{ "_id": "6a37a5343efcd9bda4421a45", "Encoding": "UTF-8", "Package": "gemR", "Type": "Package", "Title": "General Effect Modelling", "Version": "1.2.2", "Date": "2025-09-04", "Authors@R": "c(person(\"Kristian Hovde\", \"Liland\", role = c(\"aut\", \"cre\"),\nemail = \"kristian.liland@nmbu.no\"),\nperson(\"Ellen Færgestad\", \"Mosleth\", role = \"ctb\"))", "Description": "Two-step modeling with separation of sources of variation\nthrough analysis of variance and subsequent multivariate\nmodeling through a range of unsupervised and supervised\nstatistical methods. Separation can focus on removal of\ninterfering effects or isolation of effects of interest. EF\nMosleth et al. (2021) and EF\nMosleth et al. (2020) .", "License": "GPL", "LazyData": "TRUE", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://khliland.r-universe.dev", "Date/Publication": "2025-09-05 12:42:40 UTC", "RemoteUrl": "https://github.com/khliland/gemr", "RemoteRef": "HEAD", "RemoteSha": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-21 08:44:11 UTC", "User": "root" }, "Author": "Kristian Hovde Liland [aut, cre],\nEllen Færgestad Mosleth [ctb]", "Maintainer": "Kristian Hovde Liland ", "MD5sum": "460e393b11c4f2367304e22981de177b", "_user": "khliland", "_type": "src", "_file": "gemR_1.2.2.tar.gz", "_fileid": "15d2d48b3c21a1fb446d906b2319e5e61646b8ec2cf6963c13f8d5b6cb61b7e2", "_filesize": 2219668, "_sha256": "15d2d48b3c21a1fb446d906b2319e5e61646b8ec2cf6963c13f8d5b6cb61b7e2", "_created": "2026-06-21T08:44:11.000Z", "_published": "2026-06-21T08:47:48.034Z", "_distro": "noble", "_jobs": [ { "job": 82555888963, "time": 155, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7773599099" }, { "job": 82555888972, "time": 179, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7773602303" }, { "job": 82555888946, "time": 106, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7773592170" }, { "job": 82555888978, "time": 110, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7773592989" }, { "job": 82555666824, "time": 176, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7773578363" }, { "job": 82555888981, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7773595261" }, { "job": 82555888998, "time": 111, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7773593300" }, { "job": 82555889024, "time": 112, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7773593350" }, { "job": 82555889002, "time": 161, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7773599855" } ], "_buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/khliland/gemr", "_commit": { "id": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "author": "Kristian Hovde Liland ", "committer": "Kristian Hovde Liland ", "message": "gemR 1.2.2\n", "time": 1757076160 }, "_maintainer": { "name": "Kristian Hovde Liland", "email": "kristian.liland@nmbu.no", "login": "khliland", "description": "", "uuid": 9257806 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "mixlm", "role": "Imports" }, { "package": "pls", "role": "Imports" }, { "package": "plsVarSel", "role": "Imports" }, { "package": "HDANOVA", "version": ">= 0.8.4", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "glmnet", "role": "Suggests" }, { "package": "neuralnet", "role": "Suggests" } ], "_owner": "khliland", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 1 }, { "week": "2025-26", "n": 3 }, { "week": "2025-36", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "khliland", "count": 18, "uuid": 9257806 } ], "_userbio": { "uuid": 9257806, "type": "user", "name": "Kristian Hovde Liland", "followers": 44 }, "_downloads": { "count": 543, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gemR" }, "_devurl": "https://github.com/khliland/gemr", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gemR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/khliland/gemr", "_realowner": "khliland", "_cranurl": true, "_releases": [ { "version": "1.2.1", "date": "2025-06-27" }, { "version": "1.2.2", "date": "2025-09-04" } ], "_exports": [ "confints", "corrplot", "elastic", "explvar", "GEM", "grid.arrange", "knock.in", "knock.out", "loadingplot", "loadings", "mvrValstats", "neuralnet", "pca", "permutation", "pls", "R2", "sca", "scoreplot", "scores", "tableGEM" ], "_datasets": [ { "name": "Diabetes", "title": "Diabetes data", "object": "Diabetes", "class": [ "data.frame" ], "fields": [ "surgery", "T2D", "transcriptome", "meta" ], "rows": 30, "table": false, "tojson": true }, { "name": "Lactobacillus", "title": "Lactobacillus data", "object": "Lactobacillus", "class": [ "data.frame" ], "fields": [ "strain", "growthrate", "proteome", "transcriptome", "phenome" ], "rows": 12, "table": false, "tojson": true }, { "name": "MS", "title": "Multiple