| 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 |