{ "_id": "6a27ac5724555f66ed534702", "Package": "toscca", "Title": "Thresholded Ordered Sparse CCA", "Version": "1.0", "Authors@R": "person(\"Nuria\", \"Senar\", , \"n.senarvilladeamigo@amsterdamumc.nl\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1004-5785\"))", "Description": "Performs Thresholded Ordered Sparse Canonical Correlation\nAnalysis (CCA). For more details see Senar, N. (2024)\n and Senar, N. et al. (2025)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make", "Repository": "https://nuria-sv.r-universe.dev", "Date/Publication": "2026-04-09 13:40:08 UTC", "RemoteUrl": "https://github.com/nuria-sv/toscca", "RemoteRef": "HEAD", "RemoteSha": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-08 07:29:48 UTC", "User": "root" }, "Author": "Nuria Senar [aut, cre] (ORCID: )", "Maintainer": "Nuria Senar ", "MD5sum": "9dccfc7223da72d74f307be98f751ce9", "_user": "nuria-sv", "_type": "src", "_file": "toscca_1.0.tar.gz", "_fileid": "7c9bc94fa676a68b4cb084dc337c48f5f82f2ee3b582b841dff1c2c7f290e0b5", "_filesize": 772018, "_sha256": "7c9bc94fa676a68b4cb084dc337c48f5f82f2ee3b582b841dff1c2c7f290e0b5", "_created": "2026-06-08T07:29:48.000Z", "_published": "2026-06-09T06:01:59.026Z", "_distro": "noble", "_jobs": [ { "job": 80256709998, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7473976579" }, { "job": 80256710248, "time": 141, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7473975218" }, { "job": 80256710132, "time": 174, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7473978079" }, { "job": 80256709840, "time": 115, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7499671081" }, { "job": 80256709906, "time": 350, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7473933926" }, { "job": 80256709999, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7473970195" }, { "job": 80256710246, "time": 87, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7473959195" }, { "job": 80256710211, "time": 88, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7473960467" }, { "job": 80256710000, "time": 119, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7473969694" } ], "_buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/nuria-sv/toscca", "_commit": { "id": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "author": "Nuria Senar <58103870+nuria-sv@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #24 from nuria-sv/update_pkg\n\nUpdate pkg - version 1.0", "time": 1775742008 }, "_maintainer": { "name": "Nuria Senar", "email": "n.senarvilladeamigo@amsterdamumc.nl", "login": "nuria-sv", "linkedin": "in/nuria-senar-97067917b", "orcid": "0000-0002-1004-5785", "description": "👋 Hi, I'm Nuria, a stats PhD student using penalised methods to integrate high-dimensional datasets. I focus my applications on large omics data.", "uuid": 58103870 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "forecast", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "mcompanion", "role": "Imports" }, { "package": "EnvStats", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ClusterR", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "cluster", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "nuria-sv", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-37", "n": 1 }, { "week": "2025-38", "n": 1 }, { "week": "2025-49", "n": 1 }, { "week": "2026-15", "n": 1 } ], "_tags": [], "_topics": [ "canonical-correlation-analysis", "dimensionality-reduction", "high-dimensional-statistics", "soft-thresholding" ], "_stars": 1, "_contributors": [ { "user": "nuria-sv", "count": 122, "uuid": 58103870 } ], "_userbio": { "uuid": 58103870, "type": "user", "name": "Nuria Senar", "description": "👋 Hi, I'm Nuria, a stats PhD student using penalised methods to integrate high-dimensional datasets. I focus my applications on large omics data." }, "_downloads": { "count": 487, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/toscca" }, "_devurl": "https://github.com/nuria-sv/toscca", "_searchresults": 4, "_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/toscca.html", "manual.pdf" ], "_homeurl": "https://github.com/nuria-sv/toscca", "_realowner": "nuria-sv", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2025-11-07" }, { "version": "0.1.1", "date": "2026-03-24" }, { "version": "1.0", "date": "2026-04-09" } ], "_exports": [ "cpev.toscca", "getCanSubspace", "getWhich", "initialiseCanVar", "myHeatmap", "plt.selstab", "residualisation", "scale_rm", "standardVar", "toscamm.perm", "toscca", "toscca.perm", "toscca.tStat" ], "_help": [ { "page": "cpev.toscca", "title": "Calculates cpev", "topics": [ "cpev.toscca" ] }, { "page": "fastEigen", "title": "Performs eigen decomposition of a matrix in PS space.", "topics": [ "fastEigen" ] }, { "page": "getCanSubspace", "title": "Performs matrix residualisation over estimated canonical vectors by using the null space of the estimated canonical vector to construct a new matrix.", "topics": [ "getCanSubspace" ] }, { "page": "getWhich", "title": "Get location of required.", "topics": [ "getWhich" ] }, { "page": "initialiseCanVar", "title": "Initialised the canonical vector for the iterative process based on positive eigen values. Then, SVD is performed on that PS matrix.", "topics": [ "initialiseCanVar" ] }, { "page": "modes", "title": "Calculates mode.", "topics": [ "modes" ] }, { "page": "myHeatmap", "title": "Plot heatmap