{ "_id": "6ae3c98b8d250e7ad09f0ee6", "Package": "nmfkc", "Type": "Package", "Title": "Non-Negative Matrix Factorization with Kernel Covariates", "Version": "1.0.2", "Date": "2026-10-29", "Authors@R": "person(\"Kenichi\", \"Satoh\",\nemail = \"kenichi-satoh@biwako.shiga-u.ac.jp\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4436-9347\"))", "Maintainer": "Kenichi Satoh ", "URL": "https://github.com/ksatohds/nmfkc,\nhttps://ksatohds.github.io/nmfkc/", "BugReports": "https://github.com/ksatohds/nmfkc/issues", "Description": "Performs Non-negative Matrix Factorization (NMF) with\nKernel Covariates. Given an observation matrix and kernel\ncovariates, it optimizes both a basis matrix and a parameter\nmatrix. Notably, if the kernel matrix is an identity matrix,\nthe method simplifies to standard NMF. Also provides NMF with\nRandom Effects (NMF-RE) via nmfre(), which estimates a\nmixed-effects model combining covariate-driven scores with\nunit-specific random effects together with wild bootstrap\ninference, and NMF with feed-forward and feedback structure\n(NMF-FFB) via nmf.ffb(), which fits a two-block input-output\nmodel for blind source separation and path analysis.\nReferences: Satoh (2025) ; Satoh\n(2026) ; Satoh (2025)\n; Satoh (2026)\n; Satoh and Tokuda (2026)\n; Satoh (2026)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "ByteCompile": "true", "VignetteBuilder": "knitr, rmarkdown", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "7.2.3", "Repository": "https://ksatohds.r-universe.dev", "Date/Publication": "2026-10-29 22:01:26 UTC", "RemoteUrl": "https://github.com/ksatohds/nmfkc", "RemoteRef": "HEAD", "RemoteSha": "4301c529142b0189d50f68ffdf9084281c0a48c9", 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"topics": [ "nmfkc.signed.rff.gram" ] }, { "page": "nmfre", "title": "Non-negative Matrix Factorization with Random Effects", "topics": [ "nmfre" ] }, { "page": "nmfre.ecv", "title": "NMF-RE element-wise cross-validation for rank selection", "topics": [ "nmfre.ecv" ] }, { "page": "nmfre.inference", "title": "Statistical inference for the coefficient matrix C from NMF-RE", "topics": [ "nmfre.inference" ] }, { "page": "plot.nmf.cluster.criteria", "title": "Plot clustering-quality criteria across a sequence of fits", "topics": [ "plot.nmf.cluster.criteria" ] }, { "page": "plot.nmf.cluster.flow", "title": "Plot a cluster-flow (alluvial) diagram", "topics": [ "plot.nmf.cluster.flow" ] }, { "page": "plot.nmf.gmm", "title": "Plot method for nmf.gmm objects", "topics": [ "plot.nmf.gmm" ] }, { "page": "plot.nmf.gmm.select", "title": "Plot method for nmf.gmm.select objects", "topics": [ "plot.nmf.gmm.select" ] }, { "page": "plot.nmf.rank", "title": "Plot a rank-selection (nmf.rank) object", "topics": [ "plot.nmf.rank" ] }, { "page": "plot.nmfae", "title": "'plot.nmfae' displays the convergence trajectory of the objective function across iterations. The title shows the achieved R^2.", "topics": [ "plot.nmfae" ] }, { "page": "plot.nmfkc", "title": "Plot method for objects of class 'nmfkc'", "topics": [ "plot.nmfkc" ] }, { "page": "plot.nmfkc.ar.latent", "title": "Plot the latent dynamics of an NMF-VAR model", "topics": [ "plot.nmfkc.ar.latent" ] }, { "page": "plot.nmfkc.ar.stationarity", "title": "Plot the stationarity bracket of an NMF-VAR model", "topics": [ "plot.nmfkc.ar.stationarity" ] }, { "page": "plot.nmfkc.ard", "title": "Plot method for nmfkc.ard objects", "topics": [ "plot.nmfkc.ard" ] }, { "page": "plot.nmfkc.consensus", "title": "Plot a consensus rank-selection (nmfkc.consensus) object", "topics": [ "plot.nmfkc.consensus" ] }, { "page": "plot.nmfkc.DOT", "title": "Plot method for nmfkc.DOT objects", "topics": [ "plot.nmfkc.DOT" ] }, { "page": "plot.nmfkc.signed", "title": "Plot method for nmfkc.signed (convergence)", "topics": [ "plot.nmfkc.signed" ] }, { "page": "plot.nmfre", "title": "Plot convergence diagnostics for NMF models", "topics": [ "plot.nmf.ffb", "plot.nmfre" ] }, { "page": "plot.nmfre.ecv", "title": "Plot