{ "_id": "6a4a5d891e9cffeb4b83366a", "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": "2026-07-05 11:49:31 UTC", "RemoteUrl": "https://github.com/franciscorichter/phylo-species-atlas", "RemoteRef": "HEAD", "RemoteSha": "a4a1f8d0ef052fbd0eb08168008d06b34881652a", "RemoteSubdir": "phyloatlas", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-05 13:32:14 UTC", "User": "root" }, "Author": "Francisco Richter [aut, cre] (ORCID:\n)", "Maintainer": "Francisco Richter ", "_user": "franciscorichter", "_type": "src", "_file": "phyloatlas_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/d82d81ef22774840bc20a9185b72c92afc933ecbf91829526459bb0fc47667db", "_filesize": 123187, "_sha256": "d82d81ef22774840bc20a9185b72c92afc933ecbf91829526459bb0fc47667db", "_expires": "2026-10-13T13:35:04.000Z", "_created": "2026-07-05T13:32:14.000Z", "_published": "2026-07-05T13:35:05.650Z", "_jobs": [ { "job": 85227616973, "time": 113, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8092279970" }, { "job": 85227617008, "time": 132, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8092282223" }, { "job": 85227616982, "time": 65, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8092273776" }, { "job": 85227617003, "time": 70, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8092274463" }, { "job": 85227345058, "time": 210, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8092264577" }, { "job": 85227616996, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8092282633" }, { "job": 85227617013, "time": 79, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8092275730" }, { "job": 85227617022, "time": 70, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8092274413" }, { "job": 85227617006, "time": 71, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8092274486" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/franciscorichter/actions/runs/28742385312", "_status": "success", "_upstream": "https://github.com/franciscorichter/phylo-species-atlas", "_commit": { "id": "a4a1f8d0ef052fbd0eb08168008d06b34881652a", "author": "franciscorichter ", "committer": "franciscorichter ", "message": "Release v1.0.8: reconcile turtle canonical to the 274-tip Thomson 2021 chronogram; MEE integrity pass\n\n- Turtles: ship the 274-tip ultrametric MCC chronogram (crown ~212 Ma) as the\n standardized canonical, replacing the 287-tip substitution tree that violated\n time-calibration integrity (Invariant 0). Updated standardized/metadata.csv\n (593->274), data_provenance, data_estimates, Table S5, turtles.nwk.\n- Fungi: manuscript corrected to the 1,602 species-level shipped count (site\n override already ships it; 1,672 was the raw tip count).\n- Carries the earlier cacti/conifers/solanaceae dating curation and the\n Condamine DOI (ele.13382) fixes.\n- data.json rebuilt: 264 trees, 247 dated, 62 partitions; Invariant 0 passes.\n- CITATION.cff bumped to v1.0.8 (2026-07-05).\n", "time": 1783252171 }, "_maintainer": { "name": "Francisco Richter", "email": "richtf@usi.ch", "orcid": "0000-0002-0924-4613" }, "_distro": "resolute", "_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", 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"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": 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