name": "franciscorichter", "followers": 9, "description": "Mathematical Engineer and Postdoctoral researcher at the Institute of Computing at the Università della Svizzera italiana." }, "_downloads": { "count": 380, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phyloatlas" }, "_devurl": "https://github.com/franciscorichter/phylo-species-atlas", "_searchresults": 5, "_rbuild": "4.6.1", "_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", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/franciscorichter/phylo-species-atlas", "_realowner": "franciscorichter", "_cranurl": true, "_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/franciscorichter/phylo-species-atlas/raw/HEAD/phyloatlas/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": "2026-05-31 14:33:55", "modified": "2026-05-31 14:33:55", "commits": 1 } ], "_score": 4.6020599913279625, "_indexed": true, "_nocasepkg": "phyloatlas", "_universes": [ "franciscorichter" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-07-01T17:23:59.000Z", "distro": "resolute", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "40fc4da79a2cd4ab98ce3f861adc9da78216be817e56107e9abf00fec8da6e5d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-07-01T17:23:54.000Z", "distro": "resolute", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "e599920c4b7d5fe9e3215eb238a84d7df7383a4cf6c2016f84debd4a7b195c17", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-07-01T17:22:56.000Z", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "fe6d6a0d9364832a008d2041a1a2e9cc96acbe3434d86b06338a283b441f15f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" }, { "r": "4.6.1", "os": "mac", "version": "0.1.0", "date": "2026-07-01T17:22:45.000Z", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "6e3dd351c2ac749437c9c9473cbff2bd7b7e252bc162b40bb03bad94d796ba0a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-07-01T17:23:38.000Z", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "392ef3859ce04e7a8b2ef78e79d8abc416b92a13ab1337ce3a313b0ec13fdc78", "status": "success", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-07-01T17:22:08.000Z", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "9519a184ea131e604958d15b1a8c6faf68999b9775923e1f7efe4931d761c959", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-07-01T17:22:24.000Z", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "a3e853d1641b444b89ee5f2c60c48647931109dc3e5697c9303d36f482105673", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" }, { "r": "4.6.1", "os": "win", "version": "0.1.0", "date": "2026-07-01T17:23:13.000Z", "commit": "b239881edbcec018dc1b8353623ea94a657b931f", "fileid": "20e620f504cd9fbbeb26b4cf8ef570d22a35f6ebbae8f40600390cc17175f804", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28535199496" } ] }