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
GWAS                    Genome wide association study analysis
H.mat                   Combined relationship matrix H
LD.decay                Calculation of linkage disequilibrium decay
add.diallel.vars        add.diallel.vars
adiag1                  Binds arrays corner-to-corner
anova.mmes              anova form a GLMM fitted with mmes
atcg1234                Letter to number converter
atcg1234BackTransform   Letter to number converter
atm                     atm covariance structure
bathy.colors            Generate a sequence of colors for plotting
                        bathymetric data.
bbasis                  Function for creating B-spline basis functions
                        (Eilers & Marx, 2010)
build.HMM               Build a hybrid marker matrix using parental
                        genotypes from inbred individuals
coef.mmes               coef form a GLMM fitted with mmes
corImputation           Imputing a matrix using correlations
covm                    covariance between random effects
csm                     customized covariance structure
dfToMatrix              data frame to matrix
dsm                     diagonal covariance structure
fitted.mmes             fitted form a LMM fitted with mmes
fixm                    fixed indication matrix
imputev                 Imputing a numeric or character vector
ism                     identity covariance structure
jet.colors              Generate a sequence of colors alog the jet
                        colormap.
leg                     Legendre polynomial matrix
logspace                Decreasing logarithmic trend
manhattan               Creating a manhattan plot
map.plot                Creating a genetic map plot
mmer                    *m*ixed *m*odel *e*quations for *r* records
mmes                    *m*ixed *m*odel *e*quations *s*olver
neMarker                Effective population size based on marker
                        matrix
overlay                 Overlay Matrix
plot.mmes               plot form a LMM plot with mmes
pmonitor                plot the change of VC across iterations
predict.mmes            Predict form of a LMM fitted with mmes
propMissing             Proportion of missing data
r2                      Reliability
randef                  extracting random effects
redmm                   Reduced Model Matrix
residuals.mmes          Residuals form a GLMM fitted with mmes
rrm                     reduced rank covariance structure
simGECorMat             Create a GE correlation matrix for simulation
                        purposes.
sommer                  *So*lving *M*ixed *M*odel *E*quations in *R*
spl2Dc                  Two-dimensional penalised tensor-product of
                        marginal B-Spline basis.
spl2Dmats               Get Tensor Product Spline Mixed Model Incidence
                        Matrices
stan                    Standardize a vector of values in range 0 to 1
summary.mmer            summary form a GLMM fitted with mmer
summary.mmes            summary form a GLMM fitted with mmes
tps                     Get Tensor Product Spline Mixed Model Incidence
                        Matrices
tpsmmbwrapper           Get Tensor Product Spline Mixed Model Incidence
                        Matrices
transp                  Creating color with transparency
unsm                    unstructured indication matrix
usm                     unstructured covariance structure
vpredict                vpredict form of a LMM fitted with mmes
vs                      variance structure specification
vsm                     variance structure specification
vsr                     variance structure specification
wald.test               Wald Test for Model Coefficients
