{ "_id": "6a1f29bab401979e73424191", "Type": "Package", "Package": "closesamples", "Title": "Gets feasible taxon samples on a tree", "Version": "1.0", "Date": "2020-02-25", "Author": "Brian C. O'Meara", "Maintainer": "Brian C. O'Meara ", "Description": "Often you want to pick species at random, but don't have\naccess to all the possible species, and your group might be a\nnonrandom set. However, you might have a taxonomy, perhaps a\nbad one, for all the species. This will let you pick species at\nrandom on that full taxonomy and then pick a species out of the\npossible set closest to this. You could still have a biased\nsample, but way less biased.", "License": "GPL 3.0", "Encoding": "UTF-8", "RoxygenNote": "7.1.0", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev libssl-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2021-11-08 16:01:32 UTC", "RemoteUrl": "https://github.com/bomeara/closesamples", "RemoteRef": "HEAD", "RemoteSha": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 19:02:32 UTC", "User": "root" }, "MD5sum": "54fccc278bb45b531d94b99147bd59c8", "_user": "phylotastic", "_type": "src", "_file": "closesamples_1.0.tar.gz", "_fileid": "cb4952495e05e5d0abcf7be8979294659951c8fdd975dc8b6dc0b7073f9fec2b", "_filesize": 105042, "_sha256": "cb4952495e05e5d0abcf7be8979294659951c8fdd975dc8b6dc0b7073f9fec2b", "_created": "2026-06-02T19:02:32.000Z", "_published": "2026-06-02T19:06:34.099Z", "_distro": "noble", "_jobs": [ { "job": 79150211124, "time": 154, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7367265108" }, { "job": 79150211145, "time": 212, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7367286883" }, { "job": 79150211371, "time": 98, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7367263605" }, { "job": 79150211140, "time": 77, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7367254603" }, { "job": 79149567614, "time": 201, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7367208994" }, { "job": 79150211141, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367260168" }, { "job": 79150211248, "time": 120, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7367253481" }, { "job": 79150211222, "time": 99, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7367246928" }, { "job": 79150211395, "time": 130, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7367257546" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bomeara/closesamples", "_commit": { "id": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "author": "Brian O'Meara ", "committer": "Brian O'Meara ", "message": "requires Rfast2\n", "time": 1636387292 }, "_maintainer": { "name": "Brian C. OMeara", "email": "omeara.brian@gmail.com", "login": "bomeara", "mastodon": "@omearabrian@mastodon.social", "bluesky": "@omearabrian.bsky.social", "orcid": "0000-0002-0337-5997", "description": "", "uuid": 1612612 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "taxize", "role": "Imports" }, { "package": "Rfast2", "role": "Imports" }, { "package": "anRpackage", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" } ], "_owner": "bomeara", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "bomeara", "count": 16, "uuid": 1612612 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/closesamples" }, "_devurl": "https://github.com/bomeara/closesamples", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/closesamples.html", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "GetClosestSamples", "GetEnclosingTaxonomy", "LabelNodesWithFeasibleDescendants", "SubsampleTree" ], "_datasets": [ { "name": "ORCID_TOKEN", "title": "", "object": "ORCID_TOKEN", "file": "ORCID_TOKEN.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "r", "title": "", "object": "r", "file": "r.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "GetClosest", "title": "Get the closest taxon to the focal taxon", "topics": [ "GetClosest" ] }, { "page": "GetClosestSamples", "title": "Get n samples", "topics": [ "GetClosestSamples" ] }, { "page": "GetEnclosingTaxonomy", "title": "Get enclosing taxonomy for a feasible tree", "topics": [ "GetEnclosingTaxonomy" ] }, { "page": "GetSimilarity", "title": "Get similarity Uses ape's cophenetic.phylo to get patristic distances between pairs of taxa, then makes the diagonals Inf. If the tree has no branch lengths, makes every edge length 1.", "topics": [ "GetSimilarity" ] }, { "page": "LabelNodesWithChosenDescendants", "title": "Include descendant taxon ids in node labels", "topics": [ "LabelNodesWithChosenDescendants" ] }, { "page": "LabelNodesWithFeasibleDescendants", "title": "Include descendant taxon ids in node labels", "topics": [ "LabelNodesWithFeasibleDescendants" ] }, { "page": "SubsampleTree", "title": "Return a sampled tree", "topics": [ "SubsampleTree" ] } ], "_readme": "https://github.com/bomeara/closesamples/raw/HEAD/README.md", "_rundeps": [ "ape", "askpass", "backports", "BH", "checkmate", "cli", "codetools", "cpp11", "crayon", "crul", "curl", "data.table", "digest", "dplyr", "future", "future.apply", "generics", "globals", "glue", "hms", "httpcode", "httr", "igraph", "jsonlite", "lattice", "lifecycle", "listenv", "magrittr", "Matrix", "mime", "natserv", "nlme", "openssl", "osqp", "parallelly", "phangorn", "pillar", "pkgconfig", "plyr", "prettyunits", "progress", "progressr", "R6", "Rcpp", "RcppArmadillo", "RcppParallel", "rentrez", "Rfast", "Rfast2", "ritis", "rlang", "Rnanoflann", "rncl", "rotl", "rredlist", "S7", "solrium", "stringi", "sys", "taxize", "tibble", "tidyselect", "triebeard", "urltools", "utf8", "vctrs", "WikipediR", "wikitaxa", "withr", "worrms", "XML", "xml2", "zigg", "zoo" ], "_score": 1.6989700043360187, "_indexed": false, "_nocasepkg": "closesamples", "_universes": [ "phylotastic" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0", "date": "2026-06-02T19:05:06.000Z", "distro": "noble", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "14ccd14518a313f26c7a66b50ae6adb03024c74e975622ca6c4e87c76e69bc79", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" }, { "r": "4.6.0", "os": "linux", "version": "1.0", "date": "2026-06-02T19:06:04.000Z", "distro": "noble", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "1d78d4d1031e7d91be1c93c236e706eec35aaf51368fec14cb62a21800a9d803", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" }, { "r": "4.5.3", "os": "mac", "version": "1.0", "date": "2026-06-02T19:05:05.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "63c907413238d9b7854eb863da1cd8df231f8dda5b23f7a2f0b00c1f3d4a55ed", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" }, { "r": "4.6.0", "os": "mac", "version": "1.0", "date": "2026-06-02T19:04:41.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "a88d341320450d386a3ec1fac3d7829f6077bf7b4abbc8cf51c00a2773212802", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" }, { "r": "4.6.0", "os": "wasm", "version": "1.0", "date": "2026-06-02T19:05:06.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "470638f171131634bb9ecc76d1ff034ecab1df2cb88a8d3aaadcfe4197bfedff", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" }, { "r": "4.7.0", "os": "win", "version": "1.0", "date": "2026-06-02T19:04:28.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "6bca738c3612188d681994194d02335b669499b792354c49d2b7a13b084b3459", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" }, { "r": "4.5.3", "os": "win", "version": "1.0", "date": "2026-06-02T19:04:12.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "44d88c982ad1baf38bfef4a448f6674522db36a91b1a48c399d0ade15a2bcc1b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" }, { "r": "4.6.0", "os": "win", "version": "1.0", "date": "2026-06-02T19:04:39.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "a2c8d74e9a805a1962ceaf38afaa65b738db3c8bf62090ff2e82f5bf2c5eadc6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841487298" } ] }