Solving Mixed Model Equations in R


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Documentation for package ‘sommer’ version 3.2

Help Pages

A.mat Additive relationship matrix
adiag1 Binds arrays corner-to-corner
AI Average Information Algorithm
and and functionality
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
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
eig eigen decomposition functionality
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
g g functionality
grp grouping functionality
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*
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
us us functionality
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