# sommer: Solving Mixed Model Equations in R

Multivariate mixed model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well. Covariance structures for the residual component is currently supported only for balanced univariate Newton Raphson.

- Author
- Giovanny Covarrubias-Pazaran
- Date of publication
- 2016-10-02 02:01:14
- Maintainer
- Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
- License
- GPL-3
- Version
- 2.2
- URLs

## Man pages

- adiag1
- Binds arrays corner-to-corner
- AI
- Average Information Algorithm
- ai2help
- Average Information Algorithm
- A.mat
- Additive relationship matrix
- anova.mmer
- anova form a GLMM fitted with mmer
- anova.mmerM
- anova form a GLMM fitted with mmer
- anova.MMERM1
- anova form a GLMM fitted with mmer
- AR1.mat
- Autocorrelation matrix of order 1.
- ARMA.mat
- Autorregressive moving average matrix
- atcg1234
- Letter to number converter
- augment
- augment design example.
- bathy.colors
- Generate a sequence of colors for plotting bathymetric data.
- big.peaks.col
- Peak search by first derivatives
- brewer.pal
- Generate a sequence of colors for groups.
- coef.mmer
- coef form a GLMM fitted with mmer
- coef.mmerM
- coef form a GLMM fitted with mmer
- coef.MMERM1
- coef form a GLMM fitted with mmer
- cornHybrid
- Corn crosses and markers
- CPdata
- Genotypic and Phenotypic data for a CP population
- CS.mat
- Compound symmetry matrix
- design.score
- design score for the model to be tested
- D.mat
- Dominance relationship matrix
- eigenGWAS
- Unraveling selection signatures with eigenGWAS
- EM
- Expectation Maximization Algorithm
- EM2
- Expectation Maximization Algorithm
- E.mat
- Epistatic relationship matrix
- EMMA
- Efficient Mixed Model Association Algorithm
- F1geno
- Genotypes from an F1(CP) cross to show phasing
- FDdata
- half diallel data for corn hybrids
- fdr
- False Discovery Rate calculation
- fitted.mmer
- fitted form a GLMM fitted with mmer
- fitted.mmerM
- fitted form a GLMM fitted with mmer
- fitted.MMERM1
- fitted form a GLMM fitted with mmer
- h2
- Broad sense heritability calculation.
- hadamard.prod
- Hadamard product of two matrices
- HDdata
- half diallel data for corn hybrids
- hdm
- Half Diallel Matrix
- hits
- Creating a fixed effect matrix with significant GWAS markers
- is.diagonal.matrix
- Test for diagonal square matrix
- is.square.matrix
- Test for square matrix
- jet.colors
- Generate a sequence of colors alog the jet colormap.
- LD.decay
- Calculation of linkage disequilibrium decay
- MAI
- Multivariate Average Information Algorithm
- MAI2
- Multivariate Average Information Algorithm
- manhattan
- Creating a manhattan plot
- map.plot
- Creating a genetic map plot
- matrix.trace
- The trace of a matrix
- maxi.qtl
- Peak search by first derivatives
- MEMMA
- Multivariate Efficient Mixed Model Association Algorithm
- mmer
- Mixed Model Equations in R
- mmer2
- Mixed Model Equations in R v2
- MMERM
- Multivariate mixed model solver to be called inside mmer
- mmerSNOW
- Mixed Model Equations in R univariate
- MNR
- Multivariate Newton-Raphson Algorithm
- my.colors
- All typical colors in R easy to access.
- NR
- Newton-Raphson Algorithm
- NR22
- Newton-Raphson Algorithm
- NRR
- Newton-Raphson Algorithm including Residual structures
- PEV
- Selecting the best training population for genomic selection
- phase.F1
- Phasing F1 (CP) data in biparental populations
- plot.mmer
- plot form a GLMM plot with mmer
- plot.mmerM
- plot form a GLMM plot with mmer
- plot.MMERM1
- plot form a GLMM plot with mmer
- poe
- Short poems from Latin America, and other places why not?
- PolyData
- Genotypic and Phenotypic data for a potato polyploid...
- randef
- extracting random effects
- residuals.mmer
- Residuals form a GLMM fitted with mmer
- residuals.mmerM
- Residuals form a GLMM fitted with mmer
- residuals.MMERM1
- Residuals form a GLMM fitted with mmer
- RICE
- Rice lines dataset
- score.calc
- Score calculation for markers
- score.calcMV
- Score calculation for markers
- sommer-package
- Solving Mixed Model Equations in R
- summary.mmer
- summary form a GLMM fitted with mmer
- summary.mmerM
- summary form a GLMM fitted with mmer
- summary.MMERM1
- summary form a GLMM fitted with mmer
- Technow_data
- Genotypic and Phenotypic data from single cross hybrids...
- TP.prep
- Selecting the best training population for genomic selection
- transp
- Creating color with transparency
- wheatLines
- wheat lines dataset
- yates.oats
- Yield of oats in a split-block experiment

