| coef.LASSO | LASSO methods |
| coef.SSI | SSI methods |
| collect | Collecting SSI outputs |
| cov2cor2 | Conversion of a covariance matrix to a distance/correlation matrix |
| cov2dist | Conversion of a covariance matrix to a distance/correlation matrix |
| fitBLUP | Fitting a Linear Mixed model to calculate BLUP |
| fitted.LASSO | LASSO methods |
| fitted.SSI | SSI methods |
| genCOV_xy | Wheat dataset |
| genCOV_yy | Wheat dataset |
| getGenCov | Pairwise Genetic Covariance |
| LARS | Least Angle Regression to solve LASSO-type problems |
| M | Wheat dataset |
| multitrait.plot | Accuracy vs penalization from Multitrait SSI |
| net | Graphical Network |
| path.plot | Coefficients path plot |
| plot.net | Plotting a network |
| plot.SSI | Accuracy vs penalization plot |
| Prune | R-squared pruning |
| readBinary | Save/read binary files |
| resCOV_yy | Wheat dataset |
| saveBinary | Save/read binary files |
| solveEN | Coordinate Descent algorithm to solve Elastic-Net-type problems |
| SSI | Sparse Selection Index |
| SSI.CV | Sparse Selection Index |
| summary.SSI | SSI methods |
| VI_E1 | Wheat dataset |
| wheatHTP | Wheat dataset |
| X_E1 | Wheat dataset |
| Y | Wheat dataset |