| A.mat | Additive relationship matrix |
| anova_mmes | anova form a GLMM fitted with mmes |
| AR1mat | Autocorrelation matrix of order 1. |
| ARMAmat | Autocorrelation Moving average. |
| atm | atm covariance structure |
| coef_mmes | coef form a GLMM fitted with mmes |
| corImputation | Imputing a matrix using correlations |
| covm | covariance between random effects |
| csm | customized covariance structure |
| CSmat | Compound symmetry matrix |
| DEPRECATED_GWAS | Genome wide association study analysis |
| DEPRECATED_summary_mmer | summary form a GLMM fitted with mmer |
| DEPRECATED_VS | variance structure specification |
| DEPRECATED_VSR | variance structure specification |
| dfToMatrix | data frame to matrix |
| D.mat | Dominance relationship matrix |
| dsm | diagonal covariance structure |
| E.mat | Epistatic relationship matrix |
| fitted_mmes | fitted form a LMM fitted with mmes |
| fixm | fixed indication matrix |
| H.mat | Combined relationship matrix H |
| ism | identity covariance structure |
| mmer | *m*ixed *m*odel *e*quations for *r* records |
| mmes | *m*ixed *m*odel *e*quations *s*olver |
| MNR | Multivariate Newton-Raphson algorithm |
| plot_mmes | plot form a LMM plot with mmes |
| plot.monitor | plot the change of VC across iterations |
| predict_mmes | Predict form of a LMM fitted with mmes |
| r2 | Reliability |
| randef | extracting random effects |
| residuals_mmes | Residuals form a GLMM fitted with mmes |
| sommer-package | *So*lving *M*ixed *M*odel *E*quations in *R* |
| spl2Dc | Two-dimensional penalised tensor-product of marginal B-Spline... |
| spl2Dmats | Get Tensor Product Spline Mixed Model Incidence Matrices |
| summary_mmes | summary form a GLMM fitted with mmes |
| tpsmmbwrapper | Get Tensor Product Spline Mixed Model Incidence Matrices |
| unsm | unstructured indication matrix |
| usm | unstructured covariance structure |
| vpredict | vpredict form of a LMM fitted with mmes |
| vsm | variance structure specification |
