A.mat                   Additive relationship matrix
AI                      Average Information Algorithm
CPdata                  Genotypic and Phenotypic data for a CP
                        population
D.mat                   Dominance relationship matrix
E.mat                   Epistatic relationship matrix
EM                      Expectation Maximization Algorithm
EM2                     Expectation Maximization Algorithm
EMMA                    Efficient Mixed Model Association Algorithm
ExpDesigns              Data for different experimental designs
F1geno                  Genotypes from an F1(CP) cross to show phasing
FDdata                  Full diallel data for corn hybrids
HDdata                  half diallel data for corn hybrids
LD.decay                Calculation of linkage disequilibrium decay
MAI                     Multivariate Average Information Algorithm
MAI2                    Multivariate Average Information Algorithm
MEMMA                   Multivariate Efficient Mixed Model Association
                        Algorithm
MMERM                   Multivariate mixed model solver to be called
                        inside mmer
MNR                     Multivariate Newton-Raphson Algorithm
NR                      Newton-Raphson Algorithm
NR22                    Newton-Raphson Algorithm
PEV                     Selecting the best training population for
                        genomic selection
PolyData                Genotypic and Phenotypic data for a potato
                        polyploid population
RICE                    Rice lines dataset
TP.prep                 Selecting the best training population for
                        genomic selection
Technow_data            Genotypic and Phenotypic data from single cross
                        hybrids (Technow et al. (2014))
adiag1                  Binds arrays corner-to-corner
ai2help                 Average Information Algorithm
and                     and functionality
anova.MMERM             anova form a GLMM fitted with mmer
anova.mmer              anova form a GLMM fitted with mmer
anova.mmerM             anova form a GLMM fitted with mmer
at                      at functionality
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
brewer.pal              Generate a sequence of colors for groups.
coef.MMERM              coef form a GLMM fitted with mmer
coef.mmer               coef form a GLMM fitted with mmer
coef.mmerM              coef form a GLMM fitted with mmer
cornHybrid              Corn crosses and markers
design.score            design score for the model to be tested
eigenGWAS               Unraveling selection signatures with eigenGWAS
fdr                     False Discovery Rate calculation
fdr2                    False Discovery Rate calculation
fitted.MMERM            fitted form a GLMM fitted with mmer
fitted.mmer             fitted form a GLMM fitted with mmer
fitted.mmerM            fitted form a GLMM fitted with mmer
g                       g functionality
gryphondata             Gryphon data from the Journal of Animal Ecology
h2                      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                    Mixed Model Equations in R
mmer2                   Mixed Model Equations in R v2
mmerSNOW                Mixed Model Equations in R univariate
my.colors               All typical colors in R easy to access.
name.change             renaming a vector by adding zeros
nna                     Nearest neighbour adjustment
overlay                 Overlay Matrix
phase.F1                Phasing F1 (CP) data in biparental populations
plot.MMERM              plot form a GLMM plot with mmer
plot.mmer               plot form a GLMM plot with mmer
plot.mmerM              plot form a GLMM plot with mmer
poe                     Short poems from Latin America, and other
                        places why not?
randef                  extracting random effects
residuals.MMERM         Residuals form a GLMM fitted with mmer
residuals.mmer          Residuals form a GLMM fitted with mmer
residuals.mmerM         Residuals form a GLMM fitted with mmer
score.calc              Score calculation for markers
score.calcMV            Score calculation for markers
sommer                  Solving Mixed Model Equations in R
summary.MMERM           summary form a GLMM fitted with mmer
summary.mmer            summary form a GLMM fitted with mmer
summary.mmerM           summary form a GLMM fitted with mmer
transp                  Creating color with transparency
us                      us functionality
wheatLines              wheat lines dataset
yates.oats              Yield of oats in a split-block experiment
