{ "_id": "6a1ed89cb401979e7340f164", "Package": "treestructure", "Type": "Package", "Title": "Detect Population Structure Within Phylogenetic Trees", "Version": "0.7.0", "Date": "2025-09-24", "Authors@R": "c(person(given = \"Erik\",\nfamily = \"Volz\",\nrole = c(\"aut\", \"cre\"),\nemail = \"erik.volz@gmail.com\",\ncomment = c(ORCID = \"0000-0001-6268-8937\")),\nperson(given = \"Fabricia\",\nfamily = \"F. Nascimento\",\nemail = \"thednainus@yahoo.com\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9426-6835\")),\nperson(given = \"Vinicius\",\nfamily = \"B. Franceschi\",\nemail = \"vinibfranc@gmail.com\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-0006-9337\")))", "Description": "Algorithms for detecting population structure from the\nhistory of coalescent events recorded in phylogenetic trees.\nThis method classifies each tip and internal node of a tree\ninto disjoint sets characterized by similar coalescent\npatterns.", "License": "GPL (>= 2)", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "URL": "https://emvolz-phylodynamics.github.io/treestructure/,\nhttps://github.com/emvolz-phylodynamics/treestructure", "BugReports": "https://github.com/emvolz-phylodynamics/treestructure/issues", "Repository": "https://emvolz-phylodynamics.r-universe.dev", "Date/Publication": "2026-03-20 10:55:02 UTC", "RemoteUrl": "https://github.com/emvolz-phylodynamics/treestructure", "RemoteRef": "HEAD", "RemoteSha": "d90629b5585a910a7e7aaa91686a195428290482", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-20 09:40:33 UTC", "User": "root" }, "Author": "Erik Volz [aut, cre] (ORCID: ),\nFabricia F. Nascimento [ctb] (ORCID:\n),\nVinicius B. Franceschi [ctb] (ORCID:\n)", "Maintainer": "Erik Volz ", "MD5sum": "55e434a04dd59cf809947f5c9054de07", "_user": "emvolz-phylodynamics", "_type": "src", "_file": "treestructure_0.7.0.tar.gz", "_fileid": "dcfcc363d960d538d93cb32a87e337643c2ef84261573c6d50ff0655075441e0", "_filesize": 2441017, "_sha256": "dcfcc363d960d538d93cb32a87e337643c2ef84261573c6d50ff0655075441e0", "_created": "2026-05-20T09:40:33.000Z", "_published": "2026-06-02T13:20:28.522Z", "_distro": "noble", "_jobs": [ { "job": 79080030575, "time": 132, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7106576980" }, { "job": 79080030859, "time": 143, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7106580321" }, { "job": 79080030706, "time": 126, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7106574620" }, { "job": 79080030450, "time": 115, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7106570791" }, { "job": 79080031127, "time": 156, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7106576223" }, { "job": 79080030807, "time": 227, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7106603169" }, { "job": 79080030441, "time": 186, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7106582513" }, { "job": 79080030599, "time": 298, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7106626122" }, { "job": 79080030067, "time": 243, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7106529162" }, { "job": 79080029346, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7358814338" }, { "job": 79080030596, "time": 117, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7106571514" }, { "job": 79080030477, "time": 88, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7106561680" }, { "job": 79080030962, "time": 115, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7106571029" } ], "_buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/emvolz-phylodynamics/treestructure", "_commit": { "id": "d90629b5585a910a7e7aaa91686a195428290482", "author": "Fabricia Nascimento ", "committer": "Fabricia Nascimento ", "message": "fixed typo in vingnette and updated gitignore file\n", "time": 1774004102 }, "_maintainer": { "name": "Erik Volz", "email": "erik.volz@gmail.com", "login": "emvolz", "description": "Department of Infectious Disease Epidemiology, Imperial College London\n\n", "uuid": 15171743, "orcid": "0000-0001-6268-8937" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "ape", "version": ">= 5.0", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "ggtree", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "getopt", "role": "Suggests" }, { "package": "bookdown", "role": "Suggests" }, { "package": "phangorn", "role": "Suggests" }, { "package": "treeio", "role": "Suggests" } ], "_owner": "emvolz-phylodynamics", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 2 }, { "week": "2025-25", "n": 1 }, { "week": "2025-39", "n": 18 }, { "week": "2026-12", "n": 2 } ], "_tags": [], "_stars": 20, "_contributors": [ { "user": "emvolz", "count": 68, "uuid": 15171743 }, { "user": "vinibfranc", "count": 4, "uuid": 20503431 }, { "user": "ostirrup", "count": 1, "uuid": 7620537 } ], "_userbio": { "uuid": 15171763, "type": "organization", "name": "Erik Volz" }, "_downloads": { "count": 214, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/treestructure" }, "_devurl": "https://github.com/emvolz-phylodynamics/treestructure", "_pkgdown": "https://emvolz-phylodynamics.github.io/treestructure/", "_searchresults": 13, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/treestructure.html", "manual.pdf" ], "_homeurl": "https://github.com/emvolz-phylodynamics/treestructure", "_realowner": "emvolz-phylodynamics", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2020-02-17" }, { "version": "0.7.0", "date": "2025-09-27" } ], "_exports": [ "addtips", "treestructure.test", "trestruct" ], "_help": [ { "page": "addtips", "title": "Compare and add tips into new treestructure object", "topics": [ "addtips" ] }, { "page": "plot.TreeStructure", "title": "Plot TreeStructure tree with cluster and partition variables", "topics": [ "plot.TreeStructure" ] }, { "page": "treestructure.test", "title": "Test treestructure hypothesis", "topics": [ "treestructure.test" ] }, { "page": "trestruct", "title": "Detect cryptic population structure in time trees", "topics": [ "trestruct" ] } ], "_readme": "https://github.com/emvolz-phylodynamics/treestructure/raw/HEAD/README.md", "_rundeps": [ "ape", "digest", "lattice", "nlme", "Rcpp", "rlang" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "supportValues.Rmd", "filename": "supportValues.html", "title": "Node support values using treestructure", "author": "Vinicius Franceschi and Fabricia F. Nascimento", "engine": "knitr::rmarkdown", "headings": [ "Introductions", "Assign clusters without using node support", "Assign clusters using branch support", "Using the CH-index", "Final considerations", "References" ], "created": "2025-09-23 13:06:53", "modified": "2026-03-20 10:55:02", "commits": 5 }, { "source": "treestructure.Rmd", "filename": "treestructure.html", "title": "treestructure applied to structured coalescent simulation", "author": "Erik Volz", "engine": "knitr::rmarkdown", "headings": [ "Structured coalescent simulation", "Plotting results", "Parameter choice and number of clusters", "CH index" ], "created": "2025-03-28 14:14:51", "modified": "2026-03-19 09:51:55", "commits": 7 }, { "source": "updating_treestructure.Rmd", "filename": "updating_treestructure.html", "title": "Update of a treestructure object with new sequences", "author": "Vinicius Franceschi and Fabricia F Nascimento", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Assign clusters using node support", "Update a previous treestrucuture object with new sequences" ], "created": "2025-09-23 13:06:53", "modified": "2026-03-19 09:51:55", "commits": 4 } ], "_score": 6.494154594018443, "_indexed": true, "_nocasepkg": "treestructure", "_universes": [ "emvolz-phylodynamics", "emvolz" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.7.0", "date": "2026-05-20T09:42:49.000Z", "distro": "noble", "arch": "aarch64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "a4b1f69ad421daa92546bfa51ee36e7a551e0290134052dc94b971015aecba69", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.7.0", "os": "linux", "version": "0.7.0", "date": "2026-05-20T09:42:54.000Z", "distro": "noble", "arch": "x86_64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "4b33339546dcb269512f1e56228369279ae778c2ad8483646056aaf518267355", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.6.0", "os": "linux", "version": "0.7.0", "date": "2026-05-20T09:42:42.000Z", "distro": "noble", "arch": "aarch64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "a3b2f025332774d6441898ad265b599758ed33e70640bf038ad2e934140f48d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.6.0", "os": "linux", "version": "0.7.0", "date": "2026-05-20T09:42:29.000Z", "distro": "noble", "arch": "x86_64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "5b365ad341e648f6f2dc836b480a409e259ac7575ce093015a3422e8790a4205", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.5.3", "os": "mac", "version": "0.7.0", "date": "2026-05-20T09:42:48.000Z", "arch": "aarch64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "0bd53066cc3d58f4774884ca98478cef6e63ab811f5a92bfeb36bf7ff6ba20fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.5.3", "os": "mac", "version": "0.7.0", "date": "2026-05-20T09:43:48.000Z", "arch": "x86_64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "d1e2f6aff3cca284dfe06c9d80d089267893dbd1179b1b5c73aa0a98200dd2b4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.6.0", "os": "mac", "version": "0.7.0", "date": "2026-05-20T09:42:57.000Z", "arch": "aarch64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "71bfa847bb687407daa6a4299444caea9c0080536fc4ecfa7b3d833003d31dcd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.6.0", "os": "mac", "version": "0.7.0", "date": "2026-05-20T09:44:37.000Z", "arch": "x86_64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "52c695cb7df1a213857b3e8ff31760943eaec80c7c303aeee6903df3543e7fb7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.7.0", "os": "win", "version": "0.7.0", "date": "2026-05-20T09:42:08.000Z", "arch": "x86_64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "e1e1c55a6897430e2f2b51be6120056f2901a07c01af95a6d5fd6acecbf371fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.5.3", "os": "win", "version": "0.7.0", "date": "2026-05-20T09:41:45.000Z", "arch": "x86_64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "8225d3725417157030aeede71b95ea5db61e10d504376bd582d6bcac66ccb164", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.6.0", "os": "win", "version": "0.7.0", "date": "2026-05-20T09:41:58.000Z", "arch": "x86_64", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "861a88447fbe0e9aa6900d3c4a3c0b2f408b2d255f1848f7be14f621af4c80d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" }, { "r": "4.6.0", "os": "wasm", "version": "0.7.0", "date": "2026-06-02T13:19:38.000Z", "arch": "emscripten", "commit": "d90629b5585a910a7e7aaa91686a195428290482", "fileid": "4bf7fc8e5c4cbec547c1031d2ff334c3ea4ec1b399a69826ab40796a2a3ec05f", "status": "success", "buildurl": "https://github.com/r-universe/emvolz-phylodynamics/actions/runs/26154215906" } ] }