{ "_id": "6a1f36e7b401979e73428a4a", "Package": "opticskxi", "Title": "OPTICS K-Xi Density-Based Clustering", "Version": "1.2.1", "Authors@R": "person(\"Thomas\", \"Charlon\", role = c(\"aut\", \"cre\"), email = \"charlon@protonmail.com\", comment = c(ORCID = \"0000-0001-7497-0470\"))", "Description": "Density-based clustering methods are well adapted to the\nclustering of high-dimensional data and enable the discovery of\ncore groups of various shapes despite large amounts of noise.\nThis package provides a novel density-based cluster extraction\nmethod, OPTICS k-Xi, and a framework to compare k-Xi models\nusing distance-based metrics to investigate datasets with\nunknown number of clusters. The vignette first introduces\ndensity-based algorithms with simulated datasets, then presents\nand evaluates the k-Xi cluster extraction method. Finally, the\nmodels comparison framework is described and experimented on 2\ngenetic datasets to identify groups and their discriminating\nfeatures. The k-Xi algorithm is a novel OPTICS cluster\nextraction method that specifies directly the number of\nclusters and does not require fine-tuning of the steepness\nparameter as the OPTICS Xi method. Combined with a framework\nthat compares models with varying parameters, the OPTICS k-Xi\nmethod can identify groups in noisy datasets with unknown\nnumber of clusters. Results on summarized genetic data of 1,200\npatients are in Charlon T. (2019)\n. A short video\ntutorial can be found at\n.", "VignetteBuilder": "knitr", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "URL": "https://gitlab.com/thomaschln/opticskxi", "BugReports": "https://gitlab.com/thomaschln/opticskxi/-/issues", "Repository": "https://thomaschln.r-universe.dev", "Date/Publication": "2025-04-23 18:16:28 UTC", "RemoteUrl": "https://gitlab.com/thomaschln/opticskxi", "RemoteRef": "HEAD", "RemoteSha": "fd3d5603166eef11a6e32527d45f16328a844c92", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 06:05:39 UTC", "User": "root" }, "Author": "Thomas Charlon [aut, cre] (ORCID:\n)", "Maintainer": "Thomas Charlon ", "MD5sum": "afa98c1bcd3199403d1a6988b3896377", "_user": "thomaschln", "_type": "src", "_file": "opticskxi_1.2.1.tar.gz", "_fileid": "83cc51999df2d3812d77575b157d9a5b515326f6e26d779f64720b9101537170", "_filesize": 3061001, "_sha256": "83cc51999df2d3812d77575b157d9a5b515326f6e26d779f64720b9101537170", "_created": "2026-05-15T06:05:39.000Z", "_published": "2026-06-02T20:02:47.448Z", "_distro": "noble", "_jobs": [ { "job": 79160814333, "time": 170, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7011159419" }, { "job": 79160814112, "time": 164, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7011158019" }, { "job": 79160811971, "time": 158, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7011226480" }, { "job": 79160813805, "time": 141, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7011214835" }, { "job": 79160811187, "time": 219, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7011125234" }, { "job": 79160811218, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7368475397" }, { "job": 79160813437, "time": 140, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7011153011" }, { "job": 79160813520, "time": 130, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7011150966" }, { "job": 79160813620, "time": 135, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7011152047" } ], "_buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://gitlab.com/thomaschln/opticskxi", "_commit": { "id": "fd3d5603166eef11a6e32527d45f16328a844c92", "author": "Thomas Charlon ", "committer": "Thomas Charlon ", "message": "up\n", "time": 1745432188 }, "_maintainer": { "name": "Thomas Charlon", "email": "charlon@protonmail.com", "login": "thomaschln", "linkedin": "in/thomas-charlon-meng-phd-aba0a3275", "orcid": "0000-0001-7497-0470", "uuid": 2394508 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "amap", "role": "Suggests" }, { "package": "dbscan", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "fastICA", "role": "Suggests" }, { "package": "fpc", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "grDevices", "role": "Suggests" }, { "package": "gtable", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "plyr", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "gitlab-thomaschln", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_userbio": { "uuid": 2394508, "type": "user", "name": "Thomas Charlon", "description": "Harvard Medical School Researcher\r\nBiomedical Informatics @hms-dbmi\r\nCELEHS laboratory @CELEHS" }, "_downloads": { "count": 620, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/opticskxi" }, "_devurl": "https://gitlab.com/thomaschln/opticskxi", "_searchresults": 2, "_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/opticskxi.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://gitlab.com/thomaschln/opticskxi", "_realowner": "thomaschln", "_cranurl": true, "_releases": [ { "version": "0.1", "date": "2019-07-19" }, { "version": "1.1.0", "date": "2024-12-09" }, { "version": "1.2.0", "date": "2025-02-26" }, { "version": "1.2.1", "date": "2025-03-09" } ], "_exports": [ "%<>%", "%>%", "%$%", "contingency_table", "cosine_simi", "dist_matrix", "ensemble_metrics", "ensemble_models", "fortify_dimred", "fortify_ica", "fortify_pca", "get_best_kxi", "ggpairs", "ggplot_kxi_metrics", "ggplot_optics", "gtable_kxi_profiles", "nice_palette", "norm_inprod", "normalize", "opticskxi", "opticskxi_pipeline", "print_vignette_table", "residuals_table", "stddev_mean" ], "_datasets": [ { "name": "crohn", "title": "Crohn's disease data", "object": "crohn", "file": "crohn.RData", "class": [ "data.frame" ], "fields": [ "pid", "id", "fid", "mid", "sex", "crohn", "loc1.a1", "loc1.a2", "loc2.a1", "loc2.a2", "loc3.a1", "loc3.a2", "loc4.a1", "loc4.a2", "loc5.a1", "loc5.a2", "loc6.a1", "loc6.a2", "loc7.a1", "loc7.a2", "loc8.a1", "loc8.a2", "loc9.a1", "loc9.a2", "loc10.a1", "loc10.a2", "loc11.a1", "loc11.a2", "loc12.a1", "loc12.a2", "loc13.a1", "loc13.a2", "loc14.a1", "loc14.a2", "loc15.a1", "loc15.a2", "loc16.a1", "loc16.a2", "loc17.a1", "loc17.a2", "loc18.a1", "loc18.a2", "loc19.a1", "loc19.a2", "loc20.a1", "loc20.a2", "loc21.a1", "loc21.a2", "loc22.a1", "loc22.a2", "loc23.a1", "loc23.a2", "loc24.a1", "loc24.a2", "loc25.a1", "loc25.a2", "loc26.a1", "loc26.a2", "loc27.a1", "loc27.a2", "loc28.a1", "loc28.a2", "loc29.a1", "loc29.a2", "loc30.a1", "loc30.a2", "loc31.a1", "loc31.a2", "loc32.a1", "loc32.a2", "loc33.a1", "loc33.a2", "loc34.a1", "loc34.a2", "loc35.a1", "loc35.a2", "loc36.a1", "loc36.a2", "loc37.a1", "loc37.a2", "loc38.a1", "loc38.a2", "loc39.a1", "loc39.a2", "loc40.a1", "loc40.a2", "loc41.a1", "loc41.a2", "loc42.a1", "loc42.a2", "loc43.a1", "loc43.a2", "loc44.a1", "loc44.a2", "loc45.a1", "loc45.a2", "loc46.a1", "loc46.a2", "loc47.a1", "loc47.a2", "loc48.a1", "loc48.a2", "loc49.a1", "loc49.a2", "loc50.a1", "loc50.a2", "loc51.a1", "loc51.a2", "loc52.a1", "loc52.a2", "loc53.a1", "loc53.a2", "loc54.a1", "loc54.a2", "loc55.a1", "loc55.a2", "loc56.a1", "loc56.a2", "loc57.a1", "loc57.a2", "loc58.a1", "loc58.a2", "loc59.a1", "loc59.a2", "loc60.a1", "loc60.a2", "loc61.a1", "loc61.a2", "loc62.a1", "loc62.a2", "loc63.a1", "loc63.a2", "loc64.a1", "loc64.a2", "loc65.a1", "loc65.a2", "loc66.a1", "loc66.a2", "loc67.a1", "loc67.a2", "loc68.a1", "loc68.a2", "loc69