Package: lmebayesCore 0.1.0

lmebayesCore: Core C++ Sampling Engine for lmebayes

Core C++ engine for lmebayes: envelope-based iid samplers, two-block Gibbs mixed-model engines, and optional OpenCL acceleration. Full-featured developer backend for lmebayes and extensions. End users should use lmebayes for lmer/glmer-style mixed-model workflows.

Authors:Kjell Nygren [aut, cre], The R Core Team [ctb, cph], The R Foundation [cph], Ross Ihaka [ctb, cph], Robert Gentleman [ctb, cph], Simon Davies [ctb], Morten Welinder [ctb, cph], Martin Maechler [ctb]

lmebayesCore_0.1.0.tar.gz
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lmebayesCore_0.1.0.tgz(r-4.6-x86_64)lmebayesCore_0.1.0.tgz(r-4.6-arm64)lmebayesCore_0.1.0.tgz(r-4.5-x86_64)lmebayesCore_0.1.0.tgz(r-4.5-arm64)
lmebayesCore_0.1.0.tar.gz(r-4.7-arm64)lmebayesCore_0.1.0.tar.gz(r-4.7-x86_64)lmebayesCore_0.1.0.tar.gz(r-4.6-arm64)lmebayesCore_0.1.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lmebayesCore/json (API)

# Install 'lmebayesCore' in R:
install.packages('lmebayesCore', repos = c('https://knygren.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/knygren/lmebayescore/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • AMI - Amitriptyline overdose data
  • BikeSharing - Bike Sharing Dataset
  • Boston_centered - Boston housing data with mean-centered predictors
  • carinsca - Canadian Automobile Insurance Claims for 1957-1958
  • Cleveland - Cleveland Heart Disease Dataset

On CRAN:

Conda:

openblascpp

3.71 score 89 exports 19 dependencies

Last updated from:9b61cc8cd5. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK399
linux-devel-x86_64OK433
source / vignettesOK658
linux-release-arm64OK426
linux-release-x86_64OK457
macos-release-arm64OK217
macos-release-x86_64OK557
macos-oldrel-arm64OK218
macos-oldrel-x86_64OK786
windows-develOK498
windows-releaseOK598
windows-oldrelOK678
wasm-releaseFAIL298

Exports:.two_block_align_b_to_xhyper.two_block_block2_one_chainblock_rNormalGLMblock_rNormalGLM_updateblock_rNormalRegblock_rNormalReg_updatebuild_mu_allcompute_gaussian_priordBetadGammadGamma_listdiagnose_glmbayesdIndependent_Normal_GammadNormaldNormal_GammaEnvelopeBuildEnvelopeCenteringEnvelopeDispersionBuildEnvelopeEvalEnvelopeOptEnvelopeOrchestratorEnvelopeSetGridEnvelopeSetLogPEnvelopeSizeEnvelopeSortglmb_Standardize_Modelglmb.wfitglmbayesCore_has_openclglmbfamfuncglmerb_posterior_modelmerb_posterior_meanmodel_setupmulti_prior_setupmulti_rindepNormalGamma_regmulti_rlmbmulti_rNormal_regmulti_rNormalGamma_regnormalize_blockpfamilypfamily_listpinvgamma_ctplot_sweep_history_diagpnorm_ctPrior_CheckPrior_SetupPrior_Setup_lmebayesqinvgamma_ctrBeta_regrGamma_Conjugate_regrgamma_ctrGamma_regrglmbrglmerbrGLMM_Re_DrawrGLMM_regrGLMM_reg_estimated_vcovrGLMM_reg_known_vcovrGLMM_sweeprindepNormalGamma_regrindepNormalGamma_reg_with_enveloperIndepNormalGammaReg_stdrinvgamma_ctrlmbrlmerbrLMMindepNormalGamma_regrLMMindepNormalGamma_reg_estimated_vcovrLMMindepNormalGamma_reg_known_vcovrLMMNormal_regrLMMNormal_reg_estimated_vcovrLMMNormal_reg_known_vcovrnorm_ctrNormal_regrNormal_reg.wfitrNormalGamma_regrNormalGLM_stdsimfunctiontwo_block_align_b_to_xhypertwo_block_align_b_to_xhyper_cpptwo_block_block2_one_chaintwo_block_block2_one_chain_cpptwo_block_d0_pilot_starttwo_block_l_for_tvtwo_block_m_convergence_for_pilot_starttwo_block_optimize_pilot_costtwo_block_pilot_sampling_costtwo_block_ratetwo_block_rate_from_pfamily_listtwo_block_rNormal_regtwo_block_tv_bound

Dependencies:bootjsonlitelatticelme4MASSMatrixminqanlmenloptrnmathopenclopencltoolsrbibutilsRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasrlang

