Solving Mixed Model Equations in R

adiag1 | Binds arrays corner-to-corner |

A.mat | Additive relationship matrix |

anova | 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. |

BTdata | Blue Tit Data for a Quantitative Genetic Experiment |

build.HMM | Build a hybrid marker matrix using parental genotypes |

coef | coef form a GLMM fitted with mmer |

cornHybrid | Corn crosses and markers |

CPdata | Genotypic and Phenotypic data for a CP population |

design.score | design score for the model to be tested |

D.mat | Dominance relationship matrix |

EM | Expectation Maximization Algorithm |

E.mat | Epistatic relationship matrix |

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 | fitted form a GLMM fitted with mmer |

gryphondata | Gryphon data from the Journal of Animal Ecology |

GWAS | Genome Wide Association Analysis |

GWAS2 | Genome Wide Association Analysis |

h2example | Broad sense heritability calculation. |

h2.fun | Obtain heritabilities with three different methods |

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 |

impute | 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 | plot form a LMM plot with mmer |

plot.variogram | Default variogram.MMERM plotting |

PolyData | Genotypic and Phenotypic data for a potato polyploid... |

randef | extracting random effects |

residuals | Residuals form a GLMM fitted with mmer |

RICE | Rice lines dataset |

score.calcMV | Score calculation for markers |

sommer-package | *So*lving *M*ixed *M*odel *E*quations in *R* |

spatPlots | Spatial plots |

summary | summary form a GLMM fitted with mmer |

Technow_data | Genotypic and Phenotypic data from single cross hybrids... |

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 |

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