{ "_id": "6ac10a42552a13804ac7ec49", "Package": "lmebayesCore", "Type": "Package", "Title": "Core C++ Sampling Engine for 'lmebayes'", "Version": "0.1.0", "Date": "2026-08-10", "Authors@R": "c(\nperson(\"Kjell\", \"Nygren\", role = c(\"aut\", \"cre\"),\nemail = \"kjell.a.nygren@gmail.com\"),\nperson(\"The R Core Team\", role = c(\"ctb\", \"cph\"),\ncomment = \"R Mathlib sources, R stats modeling code, and derived/adapted routines\"),\nperson(\"The R Foundation\", role = \"cph\",\ncomment = \"Portions of R Mathlib and R source code\"),\nperson(\"Ross\", \"Ihaka\", role = c(\"ctb\", \"cph\"),\ncomment = \"R Mathlib and original R modeling infrastructure\"),\nperson(\"Robert\", \"Gentleman\", role = c(\"ctb\", \"cph\"),\ncomment = \"Portions of R Mathlib\"),\nperson(\"Simon\", \"Davies\", role = \"ctb\",\ncomment = \"Original R glm implementation\"),\nperson(\"Morten\", \"Welinder\", role = c(\"ctb\", \"cph\"),\ncomment = \"Portions of R Mathlib\"),\nperson(\"Martin\", \"Maechler\", role = \"ctb\",\ncomment = \"Portions of R Mathlib\")\n)", "Description": "Core C++ engine for lmebayes: envelope-based iid samplers,\ntwo-block Gibbs mixed-model engines, and optional OpenCL\nacceleration. Full-featured developer backend for lmebayes and\nextensions. End users should use lmebayes for lmer/glmer-style\nmixed-model workflows.", "License": "GPL-2", "URL": "https://github.com/knygren/lmebayesCore", "BugReports": "https://github.com/knygren/lmebayesCore/issues", "RdMacros": "Rdpack", "VignetteBuilder": "knitr", "SystemRequirements": "Optional OpenCL support. If available, GPU\nacceleration will be used; otherwise, computation runs on CPU.", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Language": "en-US", "Config/pak/sysreqs": "cmake make libicu-dev ocl-icd-opencl-dev", "Repository": "https://knygren.r-universe.dev", "Date/Publication": "2026-10-03 11:54:23 UTC", "RemoteUrl": "https://github.com/knygren/lmebayesCore", "RemoteRef": "HEAD", "RemoteSha": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-03 13:43:08 UTC", "User": "root" }, "Author": "Kjell Nygren [aut, cre],\nThe R Core Team [ctb, cph] (R Mathlib sources, R stats modeling code,\nand derived/adapted routines),\nThe R Foundation [cph] (Portions of R Mathlib and R source code),\nRoss Ihaka [ctb, cph] (R Mathlib and original R modeling\ninfrastructure),\nRobert Gentleman [ctb, cph] (Portions of R Mathlib),\nSimon Davies [ctb] (Original R glm implementation),\nMorten Welinder [ctb, cph] (Portions of R Mathlib),\nMartin Maechler [ctb] (Portions of R Mathlib)", "Maintainer": "Kjell Nygren ", "_user": "knygren", "_type": "src", "_file": "lmebayesCore_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/afe3fd371836b643ce93ba0575fe801cccf579101f12b142972b50733a45ac26", "_filesize": 3302832, "_sha256": "afe3fd371836b643ce93ba0575fe801cccf579101f12b142972b50733a45ac26", "_expires": "2027-01-11T13:59:27.000Z", "_created": "2026-10-03T13:43:08.000Z", "_published": "2026-10-03T13:59:30.121Z", "_jobs": [ { "job": 111215282285, "time": 398, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11274673595" }, { "job": 111215282271, "time": 467, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11274963273" }, { "job": 111215282417, "time": 381, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11275457816" }, { "job": 111215282364, "time": 488, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11275149923" }, { "job": 111215282267, "time": 400, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11275875383" }, { "job": 111215282282, "time": 489, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11275845667" }, { "job": 111215282237, "time": 707, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11275359944" }, { "job": 111215282242, "time": 565, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11276040142" }, { "job": 111213225444, "time": 739, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11275129169" }, { "job": 111215282212, "time": 296, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 111215282318, "time": 611, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11275885492" }, { "job": 111215282347, "time": 489, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11275682637" }, { "job": 111215282334, "time": 591, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11275920323" }, { "job": 111215282353, "time": 590, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11275699236" }, { "job": 111215282352, "time": 486, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11275509445" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423", "_status": "success", "_upstream": "https://github.com/knygren/lmebayesCore", "_commit": { "id": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "author": "knygren ", "committer": "knygren ", "message": "Restructured lmebayesCore by splitting lmerb and glmerb functionality into separate files\n", "time": 1791028463 }, "_maintainer": { "name": "Kjell Nygren", "email": "kjell.a.nygren@gmail.com", "login": "knygren", "linkedin": "in/kjellnygren", "description": "Data and analytics professional in pharma. Hobby: R package development. Creator of glmbayes — iid posterior sampling for Bayesian GLMs.", "uuid": 7188517 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "MASS", "role": "Depends" }, { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "glmbayesCore", "version": ">= 0.6.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.1.1", "role": "Imports" }, { "package": "RcppParallel", "role": "Imports" }, { "package": "Rdpack", "version": ">= 0.11-0", "role": "Imports" }, { "package": "opencltools", "version": ">= 0.8.1", "role": "Imports" }, { "package": "nmathopencl", "role": "Imports" }, { "package": "glmmTMB", "role": "Suggests" }, { "package": "bayesrules", "role": "Suggests" }, { "package": "CompQuadForm", "role": "Suggests" }, { "package": "mgcv", "role": "Suggests" }, { "package": "glmbayes", "role": "Suggests" }, { "package": "coda", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "bayestestR", "role": "Suggests" }, { "package": "LearnBayes", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "knygren", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-40", "n": 5 }, { "week": "2025-41", "n": 16 }, { "week": "2025-42", "n": 8 }, { "week": "2025-45", "n": 8 }, { "week": "2025-46", "n": 7 }, { "week": "2025-47", "n": 7 }, { "week": "2025-48", "n": 10 }, { "week": "2025-49", "n": 2 }, { "week": "2025-50", "n": 7 }, { "week": "2025-51", "n": 7 }, { "week": "2025-52", "n": 16 }, { "week": "2026-01", "n": 35 }, { "week": "2026-02", "n": 7 }, { "week": "2026-03", "n": 28 }, { "week": "2026-04", "n": 52 }, { "week": "2026-05", "n": 17 }, { "week": "2026-06", "n": 22 }, { "week": "2026-07", "n": 3 }, { "week": "2026-08", "n": 4 }, { "week": "2026-09", "n": 6 }, { "week": "2026-10", "n": 9 }, { "week": "2026-11", "n": 4 }, { "week": "2026-12", "n": 21 }, { "week": "2026-13", "n": 42 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 19 }, { "week": "2026-16", "n": 38 }, { "week": "2026-17", "n": 64 }, { "week": "2026-18", "n": 18 }, { "week": "2026-19", "n": 3 }, { "week": "2026-20", "n": 17 }, { "week": "2026-21", "n": 8 }, { "week": "2026-22", "n": 24 }, { "week": "2026-23", "n": 20 }, { "week": "2026-24", "n": 15 }, { "week": "2026-25", "n": 23 }, { "week": "2026-26", "n": 19 }, { "week": "2026-27", "n": 25 }, { "week": "2026-28", "n": 16 }, { "week": "2026-29", "n": 13 }, { "week": "2026-30", "n": 24 }, { "week": "2026-31", "n": 5 }, { "week": "2026-32", "n": 18 }, { "week": "2026-33", "n": 6 }, { "week": "2026-34", "n": 2 }, { "week": "2026-40", "n": 5 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "knygren", "count": 973, "uuid": 7188517 }, { "user": "knygrensny", "count": 266, "uuid": 224791279 }, { "user": "danieljobrien", "count": 1, "uuid": 7174733 } ], "_userbio": { "uuid": 7188517, "type": "user", "name": "Kjell Nygren", "followers": 2, "description": "Data and analytics professional in pharma. Hobby: R package development. Creator of glmbayes — iid posterior sampling for Bayesian GLMs." