{ "_id": "6ad688bdd556c3a3418a6138", "Package": "lmmix", "Title": "Linear Mixed Models with Correlated Residuals", "Version": "0.4.0", "Authors@R": "person(\"Aurélien\", \"Nicosia\", ,\n\"aurelien.nicosia@mat.ulaval.ca\",\nrole = c(\"aut\", \"cre\"))", "Description": "Fits Gaussian linear mixed models by explicitly optimizing\nthe maximum likelihood or restricted maximum likelihood\ncriterion. Random effects and correlated residual structures\ncan be combined in the same model. Fixed-effect inference\nincludes Satterthwaite and Kenward-Roger denominator degrees of\nfreedom, type III tests, likelihood-ratio model comparisons,\nand estimated marginal means.", "License": "MIT + file LICENSE", "URL": "https://github.com/AurelienNicosiaULaval/lmmix,\nhttps://aureliennicosiaulaval.github.io/lmmix/", "BugReports": "https://github.com/AurelienNicosiaULaval/lmmix/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "LazyData": "true", "Repository": "https://aureliennicosiaulaval.r-universe.dev", "Date/Publication": "2026-07-15 16:12:48 UTC", "RemoteUrl": "https://github.com/AurelienNicosiaULaval/lmmix", "RemoteRef": "HEAD", "RemoteSha": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-19 21:01:08 UTC", "User": "root" }, "Author": "Aurélien Nicosia [aut, cre]", "Maintainer": "Aurélien Nicosia ", "_user": "aureliennicosiaulaval", "_type": "src", "_file": "lmmix_0.4.0.tar.gz", "_fileid": "https://r2.ropensci.org/38c6a5f3461fcd4abd1c6f2c31b2c0df3f6674f44449fc5c94554fed0c4393fe", "_filesize": 560130, "_sha256": "38c6a5f3461fcd4abd1c6f2c31b2c0df3f6674f44449fc5c94554fed0c4393fe", "_expires": "2027-01-27T21:12:13.000Z", "_created": "2026-10-19T21:01:08.000Z", "_published": "2026-10-19T21:16:45.543Z", "_upstream": "https://github.com/AurelienNicosiaULaval/lmmix", "_status": "success", "_maintainer": { "name": "Aurélien Nicosia", "email": "aurelien.nicosia@mat.ulaval.ca", "login": "aureliennicosiaulaval", "linkedin": "in/aur%C3%A9lien-nicosia-6a52487b", "description": "Chargé d’enseignement à l’Université Laval • Passionné par la science des données, R et la pédagogie active • Créateur d’outils et de ressources pour apprendre ", "uuid": 116816597 }, "_jobs": [ { "job": 118311306157, "time": 224, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12221587004" }, { "job": 118311306710, "time": 274, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12221583274" }, { "job": 118311306312, "time": 157, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12221778462" }, { "job": 118311303863, "time": 139, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12221744381" }, { "job": 118311304844, "time": 450, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12220534290" }, { "job": 118311305511, "time": 240, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12221007857" }, { "job": 118311305314, "time": 195, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12221807238" }, { "job": 118311306467, "time": 188, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12220729698" }, { "job": 118311305670, "time": 420, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12222016676" } ], "_buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315", "_commit": { "id": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "author": "Aurélien Nicosia <116816597+AurelienNicosiaULaval@users.noreply.github.com>", "committer": "GitHub ", "message": "lmmix 0.4.0: implement audit improvements\n\n* feat: implement lmmix 0.4.0 audit improvements\n\n* test: allow published SAS rounding tolerance", "time": 1784131968 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "generics", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "numDeriv", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "emmeans", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "lme4", "role": "Suggests" }, { "package": "lmerTest", "role": "Suggests" }, { "package": "lintr", "role": "Suggests" }, { "package": "mmrm", "role": "Suggests" }, { "package": "nlme", "role": "Suggests" }, { "package": "pbkrtest", "role": "Suggests" }, { "package": "pkgdown", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "styler", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "aureliennicosiaulaval", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-29", "n": 15 } ], "_tags": [ { "name": "v0.2.0", "date": "2026-07-14" }, { "name": "v0.2.1", "date": "2026-07-14" }, { "name": "v0.3.0", "date": "2026-07-14" }, { "name": "v0.4.0", "date": "2026-07-15" } ], "_stars": 0, "_contributors": [ { "user": "aureliennicosiaulaval", "count": 21, "uuid": 116816597 } ], "_userbio": { "uuid": 116816597, "type": "user", "name": "Aurélien Nicosia", "followers": 13, "description": "Chargé d’enseignement à l’Université Laval • Passionné par la science des données, R et la pédagogie active • Créateur d’outils et de ressources pour apprendre " }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/lmmix" }, "_devurl": "https://github.com/aureliennicosiaulaval/lmmix", "_pkgdown": "https://aureliennicosiaulaval.github.io/lmmix/", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/lmmix.