Solving Mixed Model Equations in R

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Documentation for package ‘sommer’ version 4.0.4

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A.mat Additive relationship matrix
adiag1 Binds arrays corner-to-corner
Ad_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
Af_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
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
A_example Broad sense heritability calculation.
A_gryphon Gryphon data from the Journal of Animal Ecology
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
DTi_cornhybrids Corn crosses and markers
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
GTn_rice Rice lines dataset
GT_cornhybrids Corn crosses and markers
GT_cpdata Genotypic and Phenotypic data for a CP population
GT_polyploid Genotypic and Phenotypic data for a potato polyploid population
GT_rice Rice lines dataset
GT_wheat wheat lines dataset
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
Md_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
MEMMA Multivariate Efficient Mixed Model Association Algorithm
Mf_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
mmer *m*ixed *m*odel *e*quations in *R*
mmer2 *m*ixed *m*odel *e*quations in *R*
MP_cpdata Genotypic and Phenotypic data for a CP population
MP_polyploid Genotypic and Phenotypic data for a potato polyploid population
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
P_gryphon Gryphon data from the Journal of Animal Ecology
randef extracting random effects
residuals.mmer Residuals form a GLMM fitted with mmer
simGECorMat Create a GE correlation matrix for simulation purposes.
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