{ "_id": "6a1e760d1d7bb097a0a63cb4", "Package": "NIMAA", "Title": "Nominal Data Mining Analysis", "Version": "0.2.2", "Date": "2025-10-02", "Authors@R": "c(\nperson(\"Mohieddin\", \"Jafari\", role = c(\"aut\",\"cre\"),email = \"mohieddin.jafari@helsinki.fi\"),\nperson(\"Cheng\", \"Chen\", role = c(\"aut\"),email = \"cheng.chen@helsinki.fi\"),\nperson(\"Zangene\", \"Ehsan\", role = c(\"aut\"),email = \"ehsan.zangene@helsinki.fi\")\n)", "Description": "Functions for nominal data mining based on bipartite\ngraphs, which build a pipeline for analysis and missing values\nimputation. Methods are mainly from the paper: Jafari,\nMohieddin, et al. (2021) , some\nnew ones are also included.", "License": "GPL (>= 3)", "URL": "https://github.com/jafarilab/NIMAA", "BugReports": "https://github.com/jafarilab/NIMAA/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://jafarilab.r-universe.dev", "Date/Publication": "2025-10-03 09:48:18 UTC", "RemoteUrl": "https://github.com/jafarilab/nimaa", "RemoteRef": "HEAD", "RemoteSha": "8645191e55cebd7769946394cd311d4ce4ee112e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:12:16 UTC", "User": "root" }, "Author": "Mohieddin Jafari [aut, cre],\nCheng Chen [aut],\nZangene Ehsan [aut]", "Maintainer": "Mohieddin Jafari ", "MD5sum": "98157d159420749bca6c3bbe9ef5be53", "_user": "jafarilab", "_type": "src", "_file": "NIMAA_0.2.2.tar.gz", "_fileid": "5b13818d1c71e1807abbc021273c47254a87c538fd62551d21618778d17ebad7", "_filesize": 4447305, "_sha256": "5b13818d1c71e1807abbc021273c47254a87c538fd62551d21618778d17ebad7", "_created": "2026-05-31T06:12:16.000Z", "_published": "2026-06-02T06:19:57.866Z", "_distro": "noble", "_jobs": [ { "job": 79010867990, "time": 278, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7350364391" }, { "job": 79010868101, "time": 275, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7350363453" }, { "job": 79010868063, "time": 180, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7350341657" }, { "job": 79010868034, "time": 198, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7350344473" }, { "job": 79010868191, "time": 329, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314324917" }, { "job": 79010868462, "time": 172, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314342973" }, { "job": 79010867993, "time": 68, "config": "windows-devel", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 79010868026, "time": 93, "config": "windows-oldrel", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 79010867972, "time": 20, "config": "windows-release", "r": "", "check": "FAIL", "artifact": "" } ], "_buildurl": "https://github.com/r-universe/jafarilab/actions/runs/26704984814", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jafarilab/nimaa", "_commit": { "id": "8645191e55cebd7769946394cd311d4ce4ee112e", "author": "Mohieddin Jafari ", "committer": "Mohieddin Jafari ", "message": "RoxygenNote modification\n", "time": 1759484898 }, "_maintainer": { "name": "Mohieddin Jafari", "email": "mohieddin.jafari@helsinki.fi" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "plotly", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "bipartite", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "skimr", "role": "Imports" }, { "package": "bnstruct", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "fpc", "role": "Imports" }, { "package": "mice", "role": "Imports" }, { "package": "missMDA", "role": "Imports" }, { "package": "networkD3", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "softImpute", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidytext", "role": "Imports" }, { "package": "visNetwork", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "utils", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "htmltools", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "jafarilab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-37", "n": 1 }, { "week": "2025-40", "n": 5 } ], "_tags": [], "_stars": 4, "_contributors": [ { "user": "jafarilab", "count": 121, "uuid": 28731506 }, { "user": "chendebiao", "count": 4, "uuid": 45630055 }, { "user": "esnzgn", "count": 1, "uuid": 33609170 } ], "_userbio": { "uuid": 28731506, "type": "user", "name": "Mohieddin Jafari" }, "_downloads": { "count": 267, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/NIMAA" }, "_devurl": "https://github.com/jafarilab/nimaa", "_searchresults": 11, "_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/NIMAA.