Solving Mixed Model Equations in R

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Documentation for package ‘sommer’ version 4.4.4

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

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