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_ige                  Data to fit indirect genetic effects.
DT_legendre             Simulated data for random regression
DT_mohring              Full diallel data for corn hybrids
DT_polyploid            Genotypic and Phenotypic data for a potato
                        polyploid population
DT_rice                 Rice lines dataset
DT_sleepstudy           Reaction times in a sleep deprivation study
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
H.mat                   Combined relationship matrix H
LD.decay                Calculation of linkage disequilibrium decay
MEMMA                   Multivariate Efficient Mixed Model Association
                        Algorithm
add.diallel.vars        add.diallel.vars
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
dfToMatrix              data frame to matrix
ds                      diagonal covariance structure
fcm                     fixed effect constraint indication matrix
fitted.mmer             fitted form a LMM fitted with mmer
fixm                    fixed indication matrix
gvs                     general variance structure specification
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
plot.mmer               plot form a LMM plot with mmer
predict.mmer            Predict form of a LMM fitted with mmer
randef                  extracting random effects
residuals.mmer          Residuals form a GLMM fitted with mmer
simGECorMat             Create a GE correlation matrix for simulation
                        purposes.
sommer                  *So*lving *M*ixed *M*odel *E*quations in *R*
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
vpredict                vpredict form of a LMM fitted with mmer
vs                      variance structure specification
wald.test               Wald Test for Model Coefficients
