Man pages for sommer
Solving Mixed Model Equations in R

adiag1Binds arrays corner-to-corner
A.matAdditive relationship matrix
anovaanova form a GLMM fitted with mmer
AR1matAutocorrelation matrix of order 1.
ARMAmatAutocorrelation Moving average.
atat covariance structure
atcg1234Letter to number converter
bathy.colorsGenerate a sequence of colors for plotting bathymetric data.
build.HMMBuild a hybrid marker matrix using parental genotypes
coefcoef form a GLMM fitted with mmer
cscustomized covariance structure
CSmatCompound symmetry matrix
D.matDominance relationship matrix
dsdiagonal covariance structure
DT_augmentDT_augment design example.
DT_btdataBlue Tit Data for a Quantitative Genetic Experiment
DT_cornhybridsCorn crosses and markers
DT_cpdataGenotypic and Phenotypic data for a CP population
DT_exampleBroad sense heritability calculation.
DT_expdesignsData for different experimental designs
DT_fulldiallelFull diallel data for corn hybrids
DT_gryphonGryphon data from the Journal of Animal Ecology
DT_h2Broad sense heritability calculation.
DT_halfdiallelhalf diallel data for corn hybrids
DT_legendreSimulated data for random regression
DT_polyploidGenotypic and Phenotypic data for a potato polyploid...
DT_riceRice lines dataset
DT_technowGenotypic and Phenotypic data from single cross hybrids...
DT_wheatwheat lines dataset
DT_yatesoatsYield of oats in a split-block experiment
EMExpectation Maximization Algorithm
E.matEpistatic relationship matrix
EMMAMultivariate Efficient Mixed Model Association Algorithm
fcmfixed effect constraint indication matrix
fill.designFilling the design of an experiment
fittedfitted form a GLMM fitted with mmer
fixmfixed indication matrix
GWASGenome wide association study
GWAS2Genome wide association study
h2.funObtain heritabilities with three different methods
imputeImputing a numeric or character vector
jet.colorsGenerate a sequence of colors alog the jet colormap.
legLegendre polynomial matrix
list2usmatlist or vector to unstructured matrix
manhattanCreating a manhattan plot
map.plotCreating a genetic map plot
mmer*m*ixed *m*odel *e*quations in *R*
mmer2*m*ixed *m*odel *e*quations in *R*
overlayOverlay Matrix
pedtoKPedigree to matrix
pinpin functionality
plotplot form a LMM plot with mmer
predictPredict form a LMM fitted with mmer
randefextracting random effects
residualsResiduals form a GLMM fitted with mmer
sommer-package*So*lving *M*ixed *M*odel *E*quations in *R*
spatPlotsSpatial plots
spl2DTwo-dimensional penalised tensor-product of marginal B-Spline...
summarysummary form a GLMM fitted with mmer
transpCreating color with transparency
uncmunconstrained indication matrix
unsmunstructured indication matrix
usunstructured covariance structure
vsvariance structure
sommer documentation built on Dec. 9, 2018, 5:04 p.m.