Files in sommer

Solving Mixed Model Equations in R

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MD5

README.md

NAMESPACE

DESCRIPTION

CHANGELOG

cleanup

R/RcppExports.R R/mmes.R R/FUN_spatial.R R/FUN_covariance_serial.R R/FUN_threads.R R/FUN_stats.R R/FUN_covariance_factor.R R/DEPRECATED_mmer.R R/FUN_covariance_spatial.R R/FUN_mme_gpu.R R/FUN_relationships.R R/FUN_model_weights.R R/predict_mmes.R R/FUN_covariance_basic.R R/FUN_methods_mmes.R R/FUN_mme_conditional.R R/FUN_mme_capabilities.R R/FUN_markers.R R/FUN_mme_control.R R/FUN_model_helpers.R R/FUN_glmm.R R/FUN_multivariate.R R/vpredict.R R/FUN_wald.R R/FUN_emmeans.R R/FUN_fixed_rank.R R/zzz.R R/FUN_mme_conditional_ai.R R/FUN_mme_solve.R R/FUN_plotting.R R/FUN_reml_estimability.R R/FUN_mme_benchmark.R R/FUN_covfactor.R R/FUN_constraints.R R/FUN_mme_modules.R R/FUN_vsm.R R/FUN_factor_score.R

src/Makevars.win

src/mme_posterior.h

src/mme_ai_recovery.h

src/MNR.cpp

src/RcppExports.cpp

src/mme_control_r.h

src/mme_exact.h

src/mme_sparse.h

src/mme_sp2_support.h

src/mme_direct_covariance.h

src/mme_inference.cpp

src/mme_solve.cpp

src/native_utils.cpp

src/mme_layout.h

src/mme_saddle.h

src/mme_direct.cpp

src/mme_control.h

src/mme_recovery.h

src/native_relationships.cpp

src/ai_mme_sp2.cpp

src/mme_em_optimizer.h

src/mme_factors.h

src/mme_direct_em.h

src/mme_scale.h

src/mme_sufficient.h

src/mme_paths.h

src/mme_gpu.h

src/mme_covariance.h

src/mme_cuda_runtime.h

src/mme_pcg.h

src/mme_pcg_recycle.h

src/mme_fixed_rank.cpp

src/mme_rr.h

src/Makevars.in

src/mme_conditional.cpp

src/mme_pcg_estimators.h

src/mme_em.h

src/mme_gpu.cpp

src/mme_cholmod.h

src/mme_progress.h

inst/CITATION

inst/doc/sommer.mmes.options.Rmd

inst/doc/sommer.machinery.html

inst/doc/sommer.fa.and.rr.models.Rmd inst/doc/sommer.spatial.Rmd

inst/doc/sommer.mmes.options.html

inst/doc/sommer.fa.and.rr.models.html

inst/doc/sommer.vs.lme4.Rmd inst/doc/sommer.vs.lme4.R inst/doc/sommer.mmes.options.R inst/doc/sommer.gxe.R inst/doc/sommer.glmm.R

inst/doc/sommer.qg.html

inst/doc/sommer.gxe.html

inst/doc/sommer.genetic.evaluation.html

inst/doc/sommer.glmm.html

inst/doc/sommer.covariance.structures.R inst/doc/sommer.qg.Rmd inst/doc/sommer.machinery.Rmd inst/doc/sommer.gxe.Rmd inst/doc/sommer.fa.and.rr.models.R inst/doc/sommer.blas.threads.R inst/doc/sommer.covariance.structures.Rmd inst/doc/sommer.spatial.R inst/doc/sommer.genetic.evaluation.Rmd inst/doc/sommer.genetic.evaluation.R

