Man pages for sommer
Solving Mixed Model Equations in R

add.diallel.varsadd.diallel.vars
adiag1Binds arrays corner-to-corner
AIAverage Information Algorithm
A.matAdditive relationship matrix
anova_mmecanova form a GLMM fitted with mmec
anova_mmeranova form a GLMM fitted with mmer
AR1matAutocorrelation matrix of order 1.
ARMAmatAutocorrelation Moving average.
atcatc covariance structure
atcg1234Letter to number converter
atcg1234BackTransformLetter to number converter
atratr covariance structure
bathy.colorsGenerate a sequence of colors for plotting bathymetric data.
bbasisFunction for creating B-spline basis functions (Eilers &...
bivariateRunbivariateRun functionality
build.HMMBuild a hybrid marker matrix using parental genotypes from...
coef_mmeccoef form a GLMM fitted with mmec
coef_mmercoef form a GLMM fitted with mmer
corImputationImputing a matrix using correlations
covccovariance between random effects
csccustomized covariance structure
CSmatCompound symmetry matrix
csrcustomized covariance structure
dfToMatrixdata frame to matrix
D.matDominance relationship matrix
dscdiagonal covariance structure
dsrdiagonal 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_igeData to fit indirect genetic effects.
DT_legendreSimulated data for random regression
DT_mohringFull diallel data for corn hybrids
DT_polyploidGenotypic and Phenotypic data for a potato polyploid...
DT_riceRice lines dataset
DT_sleepstudyReaction times in a sleep deprivation study
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
fitted_mmecfitted form a LMM fitted with mmec
fitted_mmerfitted form a LMM fitted with mmer
fixmfixed indication matrix
gvsrgeneral variance structure specification
GWASGenome wide association study analysis
HTwo-way id by features table
H.matCombined relationship matrix H
imputeImputing a numeric or character vector
iscidentity covariance structure
jet.colorsGenerate a sequence of colors alog the jet colormap.
LD.decayCalculation of linkage disequilibrium decay
legLegendre polynomial matrix
list2usmatlist or vector to unstructured matrix
logspaceDecreasing logarithmic trend
manhattanCreating a manhattan plot
map.plotCreating a genetic map plot
mmec*m*ixed *m*odel *e*quations for *c* coefficients
mmer*m*ixed *m*odel *e*quations for *r* records
neMarkerEffective population size based on marker matrix
overlayOverlay Matrix
plot_mmecplot form a LMM plot with mmec
plot_mmerplot form a LMM plot with mmer
plot.monitorplot the change of VC across iterations
predict_mmecPredict form of a LMM fitted with mmec
predict_mmerPredict form of a LMM fitted with mmer
propMissingProportion of missing data
r2Reliability
randefextracting random effects
redmmReduced Model Matrix
residuals_mmecResiduals form a GLMM fitted with mmec
residuals_mmerResiduals form a GLMM fitted with mmer
rrcreduced rank covariance structure
simGECorMatCreate a GE correlation matrix for simulation purposes.
sommer-package*So*lving *M*ixed *M*odel *E*quations in *R*
spl2DaTwo-dimensional penalised tensor-product of marginal B-Spline...
spl2DbTwo-dimensional penalised tensor-product of marginal B-Spline...
spl2DcTwo-dimensional penalised tensor-product of marginal B-Spline...
spl2DmatsGet Tensor Product Spline Mixed Model Incidence Matrices
stackTraitStacking traits in a dataset
summary_mmecsummary form a GLMM fitted with mmec
summary_mmersummary form a GLMM fitted with mmer
tpsGet Tensor Product Spline Mixed Model Incidence Matrices
tpsmmbwrapperGet Tensor Product Spline Mixed Model Incidence Matrices
transformConstraintstransformConstraints
transpCreating color with transparency
unsmunstructured indication matrix
uscunstructured covariance structure
usrunstructured covariance structure
vpredictvpredict form of a LMM fitted with mmer
vsvariance structure specification
vscvariance structure specification
vsrvariance structure specification
waldWald Test for Model Coefficients
sommer documentation built on Sept. 11, 2024, 6:22 p.m.