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/lmebayesCore" }, "_devurl": "https://github.com/knygren/lmebayescore", "_searchresults": 0, "_topics": [ "openblas", "onetbb", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/lmebayesCore.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "beta_in_marginal_safe_set", "beta_marginal_mode", "beta_marginal_safe_set", "certificate", "check_identifiability", "deficiency_calibrate", "deficiency_spectrum", "dGamma_list", "epsilon", "epsilon_optimize", "epsilon_star", "floor_coupling_eigenvalues", "floor_coupling_spectrum", "gamma_beta_tv_certificate", "group_effects_conditional_mean", "group_precision_floor", "model_setup", "mvn_calibrate", "optimal_rosenthal_tv_bound", "pfamily_list", "plot_mean_convergence", "plot_var_convergence", "population_mode", "print_groupef", "Prior_Setup_GLMM", "Prior_SetupGroup", "rglmerb", "rGLMM_reg", "rGLMM_reg_estimated_vcov", "rGLMM_reg_known_vcov", "rlmerb", "rLMMindepNormalGamma_reg", "rLMMindepNormalGamma_reg_estimated_vcov", "rLMMindepNormalGamma_reg_estimated_vcov_v2", "rLMMindepNormalGamma_reg_known_vcov", "rLMMindepNormalGamma_reg_known_vcov_v2", "rLMMNormal_reg", "rLMMNormal_reg_estimated_vcov", "rLMMNormal_reg_known_vcov", "rLMMNormal_reg_known_vcov_iid", "rLMMNormal_reg_known_vcov_two_bg", "rNormal_reg_group", "rNormal_reg_group_safe", "rNormalGLM_reg_group", "rNormalGLM_reg_group_safe", "rosenthal_drift_constants", "rosenthal_tv_bound", "two_block_rate", "two_block_rate_from_pfamily_list" ], "_help": [ { "page": "lmebayesCore-package", "title": "lmebayesCore: Core C++ Sampling Engine for lmebayes", "topics": [ "lmebayesCore-package", "lmebayesCore" ] }, { "page": "beta_in_marginal_safe_set", "title": "Test whether group random effects lie in widetilde B(delta_2).", "topics": [ "beta_in_marginal_safe_set" ] }, { "page": "beta_marginal_mode", "title": "Marginal-mode beta posterior mode (gamma integrated out)", "topics": [ "beta_marginal_mode" ] }, { "page": "beta_marginal_safe_set", "title": "Marginal-mode beta safe set for Rosenthal / TV certificates", "topics": [ "beta_marginal_safe_set" ] }, { "page": "certificate", "title": "Restricted two-block Gibbs minorization certificate (Chapter C05).", "topics": [ "certificate" ] }, { "page": "check_identifiability", "title": "Check identifiability and estimability of a single-factor mixed-model design", "topics": [ "check_identifiability" ] }, { "page": "deficiency_calibrate", "title": "Calibrate reference radius r(delta) and deficiency d = r^2/2.", "topics": [ "deficiency_calibrate" ] }, { "page": "deficiency_spectrum", "title": "Coupling eigenvalue spectrum at the population mode.", "topics": [ "deficiency_spectrum" ] }, { "page": "dGamma_list", "title": "Build a named list of dGamma measurement-dispersion priors", "topics": [ "dGamma_list" ] }, { "page": "epsilon", "title": "Restricted-chain Doeblin multiplier epsilon from spectrum-calibrated sizing.", "topics": [ "epsilon" ] }, { "page": "epsilon_optimize", "title": "Numerical epsilon(gamma*) from the minorization profile.", "topics": [ "epsilon_optimize" ] }, { "page": "epsilon_star", "title": "Mode profile epsilon(gamma*) for the restricted Gibbs certificate.", "topics": [ "epsilon_star" ] }, { "page": "floor_coupling_eigenvalues", "title": "Floor coupling eigenvalues from data-precision lower bounds.", "topics": [ "floor_coupling_eigenvalues" ] }, { "page": "floor_coupling_spectrum", "title": "Backward-compatible wrapper combining eigenvalues and drift constants.", "topics": [ "floor_coupling_spectrum" ] }, { "page": "gamma_beta_tv_certificate", "title": "Sharpest