method for nmfre.ecv objects", "topics": [ "plot.nmfre.ecv" ] }, { "page": "predict.nmf.gmm", "title": "Class assignments / responsibilities from an NMF-GMM fit", "topics": [ "predict.nmf.gmm" ] }, { "page": "predict.nmfkc", "title": "Prediction method for objects of class 'nmfkc'", "topics": [ "predict.nmfkc" ] }, { "page": "predict.nmfkc.signed", "title": "Predict method for nmfkc.signed", "topics": [ "predict.nmfkc.signed" ] }, { "page": "predict.nmfre", "title": "Predict method for nmfre objects", "topics": [ "predict.nmfre" ] }, { "page": "print.nmf", "title": "Print method for fitted NMF models", "topics": [ "print.nmf" ] }, { "page": "print.nmf.cluster.criteria", "title": "Print method for nmf.cluster.criteria objects", "topics": [ "print.nmf.cluster.criteria" ] }, { "page": "print.nmf.cluster.flow", "title": "Print method for nmf.cluster.flow objects", "topics": [ "print.nmf.cluster.flow" ] }, { "page": "print.nmf.ffb.test", "title": "Print a calibrated test of the feed-forward null", "topics": [ "print.nmf.ffb.test" ] }, { "page": "print.nmf.gmm", "title": "Print an NMF-GMM fit", "topics": [ "print.nmf.gmm" ] }, { "page": "print.nmf.gmm.select", "title": "Print method for nmf.gmm.select objects", "topics": [ "print.nmf.gmm.select" ] }, { "page": "print.nmf.inference", "title": "Print method for NMF inference objects", "topics": [ "print.nmf.inference" ] }, { "page": "print.nmf.rank", "title": "Print method for rank-selection (nmf.rank) objects", "topics": [ "print.nmf.rank" ] }, { "page": "print.nmfae.ecv", "title": "Print method for nmf.rrr element-wise CV results", "topics": [ "print.nmfae.ecv" ] }, { "page": "print.nmfkc.ar.latent", "title": "Print method for nmfkc.ar.latent objects", "topics": [ "print.nmfkc.ar.latent" ] }, { "page": "print.nmfkc.ar.latent.inference", "title": "Print method for nmfkc.ar.latent.inference objects", "topics": [ "print.nmfkc.ar.latent.inference" ] }, { "page": "print.nmfkc.ar.stationarity", "title": "Print method for nmfkc.ar.stationarity objects", "topics": [ "print.nmfkc.ar.stationarity" ] }, { "page": "print.nmfkc.ard", "title": "Print method for nmfkc.ard objects", "topics": [ "print.nmfkc.ard" ] }, { "page": "print.nmfkc.consensus", "title": "Print method for nmfkc.consensus objects", "topics": [ "print.nmfkc.consensus" ] }, { "page": "print.nmfkc.DOT", "title": "Print method for nmfkc.DOT objects", "topics": [ "print.nmfkc.DOT" ] }, { "page": "print.nmfkc.gram", "title": "Print method for nmfkc.gram", "topics": [ "print.nmfkc.gram" ] }, { "page": "print.nmfre.ecv", "title": "Print method for nmfre.ecv objects", "topics": [ "print.nmfre.ecv" ] }, { "page": "print.summary.nmf.ffb", "title": "Print method for summary.nmf.ffb objects", "topics": [ "print.summary.nmf.ffb" ] }, { "page": "print.summary.nmf.gmm", "title": "Print method for summary.nmf.gmm objects", "topics": [ "print.summary.nmf.gmm" ] }, { "page": "print.summary.nmfkc", "title": "Print method for 'summary.nmfkc' objects", "topics": [ "print.summary.nmfkc" ] }, { "page": "print.summary.nmfkc.inference", "title": "Print method for summary.nmfkc.inference objects", "topics": [ "print.summary.nmfkc.inference" ] }, { "page": "print.summary.nmfkc.net", "title": "Print method for summary.nmfkc.net objects", "topics": [ "print.summary.nmfkc.net" ] }, { "page": "print.summary.nmfkc.net.inference", "title": "Print method for summary.nmfkc.net.inference objects", "topics": [ "print.summary.nmfkc.net.inference" ] }, { "page": "print.summary.nmfkc.net.signed", "title": "Print method for summary.nmfkc.net.signed objects", "topics": [ "print.summary.nmfkc.net.signed" ] }, { "page": "print.summary.nmfkc.signed", "title": "Print method for summary.nmfkc.signed", "topics": [ "print.summary.nmfkc.signed" ] }, { "page": "residuals.nmf", "title": "Extract residuals from NMF models", "topics": [ "residuals.nmf", "residuals.nmf.ffb", "residuals.nmfae", "residuals.nmfre" ] }, { "page": "residuals.nmf.gmm", "title": "Residuals