# Solving Mixed Model Equations in R

## Documentation for package ‘sommer’ version 2.7

- 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
ai2help | Average Information Algorithm
and | and functionality
anova.mmer | anova form a GLMM fitted with mmer
anova.MMERM | anova form a GLMM fitted with mmer
anova.mmerM | anova form a GLMM fitted with mmer
at | at functionality
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
brewer.pal | Generate a sequence of colors for groups.
coef.mmer | coef form a GLMM fitted with mmer
coef.MMERM | coef form a GLMM fitted with mmer
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
eigenGWAS | Unraveling selection signatures with eigenGWAS
EM | Expectation Maximization Algorithm
EM2 | Expectation Maximization Algorithm
EMMA | Efficient Mixed Model Association Algorithm
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
fitted.mmer | fitted form a GLMM fitted with mmer
fitted.MMERM | fitted form a GLMM fitted with mmer
fitted.mmerM | fitted form a GLMM fitted with mmer
g | g functionality
gryphondata | Gryphon data from the Journal of Animal Ecology
h2 | 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.
LD.decay | Calculation of linkage disequilibrium decay
MAI | Multivariate Average Information Algorithm
MAI2 | Multivariate Average Information Algorithm
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 | Mixed Model Equations in R
mmer2 | Mixed Model Equations in R v2
MMERM | Multivariate mixed model solver to be called inside mmer
mmerSNOW | Mixed Model Equations in R univariate
MNR | Multivariate Newton-Raphson Algorithm
my.colors | All typical colors in R easy to access.
name.change | renaming a vector by adding zeros
nna | Nearest neighbour adjustment
NR | Newton-Raphson Algorithm
NR22 | Newton-Raphson Algorithm
overlay | Overlay Matrix
PEV | Selecting the best training population for genomic selection
phase.F1 | Phasing F1 (CP) data in biparental populations
plot.mmer | plot form a GLMM plot with mmer
plot.MMERM | plot form a GLMM plot with mmer
plot.mmerM | plot form a GLMM plot with mmer
poe | Short poems from Latin America, and other places why not?
PolyData | Genotypic and Phenotypic data for a potato polyploid population
print.mmer | summary form a GLMM fitted with mmer
print.MMERM | summary form a GLMM fitted with mmer
print.mmerM | summary form a GLMM fitted with mmer
print.summary.mmer | summary form a GLMM fitted with mmer
print.summary.MMERM | summary form a GLMM fitted with mmer
print.summary.mmerM | summary form a GLMM fitted with mmer
randef | extracting random effects
residuals.mmer | Residuals form a GLMM fitted with mmer
residuals.MMERM | Residuals form a GLMM fitted with mmer
residuals.mmerM | Residuals form a GLMM fitted with mmer
RICE | Rice lines dataset
score.calc | Score calculation for markers
score.calcMV | Score calculation for markers
sommer | Solving Mixed Model Equations in R
summary.mmer | summary form a GLMM fitted with mmer
summary.MMERM | summary form a GLMM fitted with mmer
summary.mmerM | summary form a GLMM fitted with mmer
Technow_data | Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
TP.prep | Selecting the best training population for genomic selection
transp | Creating color with transparency
us | us functionality
wheatLines | wheat lines dataset
yates.oats | Yield of oats in a split-block experiment