| add.diallel.vars | add.diallel.vars |
| adiag1 | Binds arrays corner-to-corner |
| AI | Average Information Algorithm |
| A.mat | Additive relationship matrix |
| anova_mmec | anova form a GLMM fitted with mmec |
| anova_mmer | anova form a GLMM fitted with mmer |
| AR1mat | Autocorrelation matrix of order 1. |
| ARMAmat | Autocorrelation Moving average. |
| atc | atc covariance structure |
| atcg1234 | Letter to number converter |
| atcg1234BackTransform | Letter to number converter |
| atr | atr covariance structure |
| bathy.colors | Generate a sequence of colors for plotting bathymetric data. |
| bbasis | Function for creating B-spline basis functions (Eilers &... |
| bivariateRun | bivariateRun functionality |
| build.HMM | Build a hybrid marker matrix using parental genotypes from... |
| coef_mmec | coef form a GLMM fitted with mmec |
| coef_mmer | coef form a GLMM fitted with mmer |
| corImputation | Imputing a matrix using correlations |
| covc | covariance between random effects |
| csc | customized covariance structure |
| CSmat | Compound symmetry matrix |
| csr | customized covariance structure |
| dfToMatrix | data frame to matrix |
| D.mat | Dominance relationship matrix |
| dsc | diagonal covariance structure |
| dsr | diagonal covariance structure |
| DT_augment | DT_augment design example. |
| DT_btdata | Blue Tit Data for a Quantitative Genetic Experiment |
| DT_cornhybrids | Corn crosses and markers |
| DT_cpdata | Genotypic and Phenotypic data for a CP population |
| DT_example | Broad sense heritability calculation. |
| DT_expdesigns | Data for different experimental designs |
| DT_fulldiallel | Full diallel data for corn hybrids |
| DT_gryphon | Gryphon data from the Journal of Animal Ecology |
| DT_h2 | Broad sense heritability calculation. |
| DT_halfdiallel | half diallel data for corn hybrids |
| DT_ige | Data to fit indirect genetic effects. |
| DT_legendre | Simulated data for random regression |
| DT_mohring | Full diallel data for corn hybrids |
| DT_polyploid | Genotypic and Phenotypic data for a potato polyploid... |
| DT_rice | Rice lines dataset |
| DT_sleepstudy | Reaction times in a sleep deprivation study |
| DT_technow | Genotypic and Phenotypic data from single cross hybrids... |
| DT_wheat | wheat lines dataset |
| DT_yatesoats | Yield of oats in a split-block experiment |
| EM | Expectation Maximization Algorithm |
| E.mat | Epistatic relationship matrix |
| EMMA | Multivariate Efficient Mixed Model Association Algorithm |
| fcm | fixed effect constraint indication matrix |
| fitted_mmec | fitted form a LMM fitted with mmec |
| fitted_mmer | fitted form a LMM fitted with mmer |
| fixm | fixed indication matrix |
| gvsr | general variance structure specification |
| GWAS | Genome wide association study analysis |
| H | Two-way id by features table |
| H.mat | Combined relationship matrix H |
| impute | Imputing a numeric or character vector |
| isc | identity covariance structure |
| jet.colors | Generate a sequence of colors alog the jet colormap. |
| LD.decay | Calculation of linkage disequilibrium decay |
| leg | Legendre polynomial matrix |
| list2usmat | list or vector to unstructured matrix |
| logspace | Decreasing logarithmic trend |
| manhattan | Creating a manhattan plot |
| map.plot | Creating a genetic map plot |
| mmec | *m*ixed *m*odel *e*quations for *c* coefficients |
| mmer | *m*ixed *m*odel *e*quations for *r* records |
| neMarker | Effective population size based on marker matrix |
| overlay | Overlay Matrix |
| plot_mmec | plot form a LMM plot with mmec |
| plot_mmer | plot form a LMM plot with mmer |
| plot.monitor | plot the change of VC across iterations |
| predict_mmec | Predict form of a LMM fitted with mmec |
| predict_mmer | Predict form of a LMM fitted with mmer |
| propMissing | Proportion of missing data |
| r2 | Reliability |
| randef | extracting random effects |
| redmm | Reduced Model Matrix |
| residuals_mmec | Residuals form a GLMM fitted with mmec |
| residuals_mmer | Residuals form a GLMM fitted with mmer |
| rrc | reduced rank covariance structure |
| simGECorMat | Create a GE correlation matrix for simulation purposes. |
| sommer-package | *So*lving *M*ixed *M*odel *E*quations in *R* |
| spl2Da | Two-dimensional penalised tensor-product of marginal B-Spline... |
| spl2Db | Two-dimensional penalised tensor-product of marginal B-Spline... |
| spl2Dc | Two-dimensional penalised tensor-product of marginal B-Spline... |
| spl2Dmats | Get Tensor Product Spline Mixed Model Incidence Matrices |
| stackTrait | Stacking traits in a dataset |
| summary_mmec | summary form a GLMM fitted with mmec |
| summary_mmer | summary form a GLMM fitted with mmer |
| tps | Get Tensor Product Spline Mixed Model Incidence Matrices |
| tpsmmbwrapper | Get Tensor Product Spline Mixed Model Incidence Matrices |
| transformConstraints | transformConstraints |
| transp | Creating color with transparency |
| unsm | unstructured indication matrix |
| usc | unstructured covariance structure |
| usr | unstructured covariance structure |
| vpredict | vpredict form of a LMM fitted with mmer |
| vs | variance structure specification |
| vsc | variance structure specification |
| vsr | variance structure specification |
| wald | Wald Test for Model Coefficients |