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "fixef", "lmm", "lmm_control", "lsmeans", "ranef", "VarCorr" ], "_datasets": [ { "name": "multicentre", "title": "Multi-site repeated-measures experiment", "object": "multicentre", "class": [ "data.frame" ], "fields": [ "Center", "Drug", "Subject", "Time", "Y" ], "rows": 153, "table": true, "tojson": true }, { "name": "sas_growth", "title": "Repeated-measures growth example from the SAS MIXED documentation", "object": "sas_examples", "class": [ "data.frame" ], "fields": [ "Person", "Gender", "Age", "y" ], "rows": 108, "table": true, "tojson": true }, { "name": "sas_line_source", "title": "Line-source irrigation example from the SAS MIXED documentation", "object": "sas_examples", "class": [ "data.frame" ], "fields": [ "Block", "Cult", "Sbplt", "Irrig", "Dir", "Y" ], "rows": 108, "table": true, "tojson": true }, { "name": "sas_random_coefficients", "title": "Random-coefficients example from the SAS MIXED documentation", "object": "sas_examples", "class": [ "data.frame" ], "fields": [ "Batch", "Month", "Replicate", "Y" ], "rows": 108, "table": true, "tojson": true }, { "name": "sas_split_plot", "title": "Split-plot example from the SAS MIXED procedure documentation", "object": "sas_examples", "class": [ "data.frame" ], "fields": [ "Block", "A", "B", "Y" ], "rows": 24, "table": true, "tojson": true } ], "_help": [ { "page": "augment.lmm", "title": "Augment data with fitted values and residuals", "topics": [ "augment.lmm" ] }, { "page": "fixef", "title": "Extract fixed effects", "topics": [ "fixef" ] }, { "page": "glance.lmm", "title": "One-row model summary for an 'lmm' model", "topics": [ "glance.lmm" ] }, { "page": "lmm", "title": "Fit a Gaussian linear mixed model", "topics": [ "lmm" ] }, { "page": "lmm_control", "title": "Control numerical optimization for 'lmm()'", "topics": [ "lmm_control" ] }, { "page": "lmm-methods", "title": "Standard methods for 'lmm' fits", "topics": [ "AIC.lmm", "anova.lmm", "BIC.lmm", "coef.lmm", "confint.lmm", "deviance.lmm", "fitted.lmm", "formula.lmm", "lmm-methods", "logLik.lmm", "model.frame.lmm", "model.matrix.lmm", "nobs.lmm", "plot.lmm", "predict.lmm", "print.lmm", "residuals.lmm", "sigma.lmm", "simulate.lmm", "terms.lmm", "update.lmm", "vcov.lmm" ] }, { "page": "lsmeans", "title": "Estimated marginal means for an 'lmm' model", "topics": [ "lsmeans" ] }, { "page": "multicentre", "title": "Multi-site repeated-measures experiment", "topics": [ "multicentre" ] }, { "page": "ranef", "title": "Extract random effects", "topics": [ "ranef" ] }, { "page": "recover_data.lmm", "title": "Support for 'emmeans'", "topics": [ "emm_basis.lmm", "recover_data.lmm" ] }, { "page": "sas_growth", "title": "Repeated-measures growth example from the SAS MIXED documentation", "topics": [ "sas_growth" ] }, { "page": "sas_line_source", "title": "Line-source irrigation example from the SAS MIXED documentation", "topics": [ "sas_line_source" ] }, { "page": "sas_random_coefficients", "title": "Random-coefficients example from the SAS MIXED documentation", "topics": [ "sas_random_coefficients" ] }, { "page": "sas_split_plot", "title": "Split-plot example from the SAS MIXED procedure documentation", "topics": [ "sas_split_plot" ] }, { "page": "summary.lmm", "title": "Summarize an 'lmm' fit", "topics": [ "summary.lmm" ] }, { "page": "tidy.lmm", "title": "Tidy an 'lmm' model", "topics": [ "tidy.lmm" ] }, { "page": "VarCorr", "title": "Extract covariance components", "topics": [ "VarCorr" ] } ], "_readme": "https://github.com/AurelienNicosiaULaval/lmmix/raw/HEAD/README.md", "_rundeps": [ "cli", "generics", "glue", "lattice", "lifecycle", "magrittr", "Matrix", "numDeriv", "pillar", "pkgconfig", "rlang", "tibble", "utf8", "vctrs" ], "_vignettes": [ { "source": "comparison.Rmd", "filename": "comparison.html", "title": "Choosing lmmix and related R packages", "engine": "knitr::rmarkdown", "headings": [ "Purpose", "Main distinctions", "Capability matrix", "Choosing a package", "Computational boundary", "Current boundaries that affect selection" ], "created": "2026-07-15 16:12:48", "modified": "2026-07-15 16:12:48", "commits": 1 }, { "source": "boundary-inference.Rmd", "filename": "boundary-inference.html", "title": "Covariance intervals and boundary-aware model comparisons", "engine": "knitr::rmarkdown", "headings": [ "Scope", "Confidence intervals for covariance parameters", "Parametric-bootstrap likelihood-ratio test", "Reproducibility" ], "created": "2026-07-14 