displayed gamma-beta total-variation certificate.", "topics": [ "gamma_beta_tv_certificate" ] }, { "page": "group_effects_conditional_mean", "title": "Conditional means of group random effects given population effects", "topics": [ "group_effects_conditional_mean" ] }, { "page": "group_precision_floor", "title": "Certified group-level data precision lower bounds", "topics": [ "group_precision_floor" ] }, { "page": "model_setup", "title": "Model setup for generalized linear mixed models", "topics": [ "model_setup" ] }, { "page": "mvn_calibrate", "title": "Legacy MVN-calibrated reference radius (equal-weight chi-square shortcut).", "topics": [ "mvn_calibrate" ] }, { "page": "optimal_rosenthal_tv_bound", "title": "Optimize Rosenthal TV bound over alpha and/or sweep count k.", "topics": [ "optimal_rosenthal_tv_bound" ] }, { "page": "pfamily_list", "title": "Build a named list of pfamily objects from a prior-setup object", "topics": [ "pfamily_list" ] }, { "page": "plot_mean_convergence", "title": "Combined mean-convergence plot for Block~2 fixed effects (Claim 1)", "topics": [ "plot_mean_convergence", "plot_mean_convergence.default", "plot_mean_convergence.rglmerb", "plot_mean_convergence.rGLMM_reg", "plot_mean_convergence.rlmerb", "plot_mean_convergence.rLMMindepNormalGamma_reg", "plot_mean_convergence.rLMMNormal_reg" ] }, { "page": "plot_var_convergence", "title": "Combined variance-convergence plot for Block~2 fixed effects (Claim 3)", "topics": [ "plot_var_convergence", "plot_var_convergence.default", "plot_var_convergence.rglmerb", "plot_var_convergence.rGLMM_reg", "plot_var_convergence.rlmerb", "plot_var_convergence.rLMMindepNormalGamma_reg", "plot_var_convergence.rLMMNormal_reg" ] }, { "page": "population_mode", "title": "EM fixed point for the C05 population mode gamma*.", "topics": [ "population_mode" ] }, { "page": "print_groupef", "title": "Print simulated group coefficients from an LMM/GLMM result", "topics": [ "print_groupef", "print_groupef.default", "print_groupef.rglmerb", "print_groupef.rGLMM_reg", "print_groupef.rlmerb", "print_groupef.rLMMindepNormalGamma_reg", "print_groupef.rLMMNormal_reg" ] }, { "page": "print.population_mode_em_trace", "title": "Print a 'population_mode_em_trace' object.", "topics": [ "print.population_mode_em_trace" ] }, { "page": "Prior_Setup_GLMM", "title": "Prior setup for generalized linear mixed models", "topics": [ "Prior_Setup_GLMM" ] }, { "page": "Prior_SetupGroup", "title": "Prior setup for row-block regressions", "topics": [ "Prior_SetupGroup" ] }, { "page": "rglmerb", "title": "The Bayesian Generalized Linear Mixed-Effects Model Distribution", "topics": [ "rglmerb" ] }, { "page": "rGLMM_reg", "title": "Simulation Functions for Generalized Linear Mixed Models", "concept": [ "simfuncs" ], "topics": [ "print.rGLMM_reg", "rGLMM_reg", "rGLMM_reg_estimated_vcov", "rGLMM_reg_known_vcov" ] }, { "page": "rlmerb", "title": "The Bayesian Linear Mixed-Effects Model Distribution", "topics": [ "rlmerb" ] }, { "page": "rLMM_reg", "title": "Simulation Functions for Linear Mixed Models", "concept": [ "simfuncs" ], "topics": [ "print.rLMMindepNormalGamma_reg", "print.rLMMNormal_reg", "rLMMindepNormalGamma_reg", "rLMMindepNormalGamma_reg_estimated_vcov", "rLMMindepNormalGamma_reg_estimated_vcov_v2", "rLMMindepNormalGamma_reg_known_vcov", "rLMMindepNormalGamma_reg_known_vcov_v2", "rLMMNormal_reg", "rLMMNormal_reg_estimated_vcov", "rLMMNormal_reg_known_vcov", "rLMMNormal_reg_known_vcov_iid", "rLMMNormal_reg_known_vcov_two_bg", "rLMM_reg" ] }, { "page": "rNormal_reg_group_safe", "title": "Gaussian blockwise draw with widetilde-B rejection", "topics": [ "rNormal_reg_group_safe" ] }, { "page": "rNormalGLM_reg_group_safe", "title": "GLM blockwise draw with widetilde-B rejection", "topics": [ "rNormalGLM_reg_group_safe" ] }, { "page": "rosenthal_drift_constants", "title": "Foster / Rosenthal drift constants from floor coupling eigenvalues.", "topics": [ "rosenthal_drift_constants" ] }, { "page": "rosenthal_tv_bound", "title": "Rosenthal total-variation bound at fixed tuning parameter alpha.", "topics": [ "rosenthal_tv_bound" ] }, { "page": "simfuncs_group", "title": "Conditionally independent row-group simulation (Gibbs / product likelihood)", "topics": [ "rNormalGLM_reg_group", "rNormal_reg_group", "simfuncs_group" ] }, { "page": "summary.rlmerb", "title": "Summarizing Bayesian mixed model distribution functions", "topics": [ "print.summary.rlmerb", "summary.rglmerb", "summary.rlmerb" ] }, { "page": "two_block_rate", "title": "Two-block Gibbs sampler convergence rate (Remark 8 eigenvalues)", "concept": [ "simfuncs" ], "topics": [ "print.two_block_rate", "print.two_block_rate_ing", "two_block_rate", "two_block_rate_from_pfamily_list", "two_block_rate_ing" ] } ], "_readme": "https://github.com/knygren/lmebayesCore/raw/HEAD/README.md", "_rundeps": [ "backports", "boot", "broom", "cli", "colorspace", "cowplot", "cpp11", "Deriv", "doBy", "dplyr", "farver", "forecast", "fracdiff", "generics", "ggplot2", "glmbayesCore", "glmmTMB", "glue", "gtable", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "mgcv", "minqa", "modelr", "nlme", "nloptr", "nmathopencl", "nnet", "numDeriv", "opencltools", "pbkrtest", "pillar", "pkgconfig", "purrr", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "Rdpack", "reformulas", "rlang", "RTMB", "S7", "sandwich", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "timeDate", "TMB", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libtbb", "package": "libtbb12", "headers": "libtbb-dev", "source": "onetbb", "version": "2022.3.0-2", "name": "onetbb", "homepage": "https://uxlfoundation.github.io/oneTBB/", "description": "parallelism library for C++ - runtime files" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "Chapter-B00.Rmd", "filename": "Chapter-B00.html", "title": "Chapter B00: Engine roadmap and notation", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B00: Engine roadmap and notation", "Two vignette series, two audiences", "The B-series", "The model", "Symbol table", "Internal storage", "Full conditionals", "Correspondence to lme4", "Model restrictions", "Naming conventions in the code", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B01.Rmd", "filename": "Chapter-B01.html", "title": "Chapter B01: The two-block Gibbs architecture", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B01: The two-block Gibbs architecture", "Why two blocks", "One sweep", "Replicate chains, not one long chain", "The call stack", "Route selection", "Sweep-outer versus chain-outer", "Inside Block 1", "Inside Block 2", "Where C++ takes over", "What one sweep stores", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B02.Rmd", "filename": "Chapter-B02.html", "title": "Chapter B02: Ergodicity and total-variation convergence", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B02: Ergodicity and total-variation convergence", "The scalar picture", "The multivariate rate", "Computing it without forming (P_{22})", "A worked case with a closed form", "From the rate to a total-variation bound", "The full-rank conditions", "Level 1: each group's design must be full column rank", "Level 2: the retained groups must identify (\\gamma)", "Beyond the Gaussian case", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B03.Rmd", "filename": "Chapter-B03.html", "title": "Chapter B03: Calibrating m_convergence", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B03: Calibrating m_convergence", "The pipeline", "What tv_tol means", "Why one extra sweep", "Starting points and the (D_0) term", "The pilot / main cost trade-off", "From a pfamily_list", "When certification fails", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B04.Rmd", "filename": "Chapter-B04.html", "title": "Chapter