Sclerosis data", "object": "MS", "class": [ "data.frame" ], "fields": [ "MS", "group", "sex", "age", "proteins" ], "rows": 101, "table": false, "tojson": true } ], "_help": [ { "page": "confints", "title": "Confidence Intervals of Effect Differences", "topics": [ "confints", "confints.default", "confints.GEM", "plot.confints" ] }, { "page": "Diabetes", "title": "Diabetes data", "topics": [ "Diabetes" ] }, { "page": "elastic", "title": "Elastic-net modeling of GEM objects.", "topics": [ "coef.GEMglmnet", "elastic", "elastic.GEM" ] }, { "page": "GEM", "title": "General Effect Modelling", "topics": [ "GEM", "gemR", "plot.GEM", "print.GEM", "print.summary.GEM", "summary.GEM", "tableGEM" ] }, { "page": "knock.in", "title": "Knock-in and knock-out of effect(s)", "topics": [ "knock.in", "knock.out" ] }, { "page": "Lactobacillus", "title": "Lactobacillus data", "topics": [ "Lactobacillus" ] }, { "page": "MS", "title": "Multiple Sclerosis data", "topics": [ "MS" ] }, { "page": "neuralnet", "title": "Neural Network by Multilayer Perceptron", "topics": [ "neuralnet" ] }, { "page": "pca", "title": "Principal Component Analysis", "topics": [ "pca" ] }, { "page": "plot.GEMpls", "title": "Plot function and extraction method for GEM-based PLS", "topics": [ "corrplot", "explvar", "explvar.GEMpls", "loadingplot", "loadings", "mvrValstats", "plot.GEM.pls", "plot.GEMpls", "print.GEMpls", "R2", "scoreplot", "scores", "summary.GEMpls" ] }, { "page": "pls.GEM", "title": "Partial Least Squares modelling of GEM objects.", "topics": [ "pls.GEM" ] }, { "page": "sca", "title": "Simultaneous Component Analysis", "topics": [ "sca" ] } ], "_readme": "https://github.com/khliland/gemr/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "bdsmatrix", "boot", "broom", "car", "carData", "cli", "codetools", "colorspace", "cowplot", "cpp11", "crayon", "Deriv", "doBy", "dplyr", "farver", "forecast", "Formula", "fracdiff", "genalg", "generics", "ggplot2", "glue", "gridExtra", "gtable", "HDANOVA", "hms", "isoband", "labeling", "lattice", "leaps", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "mgcv", "microbenchmark", "minqa", "mixlm", "modelr", "multcomp", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "pillar", "pkgconfig", "pls", "plsVarSel", "pracma", "praznik", "prettyunits", "progress", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "RSpectra", "S7", "sandwich", "scales", "SparseM", "stringi", "stringr", "survival", "TH.data", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_score": 3.1760912590556813, "_indexed": true, "_nocasepkg": "gemr", "_universes": [ "khliland" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.2", "date": "2026-06-21T08:46:18.000Z", "distro": "noble", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "62d2b7db197a7cb4089a23f3bfef81d540e4258639f7d38a9358410f51f619af", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" }, { "r": "4.6.0", "os": "linux", "version": "1.2.2", "date": "2026-06-21T08:46:38.000Z", "distro": "noble", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "e06271ab66b84cf8284f26536f7ed580c5b6d9e9f4c2470600db3856c4d3fa04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" }, { "r": "4.5.3", "os": "mac", "version": "1.2.2", "date": "2026-06-21T08:45:37.000Z", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "99bbc8fa334fffd2a818fbbfaec66ebd22dfcec5c225dcf980dd00a0ab8d1874", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" }, { "r": "4.6.0", "os": "mac", "version": "1.2.2", "date": "2026-06-21T08:45:48.000Z", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "448644789b207daa01ea1788f81b8f72b319fbf1189fddd552e37b093147eed5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.2", "date": "2026-06-21T08:46:35.000Z", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "5b9a96e0fa5668dd09cd14dc881f01bcf4966eaeeb02041bf8446f621dd662cd", "status": "success", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" }, { "r": "4.7.0", "os": "win", "version": "1.2.2", "date": "2026-06-21T08:45:24.000Z", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "6449fb8fc35cc0e3e723a963fe46e19d8696f76dd0b098ccfbc3199becb9e3c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" }, { "r": "4.5.3", "os": "win", "version": "1.2.2", "date": "2026-06-21T08:45:25.000Z", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "2141d1f5676a6f67f7850b6a135f2db3942cff0bd07dc03c3b90652b736a8955", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" }, { "r": "4.6.0", "os": "win", "version": "1.2.2", "date": "2026-06-21T08:45:54.000Z", "commit": "e3ba228e5c6a4747f25bdccd151a4ef30f6f5719", "fileid": "2f921e296f43f86554f629699f4884d5eeef5c462609d324c05a2970d18ba259", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/27898966952" } ] }