from an NMF-GMM fit", "topics": [ "residuals.nmf.gmm" ] }, { "page": "summary.nmf.ffb", "title": "Summary method for nmf.ffb objects", "topics": [ "summary.nmf.ffb" ] }, { "page": "summary.nmf.gmm", "title": "Summary of an NMF-GMM fit", "topics": [ "summary.nmf.gmm" ] }, { "page": "summary.nmfkc", "title": "Summary method for objects of class 'nmfkc'", "topics": [ "summary.nmfkc" ] }, { "page": "summary.nmfkc.inference", "title": "Summary method for nmfkc.inference objects", "topics": [ "summary.nmfkc.inference" ] }, { "page": "summary.nmfkc.net", "title": "Summary method for nmfkc.net objects", "topics": [ "summary.nmfkc.net" ] }, { "page": "summary.nmfkc.net.inference", "title": "Summary method for nmfkc.net.inference objects", "topics": [ "summary.nmfkc.net.inference" ] }, { "page": "summary.nmfkc.net.signed", "title": "Summary method for nmfkc.net.signed objects", "topics": [ "summary.nmfkc.net.signed" ] }, { "page": "summary.nmfkc.signed", "title": "Summary method for nmfkc.signed", "topics": [ "summary.nmfkc.signed" ] }, { "page": "summary.nmfre", "title": "Summary method for objects of class 'nmfre'", "topics": [ "print.summary.nmfre", "summary.nmfre" ] } ], "_readme": "https://github.com/ksatohds/nmfkc/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "introduction-to-nmfkc.Rmd", "filename": "introduction-to-nmfkc.html", "title": "Introduction to nmfkc", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "1. 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Handling Missing Values (Imputation)", "Creating Data with Missing Values", "Running NMF with NAs", "Predicting the Unknown Rating", "Summary" ], "created": "2025-10-13 04:49:23", "modified": "2025-11-24 21:22:05", "commits": 3 } ], "_score": 6.854548935812951, "_indexed": true, "_nocasepkg": "nmfkc", "_universes": [ "ksatohds" ], "_previous": "1.0.1", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2", "date": "2026-10-29T22:30:13.000Z", "distro": "resolute", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/8789d960f759c6c1b1d2fa5767650fbb995edaa26bfcc6ed18c52f3e22eed1b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" }, { "r": "4.6.1", "os": "linux", "version": "1.0.2", "date": "2026-10-29T22:30:30.000Z", "distro": "resolute", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/3efe93e735c9482622586f52da4948f77582c3416a1c4fc049f867acd5c5bb7b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2", "date": "2026-10-29T22:31:17.000Z", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/31129874c57e569abbcc6620de7ff0218527baa0d5ede4bce485344fd0dbb98a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" }, { "r": "4.6.1", "os": "mac", "version": "1.0.2", "date": "2026-10-29T22:30:39.000Z", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/f3898510cf502ccb73398e048bd6d20f0a93bffda8b343f56cc8f7e57a259f51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2", "date": "2026-10-29T22:30:19.000Z", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/49b2870fe9eeeb4e50baf4662442902c3f5b55893d537f5860b1acb12d83e8db", "status": "success", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" }, { "r": "4.7.0", "os": "win", "version": "1.0.2", "date": "2026-10-29T22:29:24.000Z", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/b7646ba4f823d07288991c295527751307fe9914b1a81710dad0a9cd2300aaa8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" }, { "r": "4.5.3", "os": "win", "version": "1.0.2", "date": "2026-10-29T22:29:11.000Z", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/e50ae8eac80a465d768d6eff4fe6d52b15f32601998f9a8e4d8ff877ff31c9d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" }, { "r": "4.6.1", "os": "win", "version": "1.0.2", "date": "2026-10-29T22:29:43.000Z", "commit": "4301c529142b0189d50f68ffdf9084281c0a48c9", "fileid": "https://r2.ropensci.org/1f164bea57cb7b7cf847814f40e3cb58ea159ecd5dfc6a45b5d58293e680c4a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ksatohds/actions/runs/40965411549" } ] }