A.mat |
Additive relationship matrix |
adiag1 |
Binds arrays corner-to-corner |
AI |
Average Information Algorithm |
and |
and functionality |
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 |
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. |
BTdata |
Blue Tit Data for a Quantitative Genetic Experiment |
build.HMM |
Build a hybrid marker matrix using parental genotypes |
coef.MMERM |
coef form a GLMM fitted with mmer |
cornHybrid |
Corn crosses and markers |
CPdata |
Genotypic and Phenotypic data for a CP population |
D.mat |
Dominance relationship matrix |
design.score |
design score for the model to be tested |
E.mat |
Epistatic relationship matrix |
eig |
eigen decomposition functionality |
EM |
Expectation Maximization Algorithm |
example |
Broad sense heritability calculation. |
ExpDesigns |
Data for different experimental designs |
F1geno |
Genotypes from an F1(CP) cross to show phasing |
FDdata |
Full diallel data for corn hybrids |
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 |
g |
g functionality |
grp |
grouping functionality |
gryphondata |
Gryphon data from the Journal of Animal Ecology |
GWAS |
Genome Wide Association Analysis |
GWAS2 |
Genome Wide Association Analysis |
h2.fun |
Obtain heritabilities with three different methods |
h2example |
Broad sense heritability calculation. |
hadamard.prod |
Hadamard product of two matrices |
HDdata |
half diallel data for corn hybrids |
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 |
MEMMA |
Multivariate Efficient Mixed Model Association Algorithm |
mmer |
*m*ixed *m*odel *e*quations in *R* |
mmer2 |
*m*ixed *m*odel *e*quations in *R* |
MNR |
Multivariate Newton-Raphson Algorithm |
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 |
PolyData |
Genotypic and Phenotypic data for a potato polyploid population |
print.MMERM |
summary form a GLMM fitted with mmer |
print.summary.MMERM |
summary form a GLMM fitted with mmer |
randef |
extracting random effects |
residuals.MMERM |
Residuals form a GLMM fitted with mmer |
RICE |
Rice lines dataset |
score.calcMV |
Score calculation for markers |
sommer |
*So*lving *M*ixed *M*odel *E*quations in *R* |
summary.MMERM |
summary form a GLMM fitted with mmer |
Technow_data |
Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014)) |
transp |
Creating color with transparency |
us |
us functionality |
variogram |
Sample variogram |
variogram.MMERM |
Sample variogram |
vctable |
vctable functionality |
vctable.help |
vctable.help functionality |
wheatLines |
wheat lines dataset |
yates.oats |
Yield of oats in a split-block experiment |