# Solving Mixed Model Equations in R

## Documentation for package ‘sommer’ version 3.9.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A.mat | Additive relationship matrix
adiag1 | Binds arrays corner-to-corner
anova.mmer | anova form a GLMM fitted with mmer
AR1 | Autocorrelation matrix of order 1.
ARMA | Autocorrelation Moving average.
at | at covariance structure
atcg1234 | Letter to number converter
bathy.colors | Generate a sequence of colors for plotting bathymetric data.
bivariateRun | bivariateRun functionality
build.HMM | Build a hybrid marker matrix using parental genotypes
coef.mmer | coef form a GLMM fitted with mmer
CS | Compound symmetry matrix
cs | customized covariance structure
D.mat | Dominance relationship matrix
ds | diagonal covariance structure
DT_augment | DT_augment design example.
DT_btdata | Blue Tit Data for a Quantitative Genetic Experiment
DT_cornhybrids | Corn crosses and markers
DT_cpdata | Genotypic and Phenotypic data for a CP population
DT_example | Broad sense heritability calculation.
DT_expdesigns | Data for different experimental designs
DT_fulldiallel | Full diallel data for corn hybrids
DT_gryphon | Gryphon data from the Journal of Animal Ecology
DT_h2 | Broad sense heritability calculation.
DT_halfdiallel | half diallel data for corn hybrids
DT_legendre | Simulated data for random regression
DT_polyploid | Genotypic and Phenotypic data for a potato polyploid population
DT_rice | Rice lines dataset
DT_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
DT_wheat | wheat lines dataset
DT_yatesoats | Yield of oats in a split-block experiment
E.mat | Epistatic relationship matrix
EM | Expectation Maximization Algorithm
fcm | fixed effect constraint indication matrix
fill.design | Filling the design of an experiment
fitted.mmer | fitted form a GLMM fitted with mmer
fixm | fixed indication matrix
GWAS | Genome wide association study analysis
GWAS2 | Genome wide association study
h2.fun | Obtain heritabilities with three different methods
imputev | Imputing a numeric or character vector
jet.colors | Generate a sequence of colors alog the jet colormap.
leg | Legendre polynomial matrix
list2usmat | list or vector to unstructured matrix
manhattan | Creating a manhattan plot
map.plot | Creating a genetic map plot
MEMMA | Multivariate Efficient Mixed Model Association Algorithm
mmer | *m*ixed *m*odel *e*quations in *R*
mmer2 | *m*ixed *m*odel *e*quations in *R*
overlay | Overlay Matrix
pedtoK | Pedigree to matrix
pin | pin functionality
plot.mmer | plot form a LMM plot with mmer
predict.mmer | Predict form a LMM fitted with mmer
print.mmer | summary form a GLMM fitted with mmer
print.summary.mmer | summary form a GLMM fitted with mmer
randef | extracting random effects
residuals.mmer | Residuals form a GLMM fitted with mmer
sommer | *So*lving *M*ixed *M*odel *E*quations in *R*
spatPlots | Spatial plots
spl2D | Two-dimensional penalised tensor-product of marginal B-Spline basis.
summary.mmer | summary form a GLMM fitted with mmer
transformConstraints | transformConstraints
transp | Creating color with transparency
uncm | unconstrained indication matrix
unsm | unstructured indication matrix
us | unstructured covariance structure
vs | variance structure specification