A.mat                   Additive relationship matrix
AI                      Average Information Algorithm
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
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.mmec              anova form a GLMM fitted with mmec
anova.mmer              anova form a GLMM fitted with mmer
atc                     atc covariance structure
atcg1234                Letter to number converter
atr                     atr covariance structure
bathy.colors            Generate a sequence of colors for plotting
                        bathymetric data.
bbasis                  Function for creating B-spline basis functions
                        (Eilers & Marx, 2010)
bivariateRun            bivariateRun functionality
build.HMM               Build a hybrid marker matrix using parental
                        genotypes from inbred individuals
coef.mmec               coef form a GLMM fitted with mmec
coef.mmer               coef form a GLMM fitted with mmer
corImputation           Imputing a matrix using correlations
covc                    covariance between random effects
csc                     customized covariance structure
csr                     customized covariance structure
dfToMatrix              data frame to matrix
dsc                     diagonal covariance structure
dsr                     diagonal covariance structure
fcm                     fixed effect constraint indication matrix
fitted.mmec             fitted form a LMM fitted with mmec
fitted.mmer             fitted form a LMM fitted with mmer
fixm                    fixed indication matrix
gvsr                    general variance structure specification
imputev                 Imputing a numeric or character vector
isc                     identity covariance structure
jet.colors              Generate a sequence of colors alog the jet
                        colormap.
leg                     Legendre polynomial matrix
list2usmat              list or vector to unstructured matrix
logspace                Decreasing logarithmic trend
manhattan               Creating a manhattan plot
map.plot                Creating a genetic map plot
mmec                    *m*ixed *m*odel *e*quations for *c*
                        coefficients
mmer                    *m*ixed *m*odel *e*quations for *r* records
neMarker                Effective population size based on marker
                        matrix
overlay                 Overlay Matrix
plot.mmec               plot form a LMM plot with mmec
plot.mmer               plot form a LMM plot with mmer
pmonitor                plot the change of VC across iterations
predict.mmec            Predict form of a LMM fitted with mmec
predict.mmer            Predict form of a LMM fitted with mmer
r2                      Reliability
randef                  extracting random effects
redmm                   Reduced Model Matrix
residuals.mmec          Residuals form a GLMM fitted with mmec
residuals.mmer          Residuals form a GLMM fitted with mmer
rrc                     reduced rank covariance structure
simGECorMat             Create a GE correlation matrix for simulation
                        purposes.
sommer                  *So*lving *M*ixed *M*odel *E*quations in *R*
spl2Da                  Two-dimensional penalised tensor-product of
                        marginal B-Spline basis.
spl2Db                  Two-dimensional penalised tensor-product of
                        marginal B-Spline basis.
spl2Dc                  Two-dimensional penalised tensor-product of
                        marginal B-Spline basis.
spl2Dmats               Get Tensor Product Spline Mixed Model Incidence
                        Matrices
stackTrait              Stacking traits in a dataset
summary.mmec            summary form a GLMM fitted with mmec
summary.mmer            summary form a GLMM fitted with mmer
tpsmmbwrapper           Get Tensor Product Spline Mixed Model Incidence
                        Matrices
transformConstraints    transformConstraints
transp                  Creating color with transparency
unsm                    unstructured indication matrix
usc                     unstructured covariance structure
usr                     unstructured covariance structure
vpredict                vpredict form of a LMM fitted with mmer
vs                      variance structure specification
vsc                     variance structure specification
vsr                     variance structure specification
wald.test               Wald Test for Model Coefficients
