Solving Mixed Model Equations in R


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Documentation for package ‘sommer’ version 2.7

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