{ "_id": "6a51d1c29b92047c28d51432", "Package": "mixeff", "Title": "Audit-First Mixed-Effects Models via the 'mixeff-rs' Rust Crate", "Version": "0.2.0", "Authors@R": "person(\"Brad\", \"Buchsbaum\",\nemail = \"bbuchsbaum@research.baycrest.org\",\nrole = c(\"aut\", \"cre\"))", "Description": "An R wrapper for the 'mixeff-rs' Rust crate, providing\nlinear and generalized linear mixed-effects model fitting via\nlme4-style formulas. The wrapper is audit-first: every printed\nclaim traces back to a versioned JSON artifact produced by the\nRust compiler, and the package refuses to fabricate inference\nresults that the engine cannot certify. See the package\nvignettes for migration from 'lme4' and the demystification\nsurface for random-effects syntax.", "License": "MIT + file LICENSE", "URL": "https://bbuchsbaum.github.io/mixeff/,\nhttps://github.com/bbuchsbaum/mixeff", "BugReports": "https://github.com/bbuchsbaum/mixeff/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/rextendr/version": "0.5.0", "SystemRequirements": "Cargo (Rust's package manager, >= 1.78.0), rustc\n(>= 1.78.0), GNU make", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/Needs/website": "albersdown", "Config/pak/sysreqs": "make libclang-dev", "Repository": "https://bbuchsbaum.r-universe.dev", "Date/Publication": "2026-07-11 01:45:38 UTC", "RemoteUrl": "https://github.com/bbuchsbaum/mixeff", "RemoteRef": "HEAD", "RemoteSha": "fb76713b0bad59020bcd3b58979c3546852eb317", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-11 04:55:18 UTC", "User": "root" }, "Author": "Brad Buchsbaum [aut, cre]", "Maintainer": "Brad Buchsbaum ", "_user": "bbuchsbaum", "_type": "src", "_file": "mixeff_0.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/60258eb12056e3e6af5e1948d6296f0f9a4d905b92da17854fbe7c7d20d17633", "_filesize": 6947227, "_sha256": "60258eb12056e3e6af5e1948d6296f0f9a4d905b92da17854fbe7c7d20d17633", "_expires": "2026-10-19T05:16:47.000Z", "_created": "2026-07-11T04:55:18.000Z", "_published": "2026-07-11T05:16:50.517Z", "_jobs": [ { "job": 86512391889, "time": 475, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8244992892" }, { "job": 86512391913, "time": 503, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8244996285" }, { "job": 86512391894, "time": 468, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8244991905" }, { "job": 86512391896, "time": 401, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8244981566" }, { "job": 86512391879, "time": 431, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8244985772" }, { "job": 86512391885, "time": 777, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8245038244" }, { "job": 86512391891, "time": 500, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8244995749" }, { "job": 86512391892, "time": 1089, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8245085505" }, { "job": 86511744171, "time": 543, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8244924736" }, { "job": 86512391867, "time": 308, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 86512391876, "time": 523, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8244999234" }, { "job": 86512391873, "time": 638, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8245016693" }, { "job": 86512391880, "time": 674, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8245022613" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bbuchsbaum/actions/runs/29140200875", "_status": "success", "_upstream": "https://github.com/bbuchsbaum/mixeff", "_commit": { "id": "fb76713b0bad59020bcd3b58979c3546852eb317", "author": "bbuchsbaum ", "committer": "bbuchsbaum ", "message": "test: skip