# Solving Mixed Model Equations in R

## Documentation for package ‘sommer’ version 4.4.2

- 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)
anova.mmes | anova form a GLMM fitted with mmes
AR1 | Autocorrelation matrix of order 1.
ARMA | Autocorrelation Moving average.
atcg1234 | Letter to number converter
atcg1234BackTransform | Letter to number converter
atm | atm 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)
build.HMM | Build a hybrid marker matrix using parental genotypes from inbred individuals

## -- C --

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

## -- D --

D.mat | Dominance relationship matrix
dfToMatrix | data frame to matrix
dsm | 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

## -- F --

fitted.mmes | fitted form a LMM fitted with mmes
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
GWAS | Genome wide association study analysis

## -- H --

H.mat | Combined relationship matrix H

## -- I --

imputev | Imputing a numeric or character vector
ism | 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
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)
Mf_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
mmer | *m*ixed *m*odel *e*quations for *r* records
mmes | *m*ixed *m*odel *e*quations *s*olver
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.mmes | plot form a LMM plot with mmes
pmonitor | plot the change of VC across iterations
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
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.mmes | Residuals form a GLMM fitted with mmes
rrm | 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*
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
stan | Standardize a vector of values in range 0 to 1
summary.mmer | summary form a GLMM fitted with mmer
summary.mmes | summary form a GLMM fitted with mmes

## -- T --

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

## -- U --

unsm | unstructured indication matrix
usm | unstructured covariance structure

## -- V --

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

## -- W --

wald.test | Wald Test for Model Coefficients