{ "_id": "6a181604acfb0bcc41daf75b", "Package": "TreeDimensionTest", "Type": "Package", "Title": "Trajectory Presence and Heterogeneity in Multivariate Data", "Version": "0.0.2", "Date": "2022-03-11", "Authors@R": "c(\nperson(\"Lovemore\", \"Tenha\", , \"ltenha@nmsu.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-9705-2023\")),\nperson(\"Joe\", \"Song\", , \"joemsong@cs.nmsu.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6883-6547\"))\n)", "Author": "Lovemore Tenha [aut] (),\nJoe Song [aut, cre] ()", "Maintainer": "Joe Song ", "Description": "Testing for trajectory presence and heterogeneity on\nmultivariate data. Two statistical methods (Tenha & Song 2022)\n are implemented. The tree\ndimension test quantifies the statistical evidence for\ntrajectory presence. The subset specificity measure summarizes\npattern heterogeneity using the minimum subtree cover. There is\nno user tunable parameters for either method. Examples are\nincluded to illustrate how to use the methods on single-cell\ndata for studying gene and pathway expression dynamics and\npathway expression specificity.", "License": "LGPL (>= 3)", "RoxygenNote": "7.1.2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "RdMacros": "Rdpack", "Packaged": { "Date": "2026-05-28 10:11:56 UTC", "User": "root" }, "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://joemsong.r-universe.dev", "Date/Publication": "2022-03-12 09:30:07 UTC", "RemoteUrl": "https://github.com/cran/TreeDimensionTest", "RemoteRef": "HEAD", "RemoteSha": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "MD5sum": "5fb77db372157d37fb5881bf2030f3de", "_user": "joemsong", "_type": "src", "_file": "TreeDimensionTest_0.0.2.tar.gz", "_fileid": "fea0bca882c6a7c0aa623cc4236de080ed17e9b80f00cb0c008ef5ef4487b3d9", "_filesize": 2232663, "_sha256": "fea0bca882c6a7c0aa623cc4236de080ed17e9b80f00cb0c008ef5ef4487b3d9", "_created": "2026-05-28T10:11:56.000Z", "_published": "2026-05-28T10:16:36.390Z", "_distro": "noble", "_jobs": [ { "job": 78269387151, "time": 189, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7263304208" }, { "job": 78269387092, "time": 150, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7263292191" }, { "job": 78269387071, "time": 162, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7263295226" }, { "job": 78269387147, "time": 178, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7263300464" }, { "job": 78269387109, "time": 161, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7263294493" }, { "job": 78269387099, "time": 194, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7263306101" }, { "job": 78269387169, "time": 198, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7263306924" }, { "job": 78269387139, "time": 233, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7263318634" }, { "job": 78268894174, "time": 188, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7263245571" }, { "job": 78269386979, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7263282923" }, { "job": 78269387078, "time": 130, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7263285378" }, { "job": 78269387155, "time": 204, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7263310090" }, { "job": 78269387088, "time": 119, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7263282264" } ], "_buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/TreeDimensionTest", "_commit": { "id": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "author": "Joe Song ", "committer": "cran-robot ", "message": "version 0.0.2\n", "time": 1647077407 }, "_maintainer": { "name": "Joe Song", "email": "joemsong@cs.nmsu.edu", "login": "joemsong", "description": "", "uuid": 28720910, "orcid": "0000-0002-6883-6547" }, "_registered": true, "_dependencies": [ { "package": "mlpack", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "fitdistrplus", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "nFactors", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.2", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "Rdpack", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "joemsong", "count": 2, "uuid": 28720910 } ], "_userbio": { "uuid": 28720910, "type": "user", "name": "The Song Lab" }, "_downloads": { "count": 159, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TreeDimensionTest" }, "_searchresults": 1, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/TreeDimensionTest.html", "manual.pdf" ], "_realowner": "joemsong", "_cranurl": false, "_releases": [ { "version": "0.0.1", "date": "2022-01-20" }, { "version": "0.0.2", "date": "2022-03-12" } ], "_exports": [ "compute.stats", "empirical.distributions", "separability", "test.trajectory" ], "_help": [ { "page": "compute.stats", "title": "Tree Dimension Test Related Statistics", "topics": [ "compute.stats" ] }, { "page": "empirical.distributions", "title": "Empirical Null Distribution of Tree Dimension Test", "topics": [ "empirical.distributions" ] }, { "page": "plot.test", "title": "Visualizing