lme4-parity cases when the lme4/lmer REFERENCE fit itself errors\n\nR-universe's linux/R-4.6.1 + win/R-devel binary builds failed with\n'Error: Downdated VtV is not positive definite' at test-glmm.R:137 — an\nlme4 glmer() Cholesky-downdate failure on the fragile grouseticks Poisson\nmodel that throws on some platform/lme4/Matrix builds but not others\n(macOS + the builders' other R versions passed, which is why local +\n5/7 R-universe binaries were green). Parity cannot be asserted against a\nreference lme4 could not compute, and an lme4-side numerical failure is\nnot a mixeff defect.\n\nThe GLMM (mm_glmm_fit_pair) and LMM/lmerTest (mm_lme4_fit_pair,\nmm_lmerTest_fit_pair) reference fits are now guarded: fit mixeff first\n(so a genuine mixeff failure still surfaces), then tryCatch the reference\nand testthat::skip() the case if the reference tool errors. Prevents the\nsame spurious ERROR on CRAN's multi-platform check farm. Suite green\nlocally (reference fits succeed here, so no cases skip).\n\nCo-Authored-By: Claude Fable 5 \n", "time": 1783734338 }, "_maintainer": { "name": "Brad Buchsbaum", "email": "bbuchsbaum@research.baycrest.org" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "jsonlite", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "broom", "role": "Suggests" }, { "package": "broom.mixed", "role": "Suggests" }, { "package": "generics", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "emmeans", "version": ">= 1.4", "role": "Suggests" }, { "package": "estimability", "role": "Suggests" }, { "package": "jsonvalidate", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "lme4", "role": "Suggests" }, { "package": "lmerTest", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "rextendr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bbuchsbaum", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-20", "n": 5 }, { "week": "2026-21", "n": 10 }, { "week": "2026-22", "n": 3 }, { "week": "2026-23", "n": 30 }, { "week": "2026-24", "n": 10 }, { "week": "2026-27", "n": 13 }, { "week": "2026-28", "n": 5 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "bbuchsbaum", "count": 97, "uuid": 53819 } ], "_userbio": { "uuid": 53819, "type": "user", "name": "bbuchsbaum", "followers": 35 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mixeff" }, "_devurl": "https://github.com/bbuchsbaum/mixeff", "_pkgdown": "https://bbuchsbaum.github.io/mixeff/", "_searchresults": 78, "_cargo": true, "_topics": [ "rust", "cargo" ], "_rbuild": 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"recover_data.mm_glmm", "recover_data.mm_lmm", "refit", "reporting_table", "reproducibility", "revive", "roles", "test_effect", "test_random_effect", "VarCorr", "verify_convergence" ], "_help": [ { "page": "anova.mm_glmm", "title": "Analysis of deviance for GLMMs", "topics": [ "anova.mm_glmm" ] }, { "page": "as_json", "title": "Serialize a mixeff spec or fit to JSON", "topics": [ "as_json", "as_json.mm_compiled" ] }, { "page": "audit", "title": "Audit a compiled model spec or fitted model", "topics": [ "audit", "audit.default", "audit.mm_compiled" ] }, { "page": "audit_design", "title": "Deprecated alias for 'audit()'", "topics": [ "audit_design" ] }, { "page": "bootstrap_control", "title": "Fixed-effect bootstrap control", "topics": [ "bootstrap_control" ] }, { "page": "changes", "title": "Show requested, effective, and fitted model-state changes", "topics": [ "changes", "changes.mm_compiled" ] }, { "page": "compare", "title": "Compare fitted mixeff models", "topics": [ "compare", "compare.mm_lmm" ] }, { "page": "compare_covariance", "title": "Compare covariance parameterizations for current