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jafarilab/nimaa", "_realowner": "jafarilab", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2021-09-13" }, { "version": "0.2.0", "date": "2022-04-01" }, { "version": "0.2.1", "date": "2022-04-11" }, { "version": "0.2.2", "date": "2025-10-06" } ], "_exports": [ "analyseNetwork", "extractSubMatrix", "findCluster", "nominalAsBinet", "plotBipartite", "plotBipartiteInteractive", "plotCluster", "plotIncMatrix", "predictEdge", "scoreCluster", "validateCluster", "validateEdgePrediction", "visualClusterInBipartite" ], "_datasets": [ { "name": "beatAML", "title": "beatAML", "object": "beatAML", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "inhibitor", "patient_id", "median" ], "rows": 47650, "table": true, "tojson": true }, { "name": "drugComb", "title": "drugComb", "object": "drugComb", "class": [ "grouped_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "inhibitor", "cell_line", "median" ], "rows": 16816, "table": true, "tojson": true }, { "name": "herbIngredient", "title": "herbIngredient", "object": "herbIngredient", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "latin", "pubchem" ], "rows": 16340, "table": true, "tojson": true }, { "name": "robertson", "title": "robertson", "object": "robertson", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "plant", "pollinator" ], "rows": 15255, "table": true, "tojson": true } ], "_help": [ { "page": "analyseNetwork", "title": "General properties of the network", "topics": [ "analyseNetwork" ] }, { "page": "beatAML", "title": "beatAML", "topics": [ "beatAML" ] }, { "page": "drugComb", "title": "drugComb", "topics": [ "drugComb" ] }, { "page": "extractSubMatrix", "title": "Extract the non-missing submatrices from a given matrix.", "topics": [ "extractSubMatrix" ] }, { "page": "findCluster", "title": "Find clusters in projected unipartite networks", "topics": [ "findCluster" ] }, { "page": "herbIngredient", "title": "herbIngredient", "topics": [ "herbIngredient" ] }, { "page": "NIMAA", "title": "NIMAA: A package for Nominal Data Mining Analysis.", "topics": [ "NIMAA-package", "NIMAA" ] }, { "page": "nominalAsBinet", "title": "Convert nominal data to a bipartite network", "topics": [ "nominalAsBinet" ] }, { "page": "plotBipartite", "title": "Plot the bipartite network and the corresponding projected networks", "topics": [ "plotBipartite" ] }, { "page": "plotBipartiteInteractive", "title": "Use the incidence matrix to plot an interactive bipartite network", "topics": [ "plotBipartiteInteractive" ] }, { "page": "plotCluster", "title": "Plot the clusters in one projection of the bipartite network", "topics": [ "plotCluster" ] }, { "page": "plotIncMatrix", "title": "Plot the incidence matrix.", "topics": [ "plotIncMatrix" ] }, { "page": "predictEdge", "title": "Edge prediction of weighted bipartite network.", "topics": [ "predictEdge" ] }, { "page": "robertson", "title": "robertson", "topics": [ "robertson" ] }, { "page": "scoreCluster", "title": "Score the cluster analysis in a projected network based on additional internal measures.", "topics": [ "scoreCluster" ] }, { "page": "validateCluster", "title": "Validate the cluster analysis in a projected network based on additional external measures.", "topics": [ "validateCluster" ] }, { "page": "validateEdgePrediction", "title": "Validate and compare edge prediction methods.", "topics": [ "validateEdgePrediction" ] }, { "page": "visualClusterInBipartite", "title": "Plot the bipartite graph with color coding for different clusters in both parts", "topics": [ "visualClusterInBipartite" ] } ], "_pkglogo": "https://github.com/jafarilab/nimaa/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/jafarilab/nimaa/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "backports", "base64enc", "bipartite", "bit", "bit64", "bitops", "bnstruct", "boot", "broom", "bslib", "cachem", "car", "carData", "class", "cli", "clipr", "cluster", "coda", "codetools", "colorspace", "corpcor", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "data.tree", "DEoptimR", "Deriv", "digest", "diptest", "doBy", "doParallel", "dotCall64", "dplyr", "DT", "ellipse", "emmeans", "estimability", "evaluate", "FactoMineR", "farver", "fastmap", "fields", "flashClust", "flexmix", "fontawesome", "forcats", "foreach", "forecast", "Formula", "fpc", "fracdiff", "fs", "generics", "ggplot2", "ggrepel", "glmnet", "glue", "gtable", "haven", "highr", "hms", "htmltools", "htmlwidgets", "httr", "igraph", "isoband", "iterators", "janeaustenr", "jomo", "jquerylib", "jsonlite", "kernlab", "knitr", "labeling", "later", "lattice", "lazyeval", "leaps", "lifecycle", "lme4", "lmtest", "magrittr", "maps", "MASS", "Matrix", "MatrixModels", "mclust", "memoise", "mgcv", "mice", "microbenchmark", "mime", "minqa", "missMDA", "mitml", "modelr", "modeltools", "multcompView", "mvtnorm", "network", "networkD3", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "ordinal", "otel", "pan", "pbkrtest", "permute", "pillar", "pkgconfig", "plotly", "prabclus", "prettyunits", "progress", "promises", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "readr", "reformulas", "repr", "rlang", "rmarkdown", "robustbase", "rpart", "S7", "sass", "scales", "scatterplot3d", "shape", "skimr", "sna", "SnowballC", "softImpute", "spam", "SparseM", "statnet.common", "stringi", "stringr", "survival", "sys", "tibble", "tidyr", "tidyselect", "tidytext", "timeDate", "tinytex", "tokenizers", "tzdb", "ucminf", "urca", "utf8", "vctrs", "vegan", "viridisLite", "visNetwork", "vroom", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "NIMAA-vignette.Rmd", "filename": "NIMAA-vignette.html", "title": "NIMAA-vignette", "author": "Cheng Chen, Mohieddin Jafari", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "1 Exploring the data", "1.1 Plotting the original data", "1.2 Plotting the bipartite network of the original data", "1.2.1 Static plot", "1.2.2 Interactive plot", "1.3 Analysis of network properties", "2 Extracting large submatrices without missing values", "3 Cluster finding analysis of projected unipartite networks", "4 Exploring the clusters", "4.1 Displaying Clusters inside the unipartite network", "4.2 Displaying Clusters' relationship inside the bipartite network", "4.3 Scoring clusters", "4.4 Validating clusters based on prior knowledge", "5 Edge prediction", "5.1 Predicting of edge in bipartite network", "5.2 Validating edge prediction", "References" ], "created": "2021-09-07 12:33:05", "modified": "2022-04-06 10:48:09", "commits": 21 } ], "_score": 4.944482672150169, "_indexed": true, "_nocasepkg": "nimaa", "_universes": [ "jafarilab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.2", "date": "2026-06-02T06:18:01.000Z", "distro": "noble", "commit": "8645191e55cebd7769946394cd311d4ce4ee112e", "fileid": "8654dc2321586ab3617751622347596d5d9a3895b79a439a4e5708c3758ac1de", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jafarilab/actions/runs/26704984814" }, { "r": "4.6.0", "os": "linux", "version": "0.2.2", "date": "2026-06-02T06:17:59.000Z", "distro": "noble", "commit": "8645191e55cebd7769946394cd311d4ce4ee112e", "fileid": "05899243902acc5dbc3c3bd2218573e56e6b96b41623fedda75ee52f5fdbd64f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jafarilab/actions/runs/26704984814" }, { "r": "4.5.3", "os": "mac", "version": "0.2.2", "date": "2026-06-02T06:17:02.000Z", "commit": "8645191e55cebd7769946394cd311d4ce4ee112e", "fileid": "5539441b37efea941341d7f0f6412eea1f393b5e0b576bfeaaf6faaa89b2d4eb", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jafarilab/actions/runs/26704984814" }, { "r": "4.6.0", "os": "mac", "version": "0.2.2", "date": "2026-06-02T06:17:03.000Z", "commit": "8645191e55cebd7769946394cd311d4ce4ee112e", "fileid": "1e68f913f2f8ba47df90f1869b4ffac8e770f474892e0dead2cf852ab1e5aa0e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jafarilab/actions/runs/26704984814" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.2", "date": "2026-05-31T06:15:37.000Z", "commit": "8645191e55cebd7769946394cd311d4ce4ee112e", "fileid": "51d100d7bc56f484ad40d9355687fac1e052ae4a0b5178132761f937cfa9b2cb", "status": "success", "buildurl": "https://github.com/r-universe/jafarilab/actions/runs/26704984814" } ] }