B04: The known-vcov Gaussian route and the exact iid sampler", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B04: The known-vcov Gaussian route", "Route selection", "Why the route is exact", "Two engines behind one route", "The exact iid engine", "The symmetry precondition", "The Gibbs engine on an exact target", "The precision matrix P", "The compiled kernel", "Working example", "When the route does not apply", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B05.Rmd", "filename": "Chapter-B05.html", "title": "Chapter B05: Estimated variance components (ING Block 2)", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B05: Estimated variance components", "Block 2 as a regression on the random effects", "Two ways to update", "Method A: closed-form conditional mode", "Method B: rglmb(), the production path", "Plug-ins and where the prior is calibrated", "The truncation window", "What the chain looks like", "Why a pilot stage becomes necessary", "Selecting components individually", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B06.Rmd", "filename": "Chapter-B06.html", "title": "Chapter B06: The extended local rate diagnostic", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B06: The extended local rate diagnostic", "Why a single (\\lambda^*) stops being enough", "What the engine certifies instead", "The extended rate", "The new blocks", "The residuals only make it worse", "Using it", "Reading the output", "Two checks worth running", "Scanning over draws", "The marginal route", "Theorem or heuristic: the honest table", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B07.Rmd", "filename": "Chapter-B07.html", "title": "Chapter B07: Per-group measurement dispersion", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B07: Per-group measurement dispersion", "The model, and what dispformula selects", "Calibrating (\\sigma^2_j): why the within-group RSS is the wrong target", "The marginal sum of squares", "The Gamma parameters", "rate versus rate_gamma", "Folding in hyperparameter uncertainty", "The truncation window", "dGamma_list()", "What Block 1 does with it", "Effect on the rate", "Caveats", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B08.Rmd", "filename": "Chapter-B08.html", "title": "Chapter B08: Design, identifiability and rank conditions", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B08: Design, identifiability and rank conditions", "What model_setup() returns", "Level 1: within-group rank", "What failure means, and what it does not", "The estimability check", "Level 2: across-group rank", "Why this one is fatal", "Fixed-effect grammar", "Reading the print output", "A worked failure", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B09.Rmd", "filename": "Chapter-B09.html", "title": "Chapter B09: Row-block engines", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B09: Row-block engines", "The engines", "The partition object", "Block 1 of the mixed-model sampler", "lmbBlock() and glmbBlock() are not these engines", "Per-block prior calibration", "Identifiability, without a second level", "Who owns what", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-B10.Rmd", "filename": "Chapter-B10.html", "title": "Chapter B10: Sweep history and convergence plots", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Chapter B10: Sweep history and convergence plots", "Why the ensemble view is the right one", "The object", "Which engines populate it", "Reading the two plots", "plot_mean_convergence()", "plot_var_convergence()", "Multiple chains and n_chains", "Using the history programmatically", "Interpreting a pilot history", "See also" ], "created": "2026-08-10 23:18:50", "modified": "2026-08-10 23:18:50", "commits": 1 }, { "source": "Chapter-C01.Rmd", "filename": "Chapter-C01.html", "title": "Chapter C01: The Gaussian example -- model, data and design", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "The theoretical model", "Group effects", "Population effects", "What is fixed and what has a prior", "The Big Word Club data", "Variables used", "The model being estimated", "How the population effects are indexed", "The priors", "See also" ], "created": "2026-08-13 00:51:26", "modified": "2026-08-13 00:51:26", "commits": 1 }, { "source": "Chapter-C02.Rmd", "filename": "Chapter-C02.html", "title": "Chapter C02: The exact Gaussian iid sampler", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Prior specification", "Estimating the model using the default settings", "Properties of the posterior and the iid sampling procedure", "Marginal distribution of the population effects", "Conditional distribution of the group effects", "Drawing from the posterior", "Summarizing the output", "Appendix: the reference lmer fit", "See also" ], "created": "2026-08-13 00:51:26", "modified": "2026-08-13 00:51:26", "commits": 1 }, { "source": "Chapter-C03.Rmd", "filename": "Chapter-C03.html", "title": "Chapter C03: Total variation distances between multivariate normal densities", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Total variation distances between multivariate normal densities", "Definitions", "Distance between multivariate normal densities with the same variance-covariance matrix", "Distance between multivariate normal densities with the same mean vectors", "Distances between multivariate normal densities", "Convergence rates for two-block Gibbs samplers for multivariate normal densities", "Convergence of mean vectors", "Convergence of variance-covariance matrices", "Convergence bounds and geometric ergodicity for the two-block Gibbs sampler", "Proofs", "Proof for densities with shared mean vector", "Proof for densities with shared variance-covariance matrix", "Proof for convergence of variance-covariance matrices", "Proof for convergence of mean vectors", "Proof of geometric ergodicity", "Special case derivations", "How the package evaluates these results", "See also" ], "created": "2026-08-13 00:51:26", "modified": "2026-08-16 19:39:36", "commits": 2 }, { "source": "Chapter-C04.Rmd", "filename": "Chapter-C04.html", "title": "Chapter C04: The two-block Gibbs sampler", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "Prior specification", "Estimating the model using the default settings", "Properties of the posterior and the two-block Gibbs procedure", "Block 1: group effects given the population effects", "Block 2: population effects given the group effects", "One sweep and one stored draw", "Where the sweep count comes from", "The rate matrix for this design", "From the rate to a certified sweep count", "Summarizing the output", "Variance convergence during the main phase", "See also" ], "created": "2026-08-13 00:51:26", "modified": "2026-08-13 00:51:26", "commits": 1 }, { "source": "Chapter-C05.Rmd", "filename": "Chapter-C05.html", "title": "Chapter C05: Total Variation Bounds for Restricted Two-block Gibbs Samplers", "author": "Kjell Nygren", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "1.1 Problem and setting", "1.2 Statement of the main results (informal)", "1.3 Relation to Rosenthal (1995)", "2. The Conditional Bound", "2.1 Two-block Gibbs sampler and the restricted kernel", "2.2 Total variation and L1 distance", "2.3 Truncation: $\\pi(\\cdot\\mid C_d)$ vs. $\\pi$", "2.4 Theorem 1 — geometric convergence of the restricted chain", "3. The Hierarchical GLMM Model", "3.1 Model and hypotheses", "3.2 Propriety of the flat-prior posterior", "3.3 The mean map and the marginal $\\gamma$-chain", "3.4 Theorem 2 — existence of a certified safe set (statement)", "4. The Refresh Measure $Q$", "4.1 Proper population prior ($\\Lambda_\\gamma\\succ0$)", "4.2 Flat-prior limit ($\\Lambda_\\gamma\\downarrow0$)", "4.3 Summary: existence and nondegeneracy of $Q$", "5. The Minorization Constant and