sommer

swMATH15118CRANsommerMaRDI QIDQ27011FDOQ27011

Solving Mixed Model Equations in R

Giovanny Covarrubias-Pazaran

Last update: 13 November 2023

Copyright license: GNU General Public License, version 3.0, GNU General Public License, version 2.0

Software version identifier: 4.2.1.2, 4.3.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7.1, 3.7.2, 3.7.3, 3.7, 3.8, 3.9.1, 3.9.3, 4.0.1, 4.0.4, 4.0.8, 4.0.9, 4.1.0, 4.1.1, 4.1.2, 4.1.3, 4.1.4, 4.1.5, 4.1.6, 4.1.7, 4.1.8, 4.1.9, 4.2.0.1, 4.2.0, 4.3.1, 4.3.2, 4.3.3

Source code repository: https://github.com/cran/sommer

Description

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.

Cites work

• Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer
• Joint Analysis of Psychiatric Disorders Increases Accuracy of Risk Prediction for Schizophrenia, Bipolar Disorder, and Major Depressive Disorder

Cited In (8)

• statgenGWAS
• statgenQTLxT
• IPLGP
• Estimating variances in time series kriging using convex optimization and empirical BLUPs
• lmDiallel
• mlmm.gwas
• pcgen
• Do spatial designs outperform classic experimental designs?

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