Man pages for sommer
Solving Mixed Model Equations in R

adiag1Binds arrays corner-to-corner
AIAverage Information Algorithm
A.matAdditive relationship matrix
anovaanova form a GLMM fitted with mmer
atcg1234Letter to number converter
augmentaugment design example.
bathy.colorsGenerate a sequence of colors for plotting bathymetric data.
big.peaks.colPeak search by first derivatives
blockerApplying postblocking in a field
blockerLApplying linear postblocking in a field
blockerTApplying transversal postblocking in a field
brewer.palGenerate a sequence of colors for groups.
BTdataBlue Tit Data for a Quantitative Genetic Experiment
build.HMMBuild a hybrid marker matrix using parental genotypes
coefcoef form a GLMM fitted with mmer
cornHybridCorn crosses and markers
CPdataGenotypic and Phenotypic data for a CP population
design.scoredesign score for the model to be tested
D.matDominance relationship matrix
EMExpectation Maximization Algorithm
E.matEpistatic relationship matrix
exampleBroad sense heritability calculation.
ExpDesignsData for different experimental designs
F1genoGenotypes from an F1(CP) cross to show phasing
FDdataFull diallel data for corn hybrids
fdrFalse Discovery Rate calculation
fdr2False Discovery Rate calculation
fill.designFilling the design of an experiment
fittedfitted form a GLMM fitted with mmer
gryphondataGryphon data from the Journal of Animal Ecology
GWASGenome Wide Association Analysis
GWAS2Genome Wide Association Analysis
h2exampleBroad sense heritability calculation.
h2.funObtain heritabilities with three different methods
hadamard.prodHadamard product of two matrices
HDdatahalf diallel data for corn hybrids
hdmHalf Diallel Matrix
hitsCreating a fixed effect matrix with significant GWAS markers
imputeImputing a numeric or character vector
is.diagonal.matrixTest for diagonal square matrix
is.square.matrixTest for square matrix
jet.colorsGenerate a sequence of colors alog the jet colormap.
manhattanCreating a manhattan plot
map.plotCreating a genetic map plot
matrix.traceThe trace of a matrix
maxi.qtlPeak search by first derivatives
MEMMAMultivariate Efficient Mixed Model Association Algorithm
mmer*m*ixed *m*odel *e*quations in *R*
mmer2*m*ixed *m*odel *e*quations in *R*
MNRMultivariate Newton-Raphson Algorithm
my.colorsAll typical colors in R easy to access.
nnaNearest neighbour adjustment
overlayOverlay Matrix
pedtoKPedigree to matrix
phase.F1Phasing F1 (CP) data in biparental populations
pinpin functionality
plotplot form a LMM plot with mmer
plot.variogramDefault variogram.MMERM plotting
PolyDataGenotypic and Phenotypic data for a potato polyploid...
randefextracting random effects
residualsResiduals form a GLMM fitted with mmer
RICERice lines dataset
score.calcMVScore calculation for markers
sommer-package*So*lving *M*ixed *M*odel *E*quations in *R*
spatPlotsSpatial plots
summarysummary form a GLMM fitted with mmer
Technow_dataGenotypic and Phenotypic data from single cross hybrids...
transpCreating color with transparency
variogramSample variogram
vctablevctable functionality functionality
wheatLineswheat lines dataset
yates.oatsYield of oats in a split-block experiment
sommer documentation built on March 18, 2018, 2:29 p.m.