Solving Mixed Model Equations in R

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Documentation for package ‘sommer’ version 4.3.4

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A B C D E F G H I J L M N O P R S T U V W

-- A --

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)
AI Average Information Algorithm
anova.mmec anova form a GLMM fitted with mmec
anova.mmer anova form a GLMM fitted with mmer
AR1 Autocorrelation matrix of order 1.
ARMA Autocorrelation Moving average.
atc atc covariance structure
atcg1234 Letter to number converter
atcg1234BackTransform Letter to number converter
atr atr covariance structure
A_example Broad sense heritability calculation.
A_gryphon Gryphon data from the Journal of Animal Ecology
A_ige Data to fit indirect genetic effects.

-- B --

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

-- C --

coef.mmec coef form a GLMM fitted with mmec
coef.mmer coef form a GLMM fitted with mmer
corImputation Imputing a matrix using correlations
covc covariance between random effects
CS Compound symmetry matrix
csc customized covariance structure
csr customized covariance structure

-- D --

D.mat Dominance relationship matrix
dfToMatrix data frame to matrix
dsc diagonal covariance structure
dsr 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 --

E.mat Epistatic relationship matrix
EM Expectation Maximization Algorithm

-- F --

fcm fixed effect constraint indication matrix
fitted.mmec fitted form a LMM fitted with mmec
fitted.mmer fitted form a LMM fitted with mmer
fixm fixed indication matrix

-- G --

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
gvsr general variance structure specification
GWAS Genome wide association study analysis

-- H --

H.mat Combined relationship matrix H

-- I --

imputev Imputing a numeric or character vector
isc identity covariance structure

-- J --

jet.colors Generate a sequence of colors alog the jet colormap.

-- L --

LD.decay Calculation of linkage disequilibrium decay
leg Legendre polynomial matrix
list2usmat list or vector to unstructured matrix
logspace Decreasing logarithmic trend

-- M --

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)
mmec *m*ixed *m*odel *e*quations for *c* coefficients
mmer *m*ixed *m*odel *e*quations for *r* records
MP_cpdata Genotypic and Phenotypic data for a CP population
MP_polyploid Genotypic and Phenotypic data for a potato polyploid population

-- N --

neMarker Effective population size based on marker matrix

-- O --

overlay Overlay Matrix

-- P --

plot.mmec plot form a LMM plot with mmec
plot.mmer plot form a LMM plot with mmer
pmonitor plot the change of VC across iterations
predict.mmec Predict form of a LMM fitted with mmec
predict.mmer Predict form of a LMM fitted with mmer
print.mmec summary form a GLMM fitted with mmec
print.mmer summary form a GLMM fitted with mmer
print.summary.mmec summary form a GLMM fitted with mmec
print.summary.mmer summary form a GLMM fitted with mmer
print.wald.test Wald Test for Model Coefficients
propMissing Proportion of missing data
P_gryphon Gryphon data from the Journal of Animal Ecology

-- R --

r2 Reliability
randef extracting random effects
redmm Reduced Model Matrix
residuals.mmec Residuals form a GLMM fitted with mmec
residuals.mmer Residuals form a GLMM fitted with mmer
rrc reduced rank covariance structure

-- S --

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.
spl2Dc Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Dmats Get Tensor Product Spline Mixed Model Incidence Matrices
stackTrait Stacking traits in a dataset
summary.mmec summary form a GLMM fitted with mmec
summary.mmer summary form a GLMM fitted with mmer

-- T --

tpsmmbwrapper Get Tensor Product Spline Mixed Model Incidence Matrices
transformConstraints transformConstraints
transp Creating color with transparency

-- U --

unsm unstructured indication matrix
usc unstructured covariance structure
usr unstructured covariance structure

-- V --

vpredict vpredict form of a LMM fitted with mmer
vpredict.mmer vpredict form of a LMM fitted with mmer
vs variance structure specification
vsc variance structure specification
vsr variance structure specification

-- W --

wald.test Wald Test for Model Coefficients