{ "_id": "6a47d23be06c18f0a651ff7d", "Package": "TestREnlme", "Type": "Package", "Title": "Nonparametric Tests for Random Effects in Linear and Nonlinear\nMixed-Effects Models", "Version": "0.1.0", "Authors@R": "c(\nperson(\"Germaine\", \"Uwimpuhwe\",\nemail = \"germaine.uwimpuhwe@durham.ac.uk\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Reza\", \"Drikvandi\",\nemail = \"reza.drikvandi@durham.ac.uk\",\nrole = \"aut\"),\nperson(\"Shelley A.\", \"Blozis\",\nemail = \"sablozis@ucdavis.edu\",\nrole = \"aut\"))", "Description": "Provides nonparametric permutation tests for testing all\nor any subset of random effects in linear and nonlinear\nmixed-effects models, without requiring normality or other\ndistributional assumptions on random effects or errors. Three\ndistribution-free variance-component estimators are\nimplemented: Variance Least Squares ('VLS'), Method of Moments\n('MM'), and Method of Moments with First-Order Approximation\n('MMF'). A permutation procedure is used to obtain\nfinite-sample p-values. Plotting functions support data\nexploration, model evaluation, and communication of results.\nMethods are described in Uwimpuhwe, Drikvandi, and Blozis\n(2026) .", "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "8.0.0", "VignetteBuilder": "knitr", "URL": "https://github.com/germaine86/TestREnlme", "BugReports": "https://github.com/germaine86/TestREnlme/issues", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 15:12:27 UTC", "User": "root" }, "Author": "Germaine Uwimpuhwe [aut, cre], Reza Drikvandi [aut], Shelley A.\nBlozis [aut]", "Maintainer": "Germaine Uwimpuhwe ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-07-03 12:00:15 UTC", "RemoteUrl": "https://github.com/cran/TestREnlme", "RemoteRef": "HEAD", "RemoteSha": "f061c1d5b68c7503c485fd5dfbccd2038af371d5", "_user": "cran", "_type": "src", "_file": "TestREnlme_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/1b783292eb2fffa62db61be0d652e0f860b775a8c991252507f6a8e118298e60", "_filesize": 835513, "_sha256": "1b783292eb2fffa62db61be0d652e0f860b775a8c991252507f6a8e118298e60", "_expires": "2026-10-11T15:16:09.000Z", "_created": "2026-07-03T15:12:27.000Z", "_published": "2026-07-03T15:16:11.455Z", "_jobs": [ { "job": 85027966795, "time": 180, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8069926822" }, { "job": 85027966796, "time": 179, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8069926689" }, { "job": 85027390311, "time": 210, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8069867924" }, { "job": 85027966765, "time": 160, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8069920287" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/28668907440", "_status": "success", "_upstream": "https://github.com/cran/TestREnlme", "_commit": { "id": "f061c1d5b68c7503c485fd5dfbccd2038af371d5", "author": "Germaine Uwimpuhwe ", "committer": "cran-robot ", "message": "version 0.1.0\n", "time": 1783080015 }, "_maintainer": { "name": "Germaine Uwimpuhwe", "email": "germaine.uwimpuhwe@durham.ac.uk", "login": "germaine86", "description": "", "uuid": 71663077 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "nlme", "version": ">= 3.1-150", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.3-0", "role": "Imports" }, { "package": "MASS", "version": ">= 7.3-54", "role": "Imports" }, { "package": "mgsub", "version": ">= 1.7.3", "role": "Imports" }, { "package": "matrixcalc", "version": ">= 1.0-5", "role": "Imports" }, { "package": "nls.multstart", "version": ">= 2.0.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.3.5", "role": "Imports" }, { "package": "expm", "version": ">= 0.999-6", "role": "Imports" }, { "package": "withr", "version": ">= 3.0.2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggpubr", "version": ">= 0.4.0", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "reshape2", "version": ">= 1.4.4", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-27", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2026-07-03" } ], "_stars": 0, "_contributors": [ { "user": "germaine86", "count": 1, "uuid": 71663077 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 615, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TestREnlme" }, "_devurl": "https://github.com/germaine86/testrenlme", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/TestREnlme.html", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2026-07-03" } ], "_exports": [ "Beta_hat", "bootstrap_se", "Dhypothesis_test", "Dmethod", "MM_base", "plot_condition", "plot_fitted", "plot_perm_hist", "plot_profiles", "plot_residuals", "plot_variance", "Tstat", "ZandYPred" ], "_datasets": [ { "name": "SkillAcq", "title": "Skill acquisition data", "object": "SkillAcq", "class": [ "data.frame" ], "fields": [ "id", "ly1", "ly2", "ly3", "ly4", "ly5", "ly6", "ly7", "ly8", "ly9", "ly10", "ly11", "wm2" ], "rows": 204, "table": true, "tojson": true } ], "_help": [ { "page": "Beta_hat", "title": "Estimate fixed effects by nonlinear least squares", "topics": [ "Beta_hat" ] }, { "page": "bootstrap_se", "title": "Bootstrap standard errors for variance component estimates", "topics": [ "bootstrap_se" ] }, { "page": "Dhypothesis_test", "title": "Permutation test for random effects in linear and nonlinear mixed-effects models", "topics": [ "Dhypothesis_test" ] }, { "page": "Dmethod", "title": "Non-parametric approach to estimate variance components in a linear and nonlinear mixed-effects model", "topics": [ "Dmethod" ] }, { "page": "MM_base", "title": "Compute first-stage quantities for MM and MMF estimators", "topics": [ "MM_base" ] }, { "page": "plot_condition", "title": "Plot per-subject condition numbers", "topics": [ "plot_condition" ] }, { "page": "plot_fitted", "title": "Plot fitted curves overlaid on observed data", "topics": [ "plot_fitted" ] }, { "page": "plot_perm_hist", "title": "Histogram of the permutation null distribution", "topics": [ "plot_perm_hist" ] }, { "page": "plot_profiles", "title": "Plot raw individual trajectories", "topics": [ "plot_profiles" ] }, { "page": "plot_residuals", "title": "Plot residuals versus fitted values", "topics": [ "plot_residuals" ] }, { "page": "plot_variance", "title": "Compare variance component estimates across methods", "topics": [ "plot_variance" ] }, { "page": "plot.Dmethod", "title": "Plot method for 'Dmethod' objects", "topics": [ "plot.Dmethod" ] }, { "page": "plot.Dtest", "title": "Plot method for 'Dtest' objects", "topics": [ "plot.Dtest" ] }, { "page": "SkillAcq", "title": "Skill acquisition data", "topics": [ "SkillAcq" ] }, { "page": "Tstat", "title": "Compute the observed test statistic", "topics": [ "Tstat" ] }, { "page": "ZandYPred", "title": "Compute Jacobian matrix and fixed-effects predicted values", "topics": [ "ZandYPred" ] } ], "_rundeps": [ "cli", "cpp11", "dplyr", "expm", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lhs", "lifecycle", "magrittr", "MASS", "Matrix", "matrixcalc", "mgsub", "minpack.lm", "nlme", "nls.multstart", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "TestREnlme.Rmd", "filename": "TestREnlme.html", "title": "TestREnlme: Testing Random Effects in Linear and Nonlinear Mixed-Effects Models", "author": "Germaine Uwimpuhwe, Reza Drikvandi, Shelley A. Blozis", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Model Formulation", "Theophylline Pharmacokinetic Data", "Data and Model", "Exploratory Plot", "Testing All Random Effects", "Step 1: Model preparation", "Step 2: Variance components estimation", "Step 3: Bootstrap standard errors.", "Step 4: Permutation tests", "Permutation histograms", "Reduced Random Effect Strureture.", "Diagnostic plots", "Condition-number diagnostics", "Step 4: Permutation", "Skill Acquisition Data", "Full Model (Three Random Effects)", "Summary of Key Functions", "References" ], "created": "2026-07-03 12:00:15", "modified": "2026-07-03 12:00:15", "commits": 1 } ], "_score": 2, "_indexed": false, "_nocasepkg": "testrenlme", "_universes": [ "cran", "germaine86" ], "_indexurl": "https://germaine86.r-universe.dev/TestREnlme", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-07-03T15:15:04.000Z", "distro": "resolute", "commit": "f061c1d5b68c7503c485fd5dfbccd2038af371d5", "fileid": "https://r2.ropensci.org/96f653c6c8f3f6cb1fb41e2ece8fc3cef150c7d0774d4cfcedee9b51bc93f49d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28668907440" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-07-03T15:15:02.000Z", "distro": "resolute", "commit": "f061c1d5b68c7503c485fd5dfbccd2038af371d5", "fileid": "https://r2.ropensci.org/21a03d1d5fad4656f09695b9af9ff5908a60f8a6a557e8ddddf6858a04f436ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28668907440" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-07-03T15:15:30.000Z", "commit": "f061c1d5b68c7503c485fd5dfbccd2038af371d5", "fileid": "https://r2.ropensci.org/fa9228026f91411b37fba56c850dc4136a70b137dbd5b9d135bc02236d78d8da", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/28668907440" } ] }