| A.mat | Additive relationship matrix |
| adiag1 | Binds arrays corner-to-corner |
| AI | Average Information Algorithm |
| ai2help | Average Information Algorithm |
| 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 |
| 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 |
| F1geno | Genotypes from an F1(CP) cross to show phasing |
| FDdata | half diallel data for corn hybrids |
| fdr | 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 |
| 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 |
| 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. |
| 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. |
| NR | Newton-Raphson Algorithm |
| NR22 | Newton-Raphson Algorithm |
| 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 |
| S.mat | Spatial relationship matrix |
| 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 |
| wheatLines | wheat lines dataset |