random terms", "topics": [ "compare_covariance" ] }, { "page": "compile_model", "title": "Compile a mixed-effects model spec without fitting", "topics": [ "compile_model" ] }, { "page": "confint.mm_glmm", "title": "Confidence intervals for fixed effects of a mixeff GLMM", "topics": [ "confint.mm_glmm" ] }, { "page": "contrast", "title": "Contrast fixed effects", "topics": [ "contrast", "contrast.mm_glmm", "contrast.mm_lmm" ] }, { "page": "df_for_contrast", "title": "Degrees of freedom for a contrast", "topics": [ "df_for_contrast", "df_for_contrast.mm_lmm" ] }, { "page": "diagnostics", "title": "Inspect mixeff diagnostics and fit status", "topics": [ "diagnostics", "diagnostics.mm_compiled", "fit_status", "fit_status.mm_compiled", "fit_status.mm_fit" ] }, { "page": "drop1.mm_glmm", "title": "Drop one fixed-effect term at a time from a GLMM", "topics": [ "drop1.mm_glmm" ] }, { "page": "drop1.mm_lmm", "title": "Drop one fixed-effect term at a time", "topics": [ "drop1.mm_lmm" ] }, { "page": "estimability", "title": "Assess contrast estimability", "topics": [ "estimability", "estimability.mm_lmm" ] }, { "page": "explain_model", "title": "Explain the random-effects structure of a compiled model", "topics": [ "explain_model" ] }, { "page": "fit_handle_alive", "title": "Test whether a mixeff fit has a live native handle", "topics": [ "fit_handle_alive", "fit_handle_alive.mm_fit" ] }, { "page": "getME", "title": "Extract low-level model components", "topics": [ "getME", "getME.mm_lmm" ] }, { "page": "glmm", "title": "Fit a generalized linear mixed model", "topics": [ "glmm" ] }, { "page": "inference_options", "title": "Inspect inference methods available for this fit", "topics": [ "inference_options", "inference_options.mm_lmm" ] }, { "page": "inference_table", "title": "Fixed-effect inference table", "topics": [ "inference_table", "inference_table.mm_lmm" ] }, { "page": "is_singular", "title": "Test whether a fit is singular or reduced-rank", "topics": [ "is_singular", "is_singular.mm_lmm" ] }, { "page": "lmm", "title": "Fit a linear mixed-effects model", "topics": [ "lmm" ] }, { "page": "mm_control", "title": "Control mixeff fitting behavior", "topics": [ "mm_control" ] }, { "page": "mm_formula_manifest", "title": "The wrapper's formula manifest", "topics": [ "mm_formula_manifest" ] }, { "page": "mm_grid", "title": "Marginal grids, predictions, means, and comparisons", "topics": [ "mm_comparisons", "mm_comparisons.mm_lmm", "mm_grid", "mm_grid.mm_lmm", "mm_means", "mm_means.mm_lmm", "mm_predictions", "mm_predictions.mm_lmm" ] }, { "page": "mm_json_known_schemas", "title": "Closed list of schema/version pairs the wrapper understands", "topics": [ "mm_json_known_schemas" ] }, { "page": "mm_json_negotiate", "title": "Negotiate a JSON schema header against what 'mixeff' supports", "topics": [ "mm_json_negotiate" ] }, { "page": "mm_lincomb", "title": "Wald inference on a linear combination of fixed effects", "topics": [ "mm_lincomb", "mm_lincomb.default", "mm_lincomb.mm_glmm", "mm_lincomb.mm_lmm" ] }, { "page": "mm_lmm-methods", "title": "Extract components from a fitted mixeff LMM", "topics": [ "AIC.mm_glmm", "AIC.mm_lmm", "as.data.frame.mm_ranef", "as.data.frame.mm_varcorr", "BIC.mm_glmm", "BIC.mm_lmm", "coef.mm_glmm", "coef.mm_lmm", "deviance.mm_glmm", "deviance.mm_lmm", "df.residual.mm_glmm", "df.residual.mm_lmm", "extractAIC.mm_glmm", "extractAIC.mm_lmm", "fixef", "fixef.mm_glmm", "fixef.mm_lmm", "formula.mm_glmm", "formula.mm_lmm", "logLik.mm_glmm", "logLik.mm_lmm", "mm_lmm-methods", "model.frame.mm_glmm", "model.frame.mm_lmm", "model.matrix.mm_glmm", "model.matrix.mm_lmm", "ngrps", "ngrps.default", "ngrps.mm_glmm", "ngrps.mm_lmm", "nobs.mm_glmm", "nobs.mm_lmm", "ranef", "ranef.mm_glmm", "ranef.mm_lmm", "sigma.mm_glmm", "sigma.mm_lmm", "terms.mm_glmm", "terms.mm_lmm", "VarCorr", "VarCorr.mm_glmm", "VarCorr.mm_lmm", "vcov.mm_glmm", "vcov.mm_lmm", "weights.mm_glmm", "weights.mm_lmm" ] }, { "page": "mm_negative_binomial", "title": "Negative-binomial