of cv w.r.t. the penalty parameter perfotmance.", "topics": [ "myHeatmap" ] }, { "page": "plt.selstab", "title": "Plot slection stability for penalty parameter performance.", "topics": [ "plt.selstab" ] }, { "page": "powerMethod", "title": "Performs power method.", "topics": [ "powerMethod" ] }, { "page": "progressBar", "title": "Progress bar", "topics": [ "progressBar" ] }, { "page": "residualisation", "title": "Performs matrix residualisation over estimated canonical vectors. There are three types: basic (subtracts scaled estimated latent variable from data), null (uses the null space of the estimated canonical vector to construct a new matrix) and LV (uses SVD to residualise).", "topics": [ "residualisation" ] }, { "page": "scale_rm", "title": "Standardises matrices with multiple measurements per individual.", "topics": [ "scale_rm" ] }, { "page": "scaledResidualMat", "title": "Performs scalling for matrix residualisation based on calculated coefficients.", "topics": [ "scaledResidualMat" ] }, { "page": "standardVar", "title": "Stardardise a matrix", "topics": [ "standardVar" ] }, { "page": "summary.toscca_object", "title": "Plot heatmap of cv w.r.t. the penalty parameter perfotmance.", "topics": [ "summary.toscca_object" ] }, { "page": "toscamm.perm", "title": "Computes permutatied cc fot TOSCCA-MM", "topics": [ "toscamm.perm" ] }, { "page": "toscca", "title": "Sparse Canonical Correlation Analysis. Computation of CC via NIPALS with soft thresholding.", "topics": [ "toscca" ] }, { "page": "toscca.core", "title": "Sparse Canonical Correlation Analysis. Computation of CC via NIPALS with soft thresholding.", "topics": [ "toscca.core" ] }, { "page": "toscca.folds", "title": "Sparse Canonical Correlation Analysis. Computation of CC via NIPALS with soft thresholding.", "topics": [ "toscca.folds" ] }, { "page": "toscca.lv", "title": "Get latent variables", "topics": [ "toscca.lv" ] }, { "page": "toscca.perm", "title": "Permutation testing for toscca", "topics": [ "toscca.perm" ] }, { "page": "toscca.tStat", "title": "Get the estatistic for the permutations.", "topics": [ "toscca.tStat" ] }, { "page": "tosccamm", "title": "Computes TOSCCA-MM", "topics": [ "tosccamm" ] } ], "_pkglogo": "man/figures/logo.png", "_readme": "https://github.com/nuria-sv/toscca/raw/HEAD/README.md", "_rundeps": [ "boot", "cli", "codetools", "colorspace", "cpp11", "doParallel", "EnvStats", "farver", "foreach", "forecast", "fracdiff", "gbutils", "generics", "ggplot2", "glue", "gtable", "isoband", "iterators", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "mcompanion", "minqa", "nlme", "nloptr", "nnet", "nortest", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "S7", "scales", "timeDate", "urca", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "toscca-vignette.Rmd", "filename": "toscca-vignette.html", "title": "toscca-vignette", "engine": "knitr::rmarkdown", "headings": [ "toscca", "Canonical Correlation Analysis", "tosccamm", "Results", "Latent paths for $k=1$ and $k=2$" ], "created": "2026-04-09 13:40:08", "modified": "2026-04-09 13:40:08", "commits": 1 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "toscca", "_universes": [ "nuria-sv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0", "date": "2026-06-08T07:32:24.000Z", "distro": "noble", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "b485aea0088f8a5e0e2ab89ce6915fd5666097fa245cc57801ff49221c93764e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" }, { "r": "4.6.0", "os": "linux", "version": "1.0", "date": "2026-06-08T07:32:24.000Z", "distro": "noble", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "4fea7ddc4f2bc5c8998bc534d5ad53154bca8ce6e6ebf23a7a1ccd1742fba12b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" }, { "r": "4.5.3", "os": "mac", "version": "1.0", "date": "2026-06-08T07:32:40.000Z", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "c8b810aca6e495ae9bd44886a8dd3867ca0830ee8a9a2e60b94a374f2d8e696c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" }, { "r": "4.6.0", "os": "mac", "version": "1.0", "date": "2026-06-09T06:01:08.000Z", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "1d6cfdb75e282dbbff117e508957b1feb32a34d8b3eceeb89abd6287df87cf93", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" }, { "r": "4.6.0", "os": "wasm", "version": "1.0", "date": "2026-06-08T07:32:25.000Z", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "6a7b0028b4ad09156ce97e984fe18caa34d3e95a54ab8fd90c858298117010a0", "status": "success", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" }, { "r": "4.7.0", "os": "win", "version": "1.0", "date": "2026-06-08T07:31:21.000Z", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "deef67c122caaf83d85b700210ee18f0c9cdc79b40e57045579ddf327888000c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" }, { "r": "4.5.3", "os": "win", "version": "1.0", "date": "2026-06-08T07:31:28.000Z", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "6e9138247f48caf13262db72ba6c8ce8d89767633384d17fb30f1e83125fc09b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" }, { "r": "4.6.0", "os": "win", "version": "1.0", "date": "2026-06-08T07:31:56.000Z", "commit": "d9846bcd5496c0da046b0de87ee648c1ee6c87d0", "fileid": "bb03407ab206396233cbc3c244fe47d50c94f5dd62adcfe3b154585df93d62c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nuria-sv/actions/runs/27122322601" } ] }