A.mat                   Additive relationship matrix
AI                      Average Information Algorithm
BTdata                  Blue Tit Data for a Quantitative Genetic
                        Experiment
CPdata                  Genotypic and Phenotypic data for a CP
                        population
D.mat                   Dominance relationship matrix
E.mat                   Epistatic relationship matrix
EM                      Expectation Maximization Algorithm
ExpDesigns              Data for different experimental designs
F1geno                  Genotypes from an F1(CP) cross to show phasing
FDdata                  Full diallel data for corn hybrids
GWAS                    Genome Wide Association Analysis
GWAS2                   Genome Wide Association Analysis
HDdata                  half diallel data for corn hybrids
MEMMA                   Multivariate Efficient Mixed Model Association
                        Algorithm
MNR                     Multivariate Newton-Raphson Algorithm
PolyData                Genotypic and Phenotypic data for a potato
                        polyploid population
RICE                    Rice lines dataset
Technow_data            Genotypic and Phenotypic data from single cross
                        hybrids (Technow et al. (2014))
adiag1                  Binds arrays corner-to-corner
anova.MMERM             anova form a GLMM fitted with mmer
atcg1234                Letter to number converter
augment                 augment design example.
bathy.colors            Generate a sequence of colors for plotting
                        bathymetric data.
big.peaks.col           Peak search by first derivatives
blocker                 Applying postblocking in a field
blockerL                Applying linear postblocking in a field
blockerT                Applying transversal postblocking in a field
brewer.pal              Generate a sequence of colors for groups.
build.HMM               Build a hybrid marker matrix using parental
                        genotypes
coef.MMERM              coef form a GLMM fitted with mmer
cornHybrid              Corn crosses and markers
design.score            design score for the model to be tested
example                 Broad sense heritability calculation.
fdr                     False Discovery Rate calculation
fdr2                    False Discovery Rate calculation
fill.design             Filling the design of an experiment
fitted.MMERM            fitted form a GLMM fitted with mmer
gryphondata             Gryphon data from the Journal of Animal Ecology
h2.fun                  Obtain heritabilities with three different
                        methods
h2example               Broad sense heritability calculation.
hadamard.prod           Hadamard product of two matrices
hdm                     Half Diallel Matrix
hits                    Creating a fixed effect matrix with significant
                        GWAS markers
imputev                 Imputing a numeric or character vector
is.diagonal.matrix      Test for diagonal square matrix
is.square.matrix        Test for square matrix
jet.colors              Generate a sequence of colors alog the jet
                        colormap.
manhattan               Creating a manhattan plot
map.plot                Creating a genetic map plot
matrix.trace            The trace of a matrix
maxi.qtl                Peak search by first derivatives
mmer                    *m*ixed *m*odel *e*quations in *R*
mmer2                   *m*ixed *m*odel *e*quations in *R*
my.colors               All typical colors in R easy to access.
nna                     Nearest neighbour adjustment
overlay                 Overlay Matrix
pedtoK                  Pedigree to matrix
phase.F1                Phasing F1 (CP) data in biparental populations
pin                     pin functionality
plot.MMERM              plot form a LMM plot with mmer
plot.variogram.MMERM    Default variogram.MMERM plotting
randef                  extracting random effects
residuals.MMERM         Residuals form a GLMM fitted with mmer
score.calcMV            Score calculation for markers
sommer                  *So*lving *M*ixed *M*odel *E*quations in *R*
spatPlots               Spatial plots
summary.MMERM           summary form a GLMM fitted with mmer
transp                  Creating color with transparency
variogram               Sample variogram
vctable                 vctable functionality
vctable.help            vctable.help functionality
wheatLines              wheat lines dataset
yates.oats              Yield of oats in a split-block experiment
