A.mat                   Additive relationship matrix
AR1                     Autocorrelation matrix of order 1.
ARMA                    Autocorrelation Moving average.
CS                      Compound symmetry matrix
D.mat                   Dominance relationship matrix
DT_augment              DT_augment design example.
DT_btdata               Blue Tit Data for a Quantitative Genetic
                        Experiment
DT_cornhybrids          Corn crosses and markers
DT_cpdata               Genotypic and Phenotypic data for a CP
                        population
DT_example              Broad sense heritability calculation.
DT_expdesigns           Data for different experimental designs
DT_fulldiallel          Full diallel data for corn hybrids
DT_gryphon              Gryphon data from the Journal of Animal Ecology
DT_h2                   Broad sense heritability calculation.
DT_halfdiallel          half diallel data for corn hybrids
DT_legendre             Simulated data for random regression
DT_polyploid            Genotypic and Phenotypic data for a potato
                        polyploid population
DT_rice                 Rice lines dataset
DT_technow              Genotypic and Phenotypic data from single cross
                        hybrids (Technow et al. (2014))
DT_wheat                wheat lines dataset
DT_yatesoats            Yield of oats in a split-block experiment
E.mat                   Epistatic relationship matrix
EM                      Expectation Maximization Algorithm
GWAS                    Genome wide association study analysis
GWAS2                   Genome wide association study
MEMMA                   Multivariate Efficient Mixed Model Association
                        Algorithm
adiag1                  Binds arrays corner-to-corner
anova.mmer              anova form a GLMM fitted with mmer
at                      at covariance structure
atcg1234                Letter to number converter
bathy.colors            Generate a sequence of colors for plotting
                        bathymetric data.
bivariateRun            bivariateRun functionality
build.HMM               Build a hybrid marker matrix using parental
                        genotypes
coef.mmer               coef form a GLMM fitted with mmer
cs                      customized covariance structure
ds                      diagonal covariance structure
fcm                     fixed effect constraint indication matrix
fill.design             Filling the design of an experiment
fitted.mmer             fitted form a GLMM fitted with mmer
fixm                    fixed indication matrix
h2.fun                  Obtain heritabilities with three different
                        methods
imputev                 Imputing a numeric or character vector
jet.colors              Generate a sequence of colors alog the jet
                        colormap.
leg                     Legendre polynomial matrix
list2usmat              list or vector to unstructured matrix
manhattan               Creating a manhattan plot
map.plot                Creating a genetic map plot
mmer                    *m*ixed *m*odel *e*quations in *R*
mmer2                   *m*ixed *m*odel *e*quations in *R*
overlay                 Overlay Matrix
pedtoK                  Pedigree to matrix
pin                     pin functionality
plot.mmer               plot form a LMM plot with mmer
predict.mmer            Predict form a LMM fitted with mmer
randef                  extracting random effects
residuals.mmer          Residuals form a GLMM fitted with mmer
sommer                  *So*lving *M*ixed *M*odel *E*quations in *R*
spatPlots               Spatial plots
spl2D                   Two-dimensional penalised tensor-product of
                        marginal B-Spline basis.
summary.mmer            summary form a GLMM fitted with mmer
transformConstraints    transformConstraints
transp                  Creating color with transparency
uncm                    unconstrained indication matrix
unsm                    unstructured indication matrix
us                      unstructured covariance structure
vs                      variance structure specification