family for 'glmm()'", "topics": [ "mm_negative_binomial" ] }, { "page": "mm_parse_formula", "title": "Parse and canonicalize an lme4-style formula", "topics": [ "mm_parse_formula" ] }, { "page": "model_report", "title": "Produce reporting tables for a fitted mixeff model", "topics": [ "model_report", "model_report.mm_fit", "reporting_table", "reporting_table.mm_drop1", "reporting_table.mm_fit", "reporting_table.mm_model_comparison", "reporting_table.mm_random_effect_test" ] }, { "page": "optimizer_certificate", "title": "Inspect the optimizer certificate", "topics": [ "optimizer_certificate", "optimizer_certificate.mm_compiled" ] }, { "page": "parameterization", "title": "Inspect covariance parameterization", "topics": [ "parameterization", "parameterization.mm_compiled" ] }, { "page": "parametric_bootstrap", "title": "Parametric bootstrap likelihood-ratio comparison", "topics": [ "parametric_bootstrap" ] }, { "page": "predict.mm_glmm", "title": "Predict from a fitted mixeff GLMM", "topics": [ "predict.mm_glmm" ] }, { "page": "predict.mm_lmm", "title": "Predict from a fitted mixeff LMM", "topics": [ "fitted.mm_glmm", "fitted.mm_lmm", "predict.mm_lmm", "residuals.mm_glmm", "residuals.mm_lmm" ] }, { "page": "profile.mm_lmm", "title": "Profile a fitted linear mixed model", "topics": [ "profile.mm_lmm" ] }, { "page": "random_blocks", "title": "Inspect random-effect blocks", "topics": [ "random_blocks", "random_blocks.mm_compiled" ] }, { "page": "random_options", "title": "Inspect nearby random-effect spellings for one grouping factor", "topics": [ "random_options" ] }, { "page": "refit", "title": "Refit a mixeff LMM with a new response", "topics": [ "refit", "refit.mm_lmm" ] }, { "page": "reproducibility", "title": "Inspect reproducibility metadata", "topics": [ "reproducibility", "reproducibility.mm_compiled" ] }, { "page": "revive", "title": "Revive a serialized mixeff object", "topics": [ "revive", "revive.mm_fit" ] }, { "page": "roles", "title": "Declare or inspect design roles", "topics": [ "roles" ] }, { "page": "simulate.mm_lmm", "title": "Simulate from a mixeff LMM", "topics": [ "simulate.mm_lmm" ] }, { "page": "test_effect", "title": "Test a fixed-effect term", "topics": [ "test_effect", "test_effect.mm_lmm" ] }, { "page": "test_random_effect", "title": "Test a random-effect variance component", "topics": [ "test_random_effect", "test_random_effect.mm_lmm" ] }, { "page": "update.mm", "title": "Update and re-fit a mixeff model", "topics": [ "update.mm", "update.mm_glmm", "update.mm_lmm" ] }, { "page": "verify_convergence", "title": "Verify convergence of a fitted linear mixed model", "topics": [ "verify_convergence", "verify_convergence.default", "verify_convergence.mm_lmm" ] } ], "_readme": "https://github.com/bbuchsbaum/mixeff/raw/HEAD/README.md", "_rundeps": [ "jsonlite", "lattice", "Matrix", "rlang" ], "_vignettes": [ { "source": "benchmarking.Rmd", "filename": "benchmarking.html", "title": "Benchmarking mixeff", "engine": "knitr::rmarkdown", "headings": [ "What does the benchmark show?", "What should you measure?", "How do you benchmark fitting?", "How do you benchmark bootstrap?", "What does inference method choice cost?", "How do you read the result?", "What should go in a report?" ], "created": "2026-05-17 