Readme and manuals

Help Manual

Help pageTopics
lmebayesCore: Core C++ Sampling Engine for lmebayeslmebayesCore-package lmebayesCore
Amitriptyline overdose dataAMI
Bike Sharing Dataset (Processed)BikeSharing
Conditionally independent block simulation (Gibbs / product likelihood)block_rNormalGLM block_rNormalGLM_update block_rNormalReg block_rNormalReg_update block_simfuncs normalize_block
Boston housing data with mean-centered predictorsBoston_centered
Build per-group random-effect prior means for Block 1 samplingbuild_mu_all
Canadian Automobile Insurance Claims for 1957-1958carinsca
Cleveland Heart Disease DatasetCleveland
Compute Calibrated Gaussian Normal–Gamma Prior Componentscompute_gaussian_prior
Build a named list of dGamma measurement-dispersion priorsdGamma_list
Build per-group dGamma priors from a Prior_Setup_lmebayes objectdGamma_list.lmebayes_prior_setup
GPU and OpenCL diagnostics for 'glmbayes'diagnose_glmbayes glmbayesCore_has_opencl gpu_diagnostics
GPU-Accelerated Envelope Construction for Posterior SimulationEnvelopeBuild EnvelopeSetGrid EnvelopeSetLogP
Envelope Centering for Bayesian Gaussian RegressionEnvelopeCentering
Builds Dispersion-Aware Envelope for SimulationEnvelopeDispersionBuild
Evaluate Negative Log-Likelihood and GradientsEnvelopeEval
Envelope Construction Orchestrator for Bayesian Gaussian RegressionEnvelopeOrchestrator
Envelope Sizing and OptimizationEnvelopeOpt EnvelopeSize
Sorts Envelope function for simulationEnvelopeSort
Model Formulae for 'summary.rglmb' Objectsformula.summary.rglmb
The Central Gamma Distributionctrgamma Gamma_ct pgamma_ct rgamma_ct
Standardize A Non-Gaussian Modelglmb_Standardize_Model
Return family functions used during simulation and post processingglmbfamfunc print.glmbfamfunc
The Central Inverse-Gamma DistributionInvGamma_ct pinvgamma_ct qinvgamma_ct rinvgamma_ct
Joint posterior mean or mode of the two-block mixed model (ICM)glmerb_posterior_mode lmebayes_posterior_icm lmerb_posterior_mean
Bayesian mixed model setup (single-factor 'lmer'/'glmer' gate)model_setup print.model_setup
Prior setup for multiple Gaussian responsesmulti_prior_setup
Multi-response Bayesian regression and simulationmulti_rindepNormalGamma_reg multi_rlmb multi_rNormalGamma_reg
Multi-response Normal regression simulationmulti_rNormal_reg
The Central Normal DistributionNormal_ct pnorm_ct rnorm_ct
Prior Family Objects for Bayesian ModelsdBeta dGamma dIndependent_Normal_Gamma dNormal dNormal_Gamma pfamily print.pfamily
Build a named list of pfamily objectspfamily_list
Build pfamily objects from a Prior_Setup_lmebayes objectpfamily_list.lmebayes_prior_setup
Plot Block~2 sweep-history diagnostics (cross-chain mean or SD)plot_sweep_history_diag
Checks for Prior-data conflictsPrior_Check
Setup Prior Objectsprint.PriorSetup Prior_Setup
Prior setup for the two-block Gibbs lmebayes samplerprint.lmebayes_prior_setup Prior_Setup_lmebayes
Deviance Residuals for 'rglmb' and 'summary.rglmb' Objectsresiduals.rglmb residuals.rlmb residuals.summary.rglmb
The Bayesian Generalized Linear Model Distributionprint.rglmb rglmb
The Bayesian Generalized Linear Mixed-Effects Model Distributionrglmerb
Block~1 random-effect redraw for replicate chainsrGLMM_Re_Draw
Matrix-level replicate-chain Gibbs engines for Bayesian GLMMsrGLMM_reg rGLMM_reg_estimated_vcov rGLMM_reg_known_vcov
Two-block Gibbs sweep for replicate-chain sampling ('rGLMM_reg' engine)rGLMM_sweep
Independent Normal-Gamma regression with envelope artifacts returnedrindepNormalGamma_reg_with_envelope
The Bayesian Gaussian Regression with Independent Normal-Gamma Prior in Standard FormrIndepNormalGammaReg_std
The Bayesian Linear Model Distributionprint.rlmb rlmb
The Bayesian Linear Mixed-Effects Model Distributionrlmerb
Matrix-level replicate-chain Gibbs engines for Bayesian LMMsrLMMindepNormalGamma_reg rLMMindepNormalGamma_reg_estimated_vcov rLMMindepNormalGamma_reg_known_vcov rLMMNormal_reg rLMMNormal_reg_estimated_vcov rLMMNormal_reg_known_vcov rLMM_reg
Bayesian Weighted Fitting Enginesglmb.wfit rNormal_reg.wfit
The Bayesian Generalized Linear Model Distribution in Standard FormrNormalGLM_std
Simulation Functions for Bayesian Generalized Linear Modelsprint.rGamma_reg print.simfunction rBeta_reg rGamma_Conjugate_reg rGamma_reg rindepNormalGamma_reg rNormalGamma_reg rNormal_reg simfuncs simfunction
Low-Level Simulation Pipeline for Bayesian GLMsSimulationPipeline
Summarizing mrglmb Objectsprint.summary.mrglmb summary.mrglmb
Summarizing Bayesian gamma_reg Distribution Functionsprint.summary.rGamma_reg summary.rGamma_reg
Summarizing Bayesian Generalized Linear Model Distribution Functionsprint.summary.rglmb summary.rglmb summary.rlmb
Align random-effect vector to 'X_hyper' row ordertwo_block_align_b_to_xhyper two_block_align_b_to_xhyper_cpp
One-chain Block 2 update (fixed effects, tau^2, iteration counts)two_block_block2_one_chain
Block 2 one-chain update via C++ (native align + 'rglmb')two_block_block2_one_chain_cpp
Pilot / main chain cost calibration for two-block GLMM samplingtwo_block_d0_pilot_start two_block_m_convergence_for_pilot_start two_block_optimize_pilot_cost two_block_pilot_sampling_cost
Two-block Gibbs sampler convergence rate (Remark 8 eigenvalues)print.two_block_rate two_block_rate two_block_rate_from_pfamily_list
Two-block Gibbs sampler with pfamily Block 2 priorstwo_block_rNormal_reg
Total-variation bound for the two-block Gibbs samplertwo_block_l_for_tv two_block_tv_bound