{ "_id": "6a4791d08b9f0d9747cf1e7a", "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": "2026-07-02 09:42:34 UTC", "User": "root" }, "_user": "phylotastic", "_type": "src", "_file": "closesamples_1.0.tar.gz", "_fileid": "https://r2.ropensci.org/cb1cc034a00b296bf5487d1fecd076763d173f556cc991fd5b076406f306ef89", "_filesize": 106916, "_sha256": "cb1cc034a00b296bf5487d1fecd076763d173f556cc991fd5b076406f306ef89", "_expires": "2026-10-11T10:41:19.000Z", "_created": "2026-07-02T09:42:34.000Z", "_published": "2026-07-03T10:41:20.275Z", "_jobs": [ { "job": 84982756850, "time": 164, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8034892149" }, { "job": 84982756541, "time": 149, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8034886728" }, { "job": 84982756646, "time": 97, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8034865879" }, { "job": 84982756615, "time": 128, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8034878735" }, { "job": 84982756179, "time": 205, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8034827946" }, { "job": 84982756598, "time": 167, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8034893479" }, { "job": 84982756252, "time": 98, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8034866782" }, { "job": 84982756561, "time": 90, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "8034863664" }, { "job": 84982756792, "time": 101, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8034867921" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266", "_status": "success", "_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 }, "_distro": "resolute", "_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", "followers": 5 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/closesamples" }, "_devurl": "https://github.com/bomeara/closesamples", "_searchresults": 0, "_rbuild": "4.6.1", "_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", "LICENSE", "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": "2026-07-02T09:45:17.000Z", "distro": "resolute", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/85292220946cf0a11cc152147d8716c456182b93adf2c53c131017aab3927482", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" }, { "r": "4.6.1", "os": "linux", "version": "1.0", "date": "2026-07-02T09:45:04.000Z", "distro": "resolute", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/dc56ba29d74e22360d4d11cf101bba424b103e162c697d4306c9e1da0b0fc97e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" }, { "r": "4.5.3", "os": "mac", "version": "1.0", "date": "2026-07-02T09:44:12.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/901741eefc5a13f25679148dea770487afd018f59c822d9badb4b8ca5d969dcc", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" }, { "r": "4.6.1", "os": "mac", "version": "1.0", "date": "2026-07-02T09:44:39.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/23913ff8ef8a7f4a9ebb84f17f8b1f0562fc6851b016d0cac07cd507171398ef", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" }, { "r": "4.6.0", "os": "wasm", "version": "1.0", "date": "2026-07-02T09:45:35.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/015cc75dbc04b42d87c7a41b740373c04d4f0d42d656180d46bfb1125d6458b1", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" }, { "r": "4.7.0", "os": "win", "version": "1.0", "date": "2026-07-02T09:44:06.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/d6fe53b2c71805d4372f219cd4fcc62aba4602ddeda7af5f4dbf7b82b80e20c0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" }, { "r": "4.5.3", "os": "win", "version": "1.0", "date": "2026-07-02T09:44:01.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/c868605f5b1e2ffb4f555add781fcc17fb68c068f0401b9a2f8563fd69454809", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" }, { "r": "4.6.1", "os": "win", "version": "1.0", "date": "2026-07-02T09:44:12.000Z", "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30", "fileid": "https://r2.ropensci.org/91e9395dd6edd19b29a9f18de723b9f80c4b032fc2118bc9d8f7f50f54551f29", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28580443266" } ] }