A.mat |
Additive relationship matrix |
adiag1 |
Binds arrays corner-to-corner |
AI |
Average Information Algorithm |
ai2help |
Average Information Algorithm |
and |
and functionality |
anova.mmer |
anova form a GLMM fitted with mmer |
anova.MMERM |
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.mmer |
coef form a GLMM fitted with mmer |
coef.MMERM |
coef form a GLMM fitted with mmer |
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 |
eigenGWAS |
Unraveling selection signatures with eigenGWAS |
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 |
fdr |
False Discovery Rate calculation |
fdr2 |
False Discovery Rate calculation |
fitted.mmer |
fitted form a GLMM fitted with mmer |
fitted.MMERM |
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 |
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. |
LD.decay |
Calculation of linkage disequilibrium decay |
MAI |
Multivariate Average Information Algorithm |
MAI2 |
Multivariate Average Information Algorithm |
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 |
Mixed Model Equations in R |
mmer2 |
Mixed Model Equations in R v2 |
MMERM |
Multivariate mixed model solver to be called inside mmer |
mmerSNOW |
Mixed Model Equations in R univariate |
MNR |
Multivariate Newton-Raphson Algorithm |
my.colors |
All typical colors in R easy to access. |
name.change |
renaming a vector by adding zeros |
nna |
Nearest neighbour adjustment |
NR |
Newton-Raphson Algorithm |
NR22 |
Newton-Raphson Algorithm |
overlay |
Overlay Matrix |
PEV |
Selecting the best training population for genomic selection |
phase.F1 |
Phasing F1 (CP) data in biparental populations |
plot.mmer |
plot form a GLMM plot with mmer |
plot.MMERM |
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? |
PolyData |
Genotypic and Phenotypic data for a potato polyploid population |
print.mmer |
summary form a GLMM fitted with mmer |
print.MMERM |
summary form a GLMM fitted with mmer |
print.mmerM |
summary form a GLMM fitted with mmer |
print.summary.mmer |
summary form a GLMM fitted with mmer |
print.summary.MMERM |
summary form a GLMM fitted with mmer |
print.summary.mmerM |
summary form a GLMM fitted with mmer |
randef |
extracting random effects |
residuals.mmer |
Residuals form a GLMM fitted with mmer |
residuals.MMERM |
Residuals form a GLMM fitted with mmer |
residuals.mmerM |
Residuals form a GLMM fitted with mmer |
RICE |
Rice lines dataset |
score.calc |
Score calculation for markers |
score.calcMV |
Score calculation for markers |
sommer |
Solving Mixed Model Equations in R |
summary.mmer |
summary form a GLMM fitted with mmer |
summary.MMERM |
summary form a GLMM fitted with mmer |
summary.mmerM |
summary form a GLMM fitted with mmer |
Technow_data |
Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014)) |
TP.prep |
Selecting the best training population for genomic selection |
transp |
Creating color with transparency |
us |
us functionality |
wheatLines |
wheat lines dataset |
yates.oats |
Yield of oats in a split-block experiment |