15:53:50", "modified": "2026-07-14 15:53:50", "commits": 1 }, { "source": "theory-reml.Rmd", "filename": "theory-reml.html", "title": "Estimation and inference in lmmix", "engine": "knitr::rmarkdown", "headings": [ "Gaussian mixed-model representation", "Covariance parameterization", "Profiled ML and REML criteria", "Optimization and covariance-parameter uncertainty", "Satterthwaite denominator degrees of freedom", "Kenward-Roger adjustment", "Type III tests", "Estimated marginal means", "Empirical BLUPs and prediction", "Computational scope" ], "created": "2026-07-13 20:27:03", "modified": "2026-07-15 16:12:48", "commits": 6 }, { "source": "lmmix.Rmd", "filename": "lmmix.html", "title": "Using lmmix", "engine": "knitr::rmarkdown", "headings": [ "Model scope", "Prepare the data", "Fit a combined covariance model", "Inspect convergence before inference", "Fixed effects and type III tests", "Covariance parameters and random effects", "Estimated marginal means", "Predictions, residuals and tidy output", "Simulation, updating, weights, and offsets", "Diagnostic plots", "Alternative model specifications", "Practical limits" ], "created": "2026-07-13 20:27:03", "modified": "2026-07-15 16:12:48", "commits": 10 }, { "source": "validation.Rmd", "filename": "validation.html", "title": "Validation against independent R implementations and PROC MIXED", "engine": "knitr::rmarkdown", "headings": [ "Purpose and evidentiary standard", "Comparison map", "Shared longitudinal data", "Random-intercept REML comparison with nlme::lme()", "Random-slope REML comparison with nlme::lme()", "Maximum-likelihood comparison with nlme::lme()", "Marginal CS and AR(1) comparisons with nlme::gls()", "Marginal AR(1) comparison with mmrm::mmrm()", "Satterthwaite comparison with lmerTest::lmer()", "Kenward-Roger comparison with mmrm::mmrm()", "Crossed random effects and model comparison", "Combined covariance structures", "Official PROC MIXED examples", "Example 79.1: split-plot design", "Example 79.2: repeated measures", "Example 79.5: random coefficients", "Example 79.6: line-source sprinkler irrigation", "Stored PROC MIXED comparison", "Covariance parameters and likelihood criterion", "Fixed effects", "Type III tests", "LS-means", "Pairwise LS-mean differences", "Automated regression tests", "Reproducibility information", "Boundaries of the evidence" ], "created": "2026-07-13 21:42:30", "modified": "2026-07-15 16:12:48", "commits": 7 } ], "_score": 3.3979400086720375, "_indexed": true, "_nocasepkg": "lmmix", "_universes": [ "aureliennicosiaulaval" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.0", "date": "2026-10-19T21:03:22.000Z", "distro": "resolute", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/c6816a750dad88bbea1b54a6d419e29ebadc5da5637a8a5593a6f1ac39132eb4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" }, { "r": "4.6.1", "os": "linux", "version": "0.4.0", "date": "2026-10-19T21:04:55.000Z", "distro": "resolute", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/6b899c49445d5b59b8da643c8635cab89f12ffff928620ea435cef61c81d2956", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" }, { "r": "4.5.3", "os": "mac", "version": "0.4.0", "date": "2026-10-19T21:10:17.000Z", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/b75564e1b18511e88c55876e0578ee40abfd45816b7444c6c875090f68c7215e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" }, { "r": "4.6.1", "os": "mac", "version": "0.4.0", "date": "2026-10-19T21:15:21.000Z", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/be7d8c59aebcf3d5a4c11a91d7f6b592b05761c717d5236db5e2b1489234bc39", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.0", "date": "2026-10-19T21:05:24.000Z", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/2b5dc1d7347acd882ec17209acc9434356b40b7de42ac02189264604ab55655f", "status": "success", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" }, { "r": "4.7.0", "os": "win", "version": "0.4.0", "date": "2026-10-19T21:02:32.000Z", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/1b4c667426b88267ff94902cd2b0d8c37fc60570192fbdb167827b43720c871f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" }, { "r": "4.5.3", "os": "win", "version": "0.4.0", "date": "2026-10-19T21:02:20.000Z", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/52c991ce8950eeacfc2f6f1bb1a57b16a0a0e7f8bd97927975909d7e21a76808", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" }, { "r": "4.6.1", "os": "win", "version": "0.4.0", "date": "2026-10-19T21:06:24.000Z", "commit": "e69155825d18f5298a3ed6d4e2711d0c1d95ba4d", "fileid": "https://r2.ropensci.org/597e64d28ae9b87753f03638564f82a4cdbdc0b915dae5493a905c3846a3e982", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/aureliennicosiaulaval/actions/runs/39323084315" } ] }