the Certified Set", "5.1 The minorization profile $\\varepsilon(\\gamma)$", "5.2 Convexity, coercivity, and compactness of $\\widetilde C_d$", "5.3 The attained constant $\\varepsilon_d$", "5.4 Flat-prior limit ($\\Lambda_\\gamma\\downarrow0$)", "5.5 Closed form under Gaussian closure", "6. Proof of Theorem 2", "6.1 Assembly of §4–§5", "6.2 Lifting to the joint $(\\gamma,\\beta)$ chain", "7. Scope and Extensions", "7.1 Symmetric case: sharper constants", "7.2 What is and is not certified", "7.3 Open problems", "Appendix — Proofs", "A.1 Proofs for §3.2 (propriety of the flat-prior posterior) and §3.3 (mean map)", "A.2 Proofs for §4", "A.3 Proofs for §5", "A.4 Proof of Theorem 2", "References" ], "created": "2026-08-13 00:51:26", "modified": "2026-08-16 19:39:36", "commits": 2 } ], "_score": 6.343999069057162, "_indexed": true, "_nocasepkg": "lmebayescore", "_universes": [ "knygren" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-10-03T13:49:18.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/1f90704aae18d672c0eb30fb9b4f9588da83a4a346b3bf469e81e533421f3b87", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-10-03T13:49:32.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/d44d1964b8759fd2f7b38aefbfcf09dcee2387014f05b2a075bef2143de9d303", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-10-03T13:49:12.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/48b85df9631b9233a90e0bdb4f0ff2307345550c7b5688f96fc86d3b7d07c165", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-10-03T13:50:00.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/523b8b6532868e19602a0a4fafb2716c9474ef8c8fc488819ddad3320a3b257b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-10-03T13:50:46.000Z", "arch": "aarch64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/cb0c7cce0019131fbdbcecab0b7c0a20170e5f67a6169b638e8361d6d129890c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-10-03T13:52:24.000Z", "arch": "x86_64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/fd84e24001db7340ed9befc8513e50b3055cc1610b3919d7e80c04ca44b38bb2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.6.1", "os": "mac", "version": "0.1.0", "date": "2026-10-03T13:51:40.000Z", "arch": "aarch64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/a1079b7c0b29c4c93b3c7fe13295eb83cffc57d3725a30f819ddb37437ec6f34", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.6.1", "os": "mac", "version": "0.1.0", "date": "2026-10-03T13:50:22.000Z", "arch": "x86_64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/de8b3e9fd33bee630ade771ba99cf99dde9771a62bbe72e206657e9781a62000", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-10-03T13:50:49.000Z", "arch": "aarch64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/a8695ad53c01f5d11c9d0be974b4929b032b095e7ed795831e5b862b9a620c22", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-10-03T13:48:23.000Z", "arch": "x86_64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/5f8ddcfad70b8e277346096ac71e686ce52b3705e3ef28ac412be7f7c5d14bcd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-10-03T13:48:59.000Z", "arch": "x86_64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/282f4537dc42821ce1095cfba178f66ebc1304546870be305c6c2c7b2c09e8e7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.6.1", "os": "win", "version": "0.1.0", "date": "2026-10-03T13:50:34.000Z", "arch": "aarch64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/c2885311b55a807f0cccf6beb4737430bfcc6ec85a7e62ea8b14dcf068e2df1b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" }, { "r": "4.6.1", "os": "win", "version": "0.1.0", "date": "2026-10-03T13:48:35.000Z", "arch": "x86_64", "commit": "2ab2e9846bff21ff16a058424b9a83f8489f2ae5", "fileid": "https://r2.ropensci.org/7e4c14d8fbb4c73c1b59f49ff92bc8f3fa64cfbc5504ae1fc87a10c55e956c84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/knygren/actions/runs/37126647423" } ] }