Euclidean Minimum Spanning Trees", "topics": [ "plot.treedim" ] }, { "page": "separability", "title": "Separability of Labeled Data Points", "topics": [ "separability" ] }, { "page": "test.trajectory", "title": "Tree Dimension Test", "topics": [ "test.trajectory" ] } ], "_readme": "https://github.com/cran/TreeDimensionTest/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "fitdistrplus", "glue", "GPArotation", "igraph", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "mlpack", "mnormt", "nFactors", "nlme", "pkgconfig", "psych", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEnsmallen", "Rdpack", "rlang", "survival", "vctrs" ], "_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": "Tutorial.Rmd", "filename": "Tutorial.html", "title": "Tutorial: Using the 'TreeDimensionTest' package", "engine": "knitr::rmarkdown", "headings": [ "1. Testing trajectory presence", "Example 1.1 Simulated single-cell data with trajectory presence", "Example 1.2 Simulated isotropic data without trajectory presence", "Calculating test statistics without $p$-value", "2. Measuring data subset homogeneity by separability", "Example 2.1 Homogeneous data with low separability", "Example 2.2 Heterogeneous data with high separability", "3. Understanding tissue specificity of pathway gene expression dynamics via separability", "Example 3.1 Tissue specificity of the calcium signaling pathway during development", "Example 3.2 Tissue specificity of the ribosome pathway during development", "References" ], "created": "2022-01-20 07:52:44", "modified": "2022-03-12 09:30:07", "commits": 2 } ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "treedimensiontest", "_universes": [ "joemsong" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.2", "date": "2026-05-28T10:15:01.000Z", "distro": "noble", "arch": "aarch64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "6397f5dac44b5f62b32d414d2f898c55508d172cb34fd1ed438c97a37bc9e910", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.7.0", "os": "linux", "version": "0.0.2", "date": "2026-05-28T10:14:17.000Z", "distro": "noble", "arch": "x86_64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "578a3dd2f5f90bba5c110c2c3364b67770296dd11408b4421a2711c550bfd226", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.6.0", "os": "linux", "version": "0.0.2", "date": "2026-05-28T10:14:31.000Z", "distro": "noble", "arch": "aarch64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "990d88cb8410953fa8b5f166d5c082c301e256ff6bd918936a943c5a6c9c8628", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.6.0", "os": "linux", "version": "0.0.2", "date": "2026-05-28T10:14:40.000Z", "distro": "noble", "arch": "x86_64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "9991576ea373bcf294f5ae9af02df9d15ec31f4c347d5abd65f2377909092f0a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.5.3", "os": "mac", "version": "0.0.2", "date": "2026-05-28T10:13:59.000Z", "arch": "aarch64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "ffe50a4039c1713cc6bb9ea229e27b6d69ec4ee1ac3a87d963060b48daeabdad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.5.3", "os": "mac", "version": "0.0.2", "date": "2026-05-28T10:14:39.000Z", "arch": "x86_64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "a970d1d59939aee9c0159cebb512584d2eb325d76213430ab549bf5c5cd78bcb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.6.0", "os": "mac", "version": "0.0.2", "date": "2026-05-28T10:14:33.000Z", "arch": "aarch64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "9a47e7d7ec0e3f6257f90085e4d766fd5c68ca8c17c5a667c1cb8fe25e51e637", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.6.0", "os": "mac", "version": "0.0.2", "date": "2026-05-28T10:15:16.000Z", "arch": "x86_64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "52091c017981715a3512208c07f684e18512a402590069eca82595badaaa9555", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.2", "date": "2026-05-28T10:14:18.000Z", "arch": "emscripten", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "be0754253357d4e65f48568719c86066734309742f2756b747fc08610d92072c", "status": "success", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.7.0", "os": "win", "version": "0.0.2", "date": "2026-05-28T10:13:33.000Z", "arch": "x86_64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "1555b73c1b7ae4f2743a325e7d435d2e657b4e8ac087e3aad7de7ce434ead61b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.5.3", "os": "win", "version": "0.0.2", "date": "2026-05-28T10:13:48.000Z", "arch": "x86_64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "f4277ec1aeb39b8b8ee2b402cf5876e7b9130e8f2844572bbf7ac18e36c2c6d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" }, { "r": "4.6.0", "os": "win", "version": "0.0.2", "date": "2026-05-28T10:13:20.000Z", "arch": "x86_64", "commit": "92d770f047a0d4f98dc5bf71a2d63a14e163be6e", "fileid": "9384af904595cfb5ee903330fd3e369d3fa0b83223a78a137e4d8cefa10b5c1f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26568381732" } ] }