## Files in this package

sommer |

sommer/inst |

sommer/inst/CITATION |

sommer/inst/doc |

sommer/inst/doc/sommer.R |

sommer/inst/doc/sommer.pdf |

sommer/inst/doc/sommer.Rmd |

sommer/NAMESPACE |

sommer/CHANGELOG |

sommer/data |

sommer/data/PolyData.RData |

sommer/data/Technow_data.RData |

sommer/data/augment.RData |

sommer/data/HDdata.RData |

sommer/data/RICE.RData |

sommer/data/yates.oats.RData |

sommer/data/h2.RData |

sommer/data/FDdata.RData |

sommer/data/cornHybrid.RData |

sommer/data/CPdata.RData |

sommer/data/datalist |

sommer/data/my.colors.RData |

sommer/data/wheatLines.RData |

sommer/data/F1geno.RData |

sommer/R |

sommer/R/MMERM.R |

sommer/R/design.score.R |

sommer/R/D.mat.R |

sommer/R/mmer.R |

sommer/R/MAIhelp.R |

sommer/R/poe.R |

sommer/R/score.calcMV.R |

sommer/R/maxi.qtl.R |

sommer/R/hits.R |

sommer/R/MNR.R |

sommer/R/TP.prep.R |

sommer/R/A.mat.R |

sommer/R/adiag.R |

sommer/R/MEMMA.R |

sommer/R/jet.colors.R |

sommer/R/EM.R |

sommer/R/ai2help.R |

sommer/R/NR22.R |

sommer/R/Rstructures.R |

sommer/R/PEV.R |

sommer/R/map.plot.R |

sommer/R/NR.R |

sommer/R/hdm.R |

sommer/R/NRR.R |

sommer/R/mmerSNOW.R |

sommer/R/fdr.R |

sommer/R/big.peaks.col.R |

sommer/R/EM2.R |

sommer/R/transp.R |

sommer/R/phase.F1.R |

sommer/R/manhattan.R |

sommer/R/matrix.calculations.R |

sommer/R/mmer2.R |

sommer/R/E.mat.R |

sommer/R/brewer.pal.R |

sommer/R/score.calc.R |

sommer/R/LD.decay.R |

sommer/R/EMMA.R |

sommer/R/AI.R |

sommer/R/atcg1234.R |

sommer/R/eigenGWAS.R |

sommer/R/MAI.R |

sommer/R/MAI2.R |

sommer/vignettes |

sommer/vignettes/sommer.html |

sommer/vignettes/sommer.Rmd |

sommer/MD5 |

sommer/build |

sommer/build/vignette.rds |

sommer/DESCRIPTION |

sommer/man |

sommer/man/anova.MMERM1.Rd |

sommer/man/MAI.Rd |

sommer/man/RICE.Rd |

sommer/man/PEV.Rd |

sommer/man/EMMA.Rd |

sommer/man/MAI2.Rd |

sommer/man/cornHybrid.Rd |

sommer/man/fitted.mmer.Rd |

sommer/man/h2.Rd |

sommer/man/mmerSNOW.Rd |

sommer/man/mmer.Rd |

sommer/man/eigenGWAS.Rd |

sommer/man/residuals.mmerM.Rd |

sommer/man/EM.Rd |

sommer/man/MEMMA.Rd |

sommer/man/residuals.mmer.Rd |

sommer/man/MNR.Rd |

sommer/man/Technow_data.Rd |

sommer/man/AI.Rd |

sommer/man/plot.mmerM.Rd |

sommer/man/MMERM.Rd |

sommer/man/ARMA.mat.Rd |

sommer/man/fitted.MMERM1.Rd |

sommer/man/poe.Rd |

sommer/man/hadamard.prod.Rd |

sommer/man/summary.MMERM1.Rd |

sommer/man/phase.F1.Rd |

sommer/man/fitted.mmerM.Rd |

sommer/man/plot.mmer.Rd |

sommer/man/anova.mmer.Rd |

sommer/man/AR1.mat.Rd |

sommer/man/coef.MMERM1.Rd |

sommer/man/ai2help.Rd |

sommer/man/CS.mat.Rd |

sommer/man/FDdata.Rd |

sommer/man/coef.mmerM.Rd |

sommer/man/hdm.Rd |

sommer/man/summary.mmerM.Rd |

sommer/man/PolyData.Rd |

sommer/man/big.peaks.col.Rd |

sommer/man/NRR.Rd |

sommer/man/transp.Rd |

sommer/man/D.mat.Rd |

sommer/man/is.diagonal.matrix.Rd |

sommer/man/NR22.Rd |

sommer/man/adiag1.Rd |

sommer/man/manhattan.Rd |

sommer/man/bathy.colors.Rd |

sommer/man/EM2.Rd |

sommer/man/F1geno.Rd |

sommer/man/anova.mmerM.Rd |

sommer/man/map.plot.Rd |

sommer/man/coef.mmer.Rd |

sommer/man/score.calc.Rd |

sommer/man/augment.Rd |

sommer/man/summary.mmer.Rd |

sommer/man/mmer2.Rd |

sommer/man/TP.prep.Rd |

sommer/man/my.colors.Rd |

sommer/man/A.mat.Rd |

sommer/man/matrix.trace.Rd |

sommer/man/NR.Rd |

sommer/man/wheatLines.Rd |

sommer/man/sommer-package.Rd |

sommer/man/HDdata.Rd |

sommer/man/residuals.MMERM1.Rd |

sommer/man/atcg1234.Rd |

sommer/man/brewer.pal.Rd |

sommer/man/jet.colors.Rd |

sommer/man/is.square.matrix.Rd |

sommer/man/LD.decay.Rd |

sommer/man/fdr.Rd |

sommer/man/hits.Rd |

sommer/man/design.score.Rd |

sommer/man/plot.MMERM1.Rd |

sommer/man/score.calcMV.Rd |

sommer/man/maxi.qtl.Rd |

sommer/man/yates.oats.Rd |

sommer/man/CPdata.Rd |

sommer/man/randef.Rd |

sommer/man/E.mat.Rd |