00:06:19", "modified": "2026-05-31 20:37:23", "commits": 2 }, { "source": "demystifying-formulas.Rmd", "filename": "demystifying-formulas.html", "title": "Demystifying Random-Effects Formulas", "engine": "knitr::rmarkdown", "headings": [ "What does (1 | subject) say?", "What changes when you add a random slope?", "What do split blocks and || mean?", "What are the three kinds of help?", "How do you inspect nearby formulas?", "Why is there no recommendation row?", "Where do fitted-model changes appear?" ], "created": "2026-05-17 00:06:19", "modified": "2026-06-11 14:14:39", "commits": 2 }, { "source": "lmm-basics.Rmd", "filename": "lmm-basics.html", "title": "Fitting Linear Mixed Models", "engine": "knitr::rmarkdown", "headings": [ "What data are we fitting?", "What happens when you call lmm()?", "How do you read the coefficient table?", "Which familiar extractors work?", "How do prediction and residuals line up?", "Where is the design audit?", "What should you read next?" ], "created": "2026-05-17 00:06:19", "modified": "2026-05-17 00:06:19", "commits": 1 }, { "source": "glmm.Rmd", "filename": "glmm.html", "title": "GLMM Fitting and Model Comparison", "engine": "knitr::rmarkdown", "headings": [ "Family and Audit", "Fit", "Quadrature Sensitivity", "Current Boundaries" ], "created": "2026-05-17 00:06:19", "modified": "2026-07-03 15:51:03", "commits": 6 }, { "source": "inference-method-glossary.Rmd", "filename": "inference-method-glossary.html", "title": "Inference Method Glossary", "engine": "knitr::rmarkdown", "headings": [ "expected_status", 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15:51:03", "modified": "2026-07-10 18:03:17", "commits": 2 }, { "source": "lme4-migration.Rmd", "filename": "lme4-migration.html", "title": "Migrating from lme4", "engine": "knitr::rmarkdown", "headings": [ "The two edits", "Verb map", "Argument map for lmm() / glmm()", "Four things that will bite, and the fix", "What is NA-with-a-reason (and why)" ], "created": "2026-06-02 10:48:25", "modified": "2026-07-10 18:03:17", "commits": 4 }, { "source": "reporting-lmms.Rmd", "filename": "reporting-lmms.html", "title": "Reporting Linear Mixed Models", "engine": "knitr::rmarkdown", "headings": [ "What model will we report?", "What did the formula request?", "What fit was used?", "Which design facts belong in the report?", "How are estimates and p-values labelled?", "How are random effects reported?", "What is unavailable or caveated?", "What should go into your written report?" ], "created": "2026-05-17 00:06:19", "modified": "2026-07-10 18:03:17", "commits": 4 }, { "source": "reproducing-aphantasia.Rmd", "filename": "reproducing-aphantasia.html", "title": "Reproducing the Loo Aphantasia GLMMs", "engine": "knitr::rmarkdown", "headings": [ "Inferential surfaces", "Out of scope here", "Caveats", "Citation" ], "created": "2026-05-21 20:36:39", "modified": "2026-07-10 18:03:17", "commits": 7 }, { "source": "saving-and-reviving.Rmd", "filename": "saving-and-reviving.html", "title": "Saving and Reloading Fits", "engine": "knitr::rmarkdown", "headings": [ "Fit a model", "Round trip through RDS", "Rebuild design matrices when needed", "What stays explicit?", "What should you report?" ], "created": "2026-05-17 00:06:19", "modified": "2026-05-31 20:37:23", "commits": 2 }, { "source": "mixeff.Rmd", "filename": "mixeff.html", "title": "Why mixeff?", "engine": "knitr::rmarkdown", "headings": [ "The dataset", "A. The formula stays familiar", "B. When a fit is degenerate, you find out which part", "C. Expose when asymptotics are weak, then offer bootstrap", "D. 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