# Solving Mixed Model Equations in R

## Documentation for package ‘sommer’ version 4.3.4

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

## Help Pages

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