inst/doc/sommer.blas.threads.html

inst/doc/sommer.spatial.html

inst/doc/sommer.blas.threads.Rmd inst/doc/sommer.qg.R inst/doc/sommer.theory.Rmd

inst/doc/sommer.vs.lme4.html

inst/doc/sommer.machinery.R inst/doc/sommer.glmm.Rmd

inst/doc/sommer.theory.html

inst/doc/sommer.covariance.structures.html

build/vignette.rds

build/partial.rdb

tests/testthat.R tests/native/test-mme-control-transport.R

tests/native/test-mme-control-transport.cpp

tests/native/test-mme-sufficient.cpp

tests/native/test-mme-control.cpp

tests/native/test-mme-paths.cpp

tests/native/test-mme-saddle.cpp

tests/native/test-mme-ai-recovery.cpp

tests/native/test-mme-pcg.cpp

tests/native/test-mme-sparse.cpp

tests/native/test-mme-pcg-estimators.cpp

tests/testthat/test-ai-variance-floor.R tests/testthat/test-predict-fixed-rank.R tests/testthat/test-mme-control.R tests/testthat/test-pcg-controls.R tests/testthat/test-multivariate.R tests/testthat/test-mme-modules.R tests/testthat/test-start-lsq.R tests/testthat/test-ai-recovery.R tests/testthat/test-conditional-moments.R tests/testthat/test-mmes-pql.R tests/testthat/test-varu-edgecases.R tests/testthat/test-reporting-refactor.R tests/testthat/test-mmes-fixed-rank.R tests/testthat/test-mme-profile.R tests/testthat/test-fa-covariance-safeguards.R tests/testthat/test-direct-engine.R tests/testthat/test-em-directions.R tests/testthat/test-mmes-rotation.R tests/testthat/test-mmes-progress-output.R tests/testthat/test-mme-path-reporting.R tests/testthat/test-wald-mmes.R tests/testthat/test-enhancer-models.R tests/testthat/test-mme-saddle.R tests/testthat/test-mmes-acceleration.R tests/testthat/test-pcg-crossfit.R tests/testthat/test-mme-gpu.R tests/testthat/test-dmat.R tests/testthat/test-emmeans-mmes.R tests/testthat/test-readme.R tests/testthat/test-strm.R tests/testthat/helper-native.R tests/testthat/test-model-preparation.R tests/testthat/test-control-contracts.R tests/testthat/test-covariance-information.R tests/testthat/test-conditional-fa.R tests/testthat/test-r-refactor.R tests/testthat/test-pxem-directions.R tests/testthat/test-fa-factor-score-augmentation.R tests/testthat/test-mmer-cran-compatibility.R tests/testthat/test-relationships.R tests/testthat/test-common-scale.R tests/testthat/test-meffects.R tests/testthat/test-mme-cfree.R tests/testthat/test-mmes-threads.R tests/testthat/test-reduced-ai.R tests/testthat/test-reml-estimability.R tests/testthat/test-mmes-namespace-calls.R tests/testthat/test-mme-control-native.R tests/testthat/test-spatial-refactor.R tests/testthat/test-mmes-blend.R tests/testthat/test-vsm-giv-gu.R tests/testthat/test-fa-loadings-scores.R tests/testthat/test-mme-block-chain.R tests/testthat/test-vcc.R tests/testthat/test-conditional-ai.R tests/testthat/test-dense-gu-schur.R tests/testthat/test-metricm.R tests/testthat/test-mme-capabilities.R tests/testthat/test-vsm-variance-modes.R tests/testthat/test-fa-latent-schur.R tests/testthat/test-hybrid-ai.R tests/testthat/test-rr-zero-specific.R tests/testthat/helper-enhancer-models.R tests/testthat/test-mme-compression.R tests/testthat/test-mmes-reml-vs-ml.R tests/testthat/test-rr-average-information.R tests/testthat/test-apy.R tests/testthat/test-direct-em.R tests/testthat/test-pcg-compression.R tests/testthat/test-predict-reported-issues.R tests/testthat/test-mmes-fixed-design.R tests/testthat/test-postVarU.R tests/testthat/test-mme-solve.R tests/testthat/test-predict-levels-sed.R tests/testthat/test-mme-solver.R tests/testthat/test-mme-paths.R tests/testthat/test-pcg-numerics.R tests/testthat/test-predict-mmes-ci.R tests/testthat/test-mmes-spatial-residual.R tests/testthat/test-fam-dense-gu-memory.R tests/testthat/test-weighted-sparse-residual.R vignettes/sommer.mmes.options.Rmd vignettes/sommer.fa.and.rr.models.Rmd vignettes/sommer.spatial.Rmd vignettes/sommer.vs.lme4.Rmd vignettes/sommer.qg.Rmd vignettes/sommer.machinery.Rmd vignettes/sommer.gxe.Rmd vignettes/sommer.covariance.structures.Rmd vignettes/sommer.genetic.evaluation.Rmd vignettes/sommer.blas.threads.Rmd vignettes/sommer.theory.Rmd vignettes/sommer.glmm.Rmd man/usr.Rd man/rotate_back_mmes.Rd man/unsm.Rd man/familym.Rd man/r2.Rd man/H.mat.Rd man/covparams_mmes_se.Rd man/mme_workload_grid.Rd man/profile_mme_workload.Rd man/csm.Rd man/dfToMatrix.Rd man/mmer.Rd man/DEPRECATED_GWAS.Rd man/toeplitzm.Rd man/covmatrix_mmes.Rd man/atm.Rd man/sommer-package.Rd man/postVarU.Rd man/dsm.Rd man/print.sommer_mmes_control.Rd man/loadings_mmes.Rd man/corgm.Rd man/antem.Rd man/meffects_mmes.Rd man/run_mme_benchmark.Rd man/postPEV.Rd man/dsumm.Rd man/DEPRECATED_summary_mmer.Rd man/ar1m.Rd man/atr.Rd man/MNR.Rd man/plot.monitor.Rd man/print.sommer_mme_crossover.Rd man/corImputation.Rd man/plot_mmes.Rd man/covparams_mmes.Rd man/analyze_mme_crossovers.Rd man/DEPRECATED_VS.Rd man/car.Rd man/tpsmmbwrapper.Rd man/spl2Dmats.Rd man/D.mat.Rd man/fam.Rd man/print.sommer_mme_benchmark.Rd man/ism.Rd man/vpredict.Rd man/coef_mmes.Rd man/DEPRECATED_VSR.Rd man/randef.Rd man/ar3m.Rd man/binm.Rd man/scores_mmes.Rd man/print.sommer_mme_profile.Rd man/residuals_mmes.Rd man/csr.Rd man/generate_mme_workload.Rd man/spl2Dc.Rd man/sar.Rd man/summary_mmes.Rd man/ar2m.Rd man/strm.Rd man/anova_mmes.Rd man/mmes.Rd man/metricm.Rd man/maternm.Rd man/mam.Rd man/wald_mmes.Rd man/rrm.Rd man/covm.Rd man/predict_mmes.Rd man/APY.Rd man/vcc.Rd man/vsm.Rd man/fixm.Rd man/stackTraits.Rd man/ownm.Rd man/usm.Rd man/fitted_mmes.Rd man/E.mat.Rd man/mmes_control.Rd man/dsr.Rd man/A.mat.Rd

man/figures/form3.png

man/figures/form4.png

man/figures/form2.png

man/figures/form1.png

man/figures/mai.png

sommer documentation built on Oct. 25, 2026, 5:06 p.m.