Solving Mixed Model Equations in R


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Documentation for package ‘sommer’ version 4.1.5

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A.mat Additive relationship matrix
add.diallel.vars add.diallel.vars
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
A_ige Data to fit indirect genetic effects.
bathy.colors Generate a sequence of colors for plotting bathymetric data.
bbasis Function for creating B-spline basis functions (Eilers & Marx, 2010)
bivariateRun bivariateRun functionality
build.HMM Build a hybrid marker matrix using parental genotypes from inbred individuals
coef.mmer coef form a GLMM fitted with mmer
CS Compound symmetry matrix
cs customized covariance structure
D.mat Dominance relationship matrix
dfToMatrix data frame to 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_ige Data to fit indirect genetic effects.
DT_legendre Simulated data for random regression
DT_mohring Full diallel data for corn hybrids
DT_polyploid Genotypic and Phenotypic data for a potato polyploid population
DT_rice Rice lines dataset
DT_sleepstudy Reaction times in a sleep deprivation study
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
fitted.mmer fitted form a LMM 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
gvs general variance structure specification
GWAS Genome wide association study analysis
GWAS2 Genome wide association study
H.mat Combined relationship matrix H
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.
LD.decay Calculation of linkage disequilibrium decay
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
plot.mmer plot form a LMM plot with mmer
predict.mmer Predict form of a LMM fitted with mmer
print.mmer summary form a GLMM fitted with mmer
print.summary.mmer summary form a GLMM fitted with mmer
print.wald.test Wald Test for Model Coefficients
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*
spl2Da Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Db 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
tpsmmbwrapper Get Tensor Product Spline Mixed Model Incidence Matrices
transformConstraints transformConstraints
transp Creating color with transparency
uncm unconstrained indication matrix
unsm unstructured indication matrix
us unstructured covariance structure
vpredict vpredict form of a LMM fitted with mmer
vpredict.mmer vpredict form of a LMM fitted with mmer
vs variance structure specification
wald.test Wald Test for Model Coefficients