.a1", "loc69.a2", "loc70.a1", "loc70.a2", "loc71.a1", "loc71.a2", "loc72.a1", "loc72.a2", "loc73.a1", "loc73.a2", "loc74.a1", "loc74.a2", "loc75.a1", "loc75.a2", "loc76.a1", "loc76.a2", "loc77.a1", "loc77.a2", "loc78.a1", "loc78.a2", "loc79.a1", "loc79.a2", "loc80.a1", "loc80.a2", "loc81.a1", "loc81.a2", "loc82.a1", "loc82.a2", "loc83.a1", "loc83.a2", "loc84.a1", "loc84.a2", "loc85.a1", "loc85.a2", "loc86.a1", "loc86.a2", "loc87.a1", "loc87.a2", "loc88.a1", "loc88.a2", "loc89.a1", "loc89.a2", "loc90.a1", "loc90.a2", "loc91.a1", "loc91.a2", "loc92.a1", "loc92.a2", "loc93.a1", "loc93.a2", "loc94.a1", "loc94.a2", "loc95.a1", "loc95.a2", "loc96.a1", "loc96.a2", "loc97.a1", "loc97.a2", "loc98.a1", "loc98.a2", "loc99.a1", "loc99.a2", "loc100.a1", "loc100.a2", "loc101.a1", "loc101.a2", "loc102.a1", "loc102.a2", "loc103.a1", "loc103.a2" ], "rows": 387, "table": true, "tojson": true }, { "name": "hla", "title": "The HLA data", "object": "hla", "file": "hla.rda", "class": [ "data.frame" ], "fields": [ "id", "y", "DQR.a1", "DQR.a2", "DQA.a1", "DQA.a2", "DQB.a1", "DQB.a2" ], "rows": 271, "table": true, "tojson": true }, { "name": "m_psych_embeds", "title": "A dataset containing the embeddings matrix of psychological related words", "object": "m_psych_embeds", "file": "m_psych_embeds.rda", "class": [ "matrix", "array" ], "fields": {}, "rows": 831, "table": true, "tojson": true }, { "name": "multishapes", "title": "A dataset containing clusters of multiple shapes", "object": "multishapes", "file": "multishapes.rda", "class": [ "data.frame" ], "fields": [ "x", "y", "shape" ], "rows": 1100, "table": true, "tojson": true } ], "_help": [ { "page": "compound", "title": "Assignment pipe", "topics": [ "%<>%" ] }, { "page": "pipe", "title": "Pipe", "topics": [ "%>%" ] }, { "page": "exposition", "title": "Exposition pipe", "topics": [ "%$%" ] }, { "page": "contingency_table", "title": "Contingency table", "topics": [ "contingency_table" ] }, { "page": "cosine_simi", "title": "Cosine similarity between vectors and/or matrices.", "topics": [ "cosine_simi" ] }, { "page": "crohn", "title": "Crohn's disease data", "topics": [ "crohn" ] }, { "page": "dist_matrix", "title": "dist_matrix", "topics": [ "dist_matrix" ] }, { "page": "ensemble_metrics", "title": "Compute ensemble metrics", "topics": [ "ensemble_metrics" ] }, { "page": "ensemble_metrics_bootstrap", "title": "Select models based on ensemble metrics", "topics": [ "ensemble_metrics_bootstrap" ] }, { "page": "ensemble_models", "title": "Select best models based on ensemble metrics", "topics": [ "ensemble_models" ] }, { "page": "fortify_dimred", "title": "Fortify a dimension reduction object", "topics": [ "fortify_dimred" ] }, { "page": "fortify_ica", "title": "Get and fortify ICA", "topics": [ "fortify_ica" ] }, { "page": "fortify_pca", "title": "Get and fortify PCA", "topics": [ "fortify_pca" ] }, { "page": "get_best_kxi", "title": "Get best k-Xi model", "topics": [ "get_best_kxi" ] }, { "page": "ggpairs", "title": "Plot multiple axes of a data frame or a fortified dimension reduction.", "topics": [ "ggpairs" ] }, { "page": "ggplot_kxi_metrics", "title": "Ggplot OPTICS k-Xi metrics", "topics": [ "ggplot_kxi_metrics" ] }, { "page": "ggplot_optics", "title": "Ggplot optics", "topics": [ "ggplot_optics" ] }, { "page": "gtable_kxi_profiles", "title": "Gtable OPTICS k-Xi distance profiles", "topics": [ "gtable_kxi_profiles" ] }, { "page": "hla", "title": "The HLA data", "topics": [ "hla" ] }, { "page": "m_psych_embeds", "title": "A dataset containing the embeddings matrix of psychological related words", "topics": [ "m_psych_embeds" ] }, { "page": "multishapes", "title": "A dataset