# Solving Mixed Model Equations in R

## Documentation for package ‘sommer’ version 3.4

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

## Help Pages

A.mat | Additive relationship matrix
adiag1 | Binds arrays corner-to-corner
AI | Average Information Algorithm
anova.MMERM | anova form a GLMM fitted with mmer
atcg1234 | Letter to number converter
augment | augment design example.
bathy.colors | Generate a sequence of colors for plotting bathymetric data.
big.peaks.col | Peak search by first derivatives
blocker | Applying postblocking in a field
blockerL | Applying linear postblocking in a field
blockerT | Applying transversal postblocking in a field
brewer.pal | Generate a sequence of colors for groups.
BTdata | Blue Tit Data for a Quantitative Genetic Experiment
build.HMM | Build a hybrid marker matrix using parental genotypes
coef.MMERM | coef form a GLMM fitted with mmer
cornHybrid | Corn crosses and markers
CPdata | Genotypic and Phenotypic data for a CP population
D.mat | Dominance relationship matrix
design.score | design score for the model to be tested
E.mat | Epistatic relationship matrix
EM | Expectation Maximization Algorithm
example | Broad sense heritability calculation.
ExpDesigns | Data for different experimental designs
F1geno | Genotypes from an F1(CP) cross to show phasing
FDdata | Full diallel data for corn hybrids
fdr | False Discovery Rate calculation
fdr2 | False Discovery Rate calculation
fill.design | Filling the design of an experiment
fitted.MMERM | fitted form a GLMM fitted with mmer
gryphondata | Gryphon data from the Journal of Animal Ecology
GWAS | Genome Wide Association Analysis
GWAS2 | Genome Wide Association Analysis
h2.fun | Obtain heritabilities with three different methods
h2example | Broad sense heritability calculation.
hadamard.prod | Hadamard product of two matrices
HDdata | half diallel data for corn hybrids
hdm | Half Diallel Matrix
hits | Creating a fixed effect matrix with significant GWAS markers
imputev | Imputing a numeric or character vector
is.diagonal.matrix | Test for diagonal square matrix
is.square.matrix | Test for square matrix
jet.colors | Generate a sequence of colors alog the jet colormap.
manhattan | Creating a manhattan plot
map.plot | Creating a genetic map plot
matrix.trace | The trace of a matrix
maxi.qtl | Peak search by first derivatives
MEMMA | Multivariate Efficient Mixed Model Association Algorithm
mmer | *m*ixed *m*odel *e*quations in *R*
mmer2 | *m*ixed *m*odel *e*quations in *R*
MNR | Multivariate Newton-Raphson Algorithm
my.colors | All typical colors in R easy to access.
nna | Nearest neighbour adjustment
overlay | Overlay Matrix
pedtoK | Pedigree to matrix
phase.F1 | Phasing F1 (CP) data in biparental populations
pin | pin functionality
plot.MMERM | plot form a LMM plot with mmer
plot.variogram.MMERM | Default variogram.MMERM plotting
PolyData | Genotypic and Phenotypic data for a potato polyploid population
print.MMERM | summary form a GLMM fitted with mmer
print.summary.MMERM | summary form a GLMM fitted with mmer
randef | extracting random effects
residuals.MMERM | Residuals form a GLMM fitted with mmer
RICE | Rice lines dataset
score.calcMV | Score calculation for markers
sommer | *So*lving *M*ixed *M*odel *E*quations in *R*
spatPlots | Spatial plots
summary.MMERM | summary form a GLMM fitted with mmer
Technow_data | Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
transp | Creating color with transparency
variogram | Sample variogram
variogram.MMERM | Sample variogram
vctable | vctable functionality
vctable.help | vctable.help functionality
wheatLines | wheat lines dataset
yates.oats | Yield of oats in a split-block experiment