{ "_id": "69903bfb5fcc687c950da2c4", "Package": "treestartr", "Type": "Package", "Title": "Generate Starting Trees For Combined Molecular, Morphological\nand Stratigraphic Data", "Version": "0.1.0", "Authors@R": "person(\"April\", \"Wright\", role = c(\"aut\", \"cre\"),\nemail = \"april.wright@selu.edu\")", "Description": "Combine a list of taxa with a phylogeny to generate a\nstarting tree for use in total evidence dating analyses.", "URL": "https://docs.ropensci.org/treestartr/", "BugReports": "https://github.com/ropensci/treeStartR/issues", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "6.1.0", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2019-12-05 19:03:31 UTC", "RemoteUrl": "https://github.com/ropensci/treestartr", "RemoteRef": "master", "RemoteSha": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-02-14 09:07:11 UTC", "User": "root" }, "Author": "April Wright [aut, cre]", "Maintainer": "April Wright ", "MD5sum": "9fdc6cc22524576dd1686a6339c83918", "_user": "ropensci", "_type": "src", "_file": "treestartr_0.1.0.tar.gz", "_fileid": "a9e0edfd59f28d047e6cdb6976c44de362bd0647f56564051ca4e49ba56b5926", "_filesize": 132644, "_sha256": "a9e0edfd59f28d047e6cdb6976c44de362bd0647f56564051ca4e49ba56b5926", "_created": "2026-02-14T09:07:11.000Z", "_published": "2026-02-14T09:10:19.317Z", "_distro": "noble", "_jobs": [ { "job": 63614697291, "time": 141, "config": "linux-devel-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "5510171747" }, { "job": 63614697299, "time": 142, "config": "linux-release-x86_64", "r": "4.5.2", "check": "NOTE", "artifact": "5510171800" }, { "job": 63614697305, "time": 93, "config": "macos-devel-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "5510168489" }, { "job": 63614697298, "time": 117, "config": "macos-release-arm64", "r": "4.5.2", "check": "NOTE", "artifact": "5510170063" }, { "job": 63614594042, "time": 147, "config": "pkgdown", "r": "4.5.2", "check": "OK", "artifact": "5510160051" }, { "job": 63614594053, "time": 178, "config": "source", "r": "4.5.2", "check": "OK", "artifact": "5510162186" }, { "job": 63614697286, "time": 108, "config": "wasm-release", "r": "4.5.1", "check": "OK", "artifact": "5510169384" }, { "job": 63614697315, "time": 91, "config": "windows-devel", "r": "4.6.0", "check": "NOTE", "artifact": "5510168373" }, { "job": 63614697294, "time": 91, "config": "windows-oldrel", "r": "4.4.3", "check": "NOTE", "artifact": "5510168418" }, { "job": 63614697303, "time": 90, "config": "windows-release", "r": "4.5.2", "check": "NOTE", "artifact": "5510168356" } ], "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ropensci/treestartr", "_commit": { "id": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "author": "Jeroen Ooms ", "committer": "Jeroen Ooms ", "message": "Update docs url\n", "time": 1575572611 }, "_maintainer": { "name": "April Wright", "email": "april.wright@selu.edu", "login": "wrightaprilm", "uuid": 1715446 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "phytools", "version": ">= 0.6-4", "role": "Depends" }, { "package": "ape", "version": ">= 5.0", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "ropensci", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 9, "_contributors": [ { "user": "wrightaprilm", "count": 89, "uuid": 1715446 }, { "user": "jeroen", "count": 1, "uuid": 216319 } ], "_userbio": { "uuid": 1200269, "type": "organization", "name": "rOpenSci", "description": "Tools and R Packages for Open Science" }, "_downloads": { "count": 157, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/treestartr" }, "_devurl": "https://github.com/ropensci/treestartr", "_pkgdown": "https://docs.ropensci.org/treestartr/", "_searchresults": 18, "_metadata": { "review": { "id": 239, "status": "reviewed", "version": "0.1.0", "organization": "rOpenSci Software Review", "url": "https://github.com/ropensci/software-review/issues/239" }, "ropensci_category": "data-extraction" }, "_rbuild": "4.5.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/treestartr.html", "manual.pdf" ], "_homeurl": "https://github.com/ropensci/treestartr", "_realowner": "ropensci", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2019-01-09" } ], "_exports": [ "absent_tippr", "dataf_parsr", "echo_rb", "echo_subtree", "genera_strippr", "present_tippr", "rand_absent_tippr", "text_placr" ], "_datasets": [ { "name": "absent_list", "title": "bears", "object": "bears", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "bears", "title": "bears", "object": "bears", "class": [ "data.frame" ], "fields": [ "taxon", "age" ], "rows": 22, "table": true, "tojson": true }, { "name": "mrca_df", "title": "bears", "object": "bears", "class": [ "data.frame" ], "fields": [ "taxon", "clade" ], "rows": 5, "table": true, "tojson": true }, { "name": "tax_frame", "title": "bears", "object": "bears", "class": [ "data.frame" ], "fields": [ "taxon", "age" ], "rows": 22, "table": true, "tojson": true }, { "name": "tree", "title": "bears", "object": "bears", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "absent_tippR", "title": "Add tips to tree via user input", "topics": [ "absent_tippr" ] }, { "page": "bears", "title": "bears", "topics": [ "absent_list", "bears", "mrca_df", "tax_frame", "tree" ] }, { "page": "dataf_parsR", "title": "Detect file format of taxon file", "topics": [ "dataf_parsr" ] }, { "page": "echo_rb", "title": "Print RevBayes-formatted clade constriants.", "topics": [ "echo_rb" ] }, { "page": "echo_subtree", "title": "Print subtrees with tips added.", "topics": [ "echo_subtree" ] }, { "page": "fileFormat", "title": "Utility function to check if file is a csv or tsv.", "topics": [ "fileformat" ] }, { "page": "genera_strippR", "title": "Check if tip is on tree", "topics": [ "genera_strippr" ] }, { "page": "get_found", "title": "Get dataframe of tips that do not have congeners on tree.", "topics": [ "get_found" ] }, { "page": "get_lost", "title": "Determine if a tip is present on a tree", "topics": [ "get_lost" ] }, { "page": "make_absentdf", "title": "Determine which tips are not on the tree, and get their genera.", "topics": [ "make_absentdf" ] }, { "page": "make_treedf", "title": "Determine which tips are on the tree, and get their genera.", "topics": [ "make_treedf" ] }, { "page": "present_tippR", "title": "Add tips to the tree based on taxonomy.", "topics": [ "present_tippr" ] }, { "page": "rand_absent_tippR", "title": "Random addition of taxa", "topics": [ "rand_absent_tippr" ] }, { "page": "taxon_testr", "title": "Utility function to check taxon_names in parsed data file", "topics": [ "taxon_testr" ] }, { "page": "text_placR", "title": "Add tips to tree via taxon list", "topics": [ "text_placr" ] }, { "page": "treestartr", "title": "treestartr: A package for generating reasonable starting trees for phylogenetic analysis.", "topics": [ "treestartr-package", "treestartr" ] } ], "_readme": "https://github.com/ropensci/treestartr/raw/master/README.md", "_rundeps": [ "ape", "cli", "clusterGeneration", "coda", "codetools", "combinat", "cpp11", "DEoptim", "digest", "doParallel", "expm", "fastmatch", "foreach", "generics", "glue", "igraph", "iterators", "lattice", "lifecycle", "magrittr", "maps", "MASS", "Matrix", "mnormt", "nlme", "numDeriv", "optimParallel", "phangorn", "phytools", "pkgconfig", "quadprog", "Rcpp", "rlang", "scatterplot3d", "vctrs" ], "_score": 3.9084850188786495, "_indexed": true, "_nocasepkg": "treestartr", "_universes": [ "ropensci", "wrightaprilm" ], "_binaries": [ { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-02-14T09:09:15.000Z", "distro": "noble", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "ff866419e457bc05b4f59ec6c4cfe0b0aae43350197e1226607154bc50bb5041", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" }, { "r": "4.5.2", "os": "linux", "version": "0.1.0", "date": "2026-02-14T09:09:17.000Z", "distro": "noble", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "e325b8953a763e25f8973aeafa229a5dcb65978532afe34b8ca03d4cb6624c27", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" }, { "r": "4.6.0", "os": "mac", "version": "0.1.0", "date": "2026-02-14T09:08:41.000Z", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "110d82c6129b551365758aa7b7e1aefb3a4471012ace493ca00bd512395f5208", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" }, { "r": "4.5.2", "os": "mac", "version": "0.1.0", "date": "2026-02-14T09:09:02.000Z", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "de13506a8f8b41088b9a33433ebdd9fd3b377415d77fad53f7f715f2861eec38", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" }, { "r": "4.5.1", "os": "wasm", "version": "0.1.0", "date": "2026-02-14T09:09:16.000Z", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "71f8aff9621c1cdcbe37781dc2fb5762293a7822a99bf174ffe1c5693acfa2c9", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" }, { "r": "4.6.0", "os": "win", "version": "0.1.0", "date": "2026-02-14T09:08:24.000Z", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "cbbf87fd30396a22118df0631dc9733caf561cfd2c4130c6ce5176b09fbf272e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" }, { "r": "4.4.3", "os": "win", "version": "0.1.0", "date": "2026-02-14T09:08:25.000Z", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "997c04c6c80516cdcffb932098e8db263c4a5b9b85f3747578c70179760ed36c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" }, { "r": "4.5.2", "os": "win", "version": "0.1.0", "date": "2026-02-14T09:08:24.000Z", "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b", "fileid": "74a83c9b9f8197e019896f11400655ef247dbb00b39ab3394d81467337bed0de", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014704045" } ] }