containing clusters of multiple shapes", "topics": [ "multishapes" ] }, { "page": "nice_palette", "title": "Nice palette", "topics": [ "nice_palette" ] }, { "page": "norm_inprod", "title": "norm_inprod", "topics": [ "norm_inprod" ] }, { "page": "normalize", "title": "Matrix normalization", "topics": [ "normalize" ] }, { "page": "opticskxi", "title": "OPTICS k-Xi clustering algorithm", "topics": [ "opticskxi" ] }, { "page": "opticskxi_pipeline", "title": "OPTICS k-Xi models comparison pipeline", "topics": [ "opticskxi_pipeline" ] }, { "page": "print_vignette_table", "title": "Print vignette table", "topics": [ "print_vignette_table" ] }, { "page": "residuals_table", "title": "Residuals table", "topics": [ "residuals_table" ] }, { "page": "stddev_mean", "title": "stddev_mean", "topics": [ "stddev_mean" ] } ], "_readme": "https://gitlab.com/thomaschln/opticskxi/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "ensemble_metrics.Rnw", "filename": "ensemble_metrics.pdf", "title": "Ensemble Metrics And Models For Density-Based Clustering", "engine": "utils::Sweave", "headings": [], "created": "2025-01-21 02:08:03", "modified": "2025-02-26 20:11:36", "commits": 4 }, { "source": "opticskxi.Rnw", "filename": "opticskxi.pdf", "title": "OPTICS K-Xi Density-Based Clustering", "engine": "utils::Sweave", "headings": [], "created": "2019-07-15 16:09:02", "modified": "2025-03-22 09:42:04", "commits": 3 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "opticskxi", "_universes": [ "thomaschln", "gitlab-thomaschln" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.1", "date": "2026-05-15T06:07:46.000Z", "distro": "noble", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "0885de6b72e32a7cf15163db37ee83926f10d3046e4a31122888c536cd777a73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" }, { "r": "4.6.0", "os": "linux", "version": "1.2.1", "date": "2026-05-15T06:07:42.000Z", "distro": "noble", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "1edd3c9c18bbd7dbe153ac9a163ea1654aa4c84cfc24e2057b06a79cb17f8916", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" }, { "r": "4.5.3", "os": "mac", "version": "1.2.1", "date": "2026-05-15T06:13:25.000Z", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "735b8e4d974cb16847e1e24b753f825ee5dea46c6120dd0d3cc32d68f7a4ce08", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" }, { "r": "4.6.0", "os": "mac", "version": "1.2.1", "date": "2026-05-15T06:12:36.000Z", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "b7b7a703bac3c37de62462451a9d1f00c7610f75f471f4daa729c28a80e078e1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" }, { "r": "4.7.0", "os": "win", "version": "1.2.1", "date": "2026-05-15T06:07:10.000Z", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "1b9b227e89edf543d4627e51f1a1621b086c680b0f2986a13780e9b7f43b4389", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" }, { "r": "4.5.3", "os": "win", "version": "1.2.1", "date": "2026-05-15T06:07:02.000Z", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "b835b524fa6a4d8f4e5343d7f57a634efcfaae19cc517c281e68ff96d5cc4fd8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" }, { "r": "4.6.0", "os": "win", "version": "1.2.1", "date": "2026-05-15T06:06:58.000Z", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "b24a8de77c26ddf642ce1195497ddbcae5c2c2a5121c51943193b54cc533e55d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.1", "date": "2026-06-02T20:02:19.000Z", "commit": "fd3d5603166eef11a6e32527d45f16328a844c92", "fileid": "dfde965d9f42d7fadd79f5a3625415de1e62b17e51bcbe89eea3b107407f66ce", "status": "success", "buildurl": "https://github.com/r-universe/thomaschln/actions/runs/25903048206" } ] }