Package: EMMREML 5.2

EMMREML: Fitting Mixed Models with Known Covariance Structures and GWAS

An improved mixed model solver that handles a variety of covariance structures. The main functions are 'emmreml', 'emmremlMultiKernel', and 'emmremlMultivariate'. The 'emmreml' function solves mixed models with known covariance structure using the 'EMMA' algorithm. 'emmremlMultiKernel' allows for fitting models with multiple random components with known covariance structures. The 'emmremlMultivariate' function solves multivariate Gaussian mixed models with known covariance structures using the 'ECM' algorithm. The package now offers both the original matrix interface (fully backward compatible with v3.1) and a modern formula interface. The 'emmremlMultivariate' function restores 'Gpred' and all test outputs from v3.1 while fixing ECM convergence. The new 'gwas' function provides genome-wide association studies with mixed models, including an accelerated algorithm and visualization options.

Authors:Deniz Akdemir, Okeke Uche Godfrey

EMMREML_5.2.tar.gz
EMMREML_5.2.zip(r-4.7-any)EMMREML_5.2.zip(r-4.6-any)EMMREML_5.2.zip(r-4.5-any)
EMMREML_5.2.tgz(r-4.6-any)EMMREML_5.2.tgz(r-4.5-any)
EMMREML_5.2.tar.gz(r-4.7-any)EMMREML_5.2.tar.gz(r-4.6-any)
EMMREML_5.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
EMMREML/json (API)

# Install 'EMMREML' in R:

install.packages('EMMREML', repos = c('https://denizakdemir.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dakdemir/emmreml/issues

On CRAN:

6.07 score 179 scripts 1.3k downloads 22 mentions 36 exports 2 dependencies

Last updated from:876aa2b4d4. Checks:6 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	138
source / vignettes	OK	262
macos-release	NOTE	129
macos-oldrel	NOTE	130
windows-devel	NOTE	138
windows-release	NOTE	89
windows-oldrel	NOTE	92
wasm-release	OK	129

Exports:calculate_allele_frequencies calculate_kinship compare_kinship convert_marker_coding demo_gwas demo_K_optimization demo_kinship demo_multivariate emmreml emmremlMultiKernel emmremlMultiKernel_core emmremlMultivariate emmremlMultivariate_core filter_markers generate_example_data gwas identify_marker_coding impute_markers is_diagonal_matrix is_identity_matrix marker_statistics plot_marker_stats plot.emmreml_gwas predict.emmreml print.emmreml print.emmreml_gwas print.emmreml_multi print.summary.emmreml print.summary.emmreml_gwas print.summary.emmreml_multi subset_markers_by_maf summarize_marker_data summary.emmreml summary.emmreml_gwas summary.emmreml_multi visualize_kinship

Dependencies:lattice Matrix

Introduction to EMMREML

Rendered fromemmreml.Rmdusingknitr::rmarkdown

Last update: 2026-09-30
Started: 2026-09-30

Help page	Topics
Calculate allele frequencies from marker data	calculate_allele_frequencies
Calculate a genomic relationship matrix (GRM/kinship matrix)	calculate_kinship
Compare different kinship matrices	compare_kinship
Convert marker coding between different types	convert_marker_coding
Example of using GWAS functionality	demo_gwas
Example of using EMMREML with K optimization	demo_K_optimization
Demonstrate the kinship matrix calculation functionality	demo_kinship
Example of using the multivariate EMMREML	demo_multivariate
Solver for Gaussian mixed model with known covariance structure.	emmreml
Fitting mixed models with known covariance structures.	EMMREML
Function to fit Gaussian mixed model with multiple mixed effects with known covariances.	emmremlMultiKernel
Fit a Multivariate Gaussian Mixed Model with Known Covariance Structure	emmremlMultivariate
Fit a Multivariate Gaussian Mixed Model with Known Covariance Structure	emmremlMultivariate_core
Filter markers based on various criteria	filter_markers
Generate example data for EMMREML demonstrations	generate_example_data
Genome-Wide Association Study Analysis	gwas
Kinship Matrix Calculation and Marker Data Processing	identify_marker_coding
Impute missing marker data	impute_markers
Kinship Matrix Calculation and Marker Data Functions	kinship
Calculate minor allele frequencies and return marker statistics	marker_statistics
Plot marker data summary statistics	plot_marker_stats
Plot Method for emmreml_gwas Objects	plot.emmreml_gwas
Predict Method for emmreml Objects	predict.emmreml
Print Method for emmreml Objects	print.emmreml
Print Method for emmreml_gwas Objects	print.emmreml_gwas
Print Method for emmreml_multi Objects	print.emmreml_multi
Print Method for summary.emmreml Objects	print.summary.emmreml
Print Method for summary.emmreml_gwas Objects	print.summary.emmreml_gwas
Print Method for summary.emmreml_multi Objects	print.summary.emmreml_multi
Subset a marker matrix based on MAF buckets	subset_markers_by_maf
Create a summary table of marker data properties	summarize_marker_data
Summary Method for emmreml Objects	summary.emmreml
Summary Method for emmreml_gwas Objects	summary.emmreml_gwas
Summary Method for emmreml_multi Objects	summary.emmreml_multi
Visualize a kinship matrix as a heatmap	visualize_kinship

Package: EMMREML 5.2

EMMREML: Fitting Mixed Models with Known Covariance Structures and GWAS

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