Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., unstructured, diagonal, autoregressive, factor analytic, reduced rank, among others) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 ; Maier et al., 2015 ; 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).

sommer: Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016; Maier et al., 2015; 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.

Installation

You can install the development version of sommer from GitHub:

remotes::install_github('covaruber/sommer')

Home website

Want to know more about the sommer project or you need professional services? Visit https://covaruber.github.io/sommer/

Using sommer code and the GPL license

Please be aware that the sommer project is open-source software released under the GNU General Public License (GPL). The GPL gives you the freedom to use, study, modify, and redistribute the software, subject to the conditions of the license.

In particular, if you copy, modify, or create a work based on GPL-covered sommer source code and distribute that work, the GPL imposes requirements on how the resulting work may be licensed and distributed. Among other things, recipients must retain the freedoms provided by the GPL, and when GPL-covered software is distributed in binary or other non-source form, the corresponding source code must also be made available in accordance with the GPL.

Therefore, the fact that sommer is free and open-source does not mean that its source code can be copied into another software package, modified, redistributed as a proprietary product, and kept secret. If your project contains or is based on GPL-covered sommer code, please carefully review the GPL requirements before distributing it.

The purpose of the sommer project is to encourage open collaboration, reproducibility, and continued improvement of statistical and quantitative-genetics software. Contributions and derivative work are welcome, but they should respect the freedoms and obligations established by the GPL.

Please read the full GPL license distributed with sommer before incorporating sommer source code into another project.