# Solving Mixed Model Equations in R

## Documentation for package ‘sommer’ version 4.4.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

A.mat | Additive relationship matrix
anova.mmer | anova form a GLMM fitted with mmes
anova.mmes | anova form a GLMM fitted with mmes
AR1 | Autocorrelation matrix of order 1.
ARMA | Autocorrelation Moving average.
atm | atm covariance structure
atr | atm covariance structure
coef.mmer | coef form a GLMM fitted with mmes
coef.mmes | coef form a GLMM fitted with mmes
corImputation | Imputing a matrix using correlations
covm | covariance between random effects
CS | Compound symmetry matrix
csm | customized covariance structure
csr | customized covariance structure
D.mat | Dominance relationship matrix
dfToMatrix | data frame to matrix
dsm | diagonal covariance structure
dsr | diagonal covariance structure
E.mat | Epistatic relationship matrix
fitted.mmer | fitted form a LMM fitted with mmes
fitted.mmes | fitted form a LMM fitted with mmes
fixm | fixed indication matrix
GWAS | Genome wide association study analysis
H.mat | Combined relationship matrix H
ism | identity covariance structure
mmer | *m*ixed *m*odel *e*quations for *r* records
mmes | *m*ixed *m*odel *e*quations *s*olver
MNR | Multivariate Newton-Raphson algorithm
plot.mmer | plot form a LMM plot with mmes
plot.mmes | plot form a LMM plot with mmes
pmonitor | plot the change of VC across iterations
predict.mmer | Predict form of a LMM fitted with mmes
predict.mmes | Predict form of a LMM fitted with mmes
print.mmer | summary form a GLMM fitted with mmer
print.mmes | summary form a GLMM fitted with mmes
print.summary.mmer | summary form a GLMM fitted with mmer
print.summary.mmes | summary form a GLMM fitted with mmes
r2 | Reliability
randef | extracting random effects
residuals.mmer | Residuals form a GLMM fitted with mmes
residuals.mmes | Residuals form a GLMM fitted with mmes
sommer | *So*lving *M*ixed *M*odel *E*quations in *R*
spl2Da | Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Db | Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Dc | Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Dmats | Get Tensor Product Spline Mixed Model Incidence Matrices
summary.mmer | summary form a GLMM fitted with mmer
summary.mmes | summary form a GLMM fitted with mmes
tpsmmbwrapper | Get Tensor Product Spline Mixed Model Incidence Matrices
unsm | unstructured indication matrix
unsm2 | unstructured indication matrix
usm | unstructured covariance structure
usr | unstructured covariance structure
vpredict | vpredict form of a LMM fitted with mmes
vpredict.mmes | vpredict form of a LMM fitted with mmes
vs | variance structure specification
vsm | variance structure specification
vsr | variance structure specification