| NAM-package | Nested Association Mapping |
| BCpi | Internal functions |
| ben | Genome-wide prediction |
| BRR2 | Internal functions |
| calcSize | Internal functions |
| chr | Tetra-seed Pods |
| cleanREP | SNP Quality Control |
| CNT | Internal functions |
| covar | Internal functions |
| eigX | Internal functions |
| emBA | Internal functions |
| emBB | Internal functions |
| emBC | Internal functions |
| emBD | Internal functions |
| emBL | Internal functions |
| emCV | Internal functions |
| emDE | Internal functions |
| emEN | Internal functions |
| emGWA | Internal functions |
| emML | Internal functions |
| emML2 | Internal functions |
| emMX | Internal functions |
| emRR | Internal functions |
| fam | Tetra-seed Pods |
| Fst | Fixation Index |
| funI | Internal functions |
| funX | Internal functions |
| G2A_Kernels | Internal functions |
| GAU | Internal functions |
| Gdist | Internal functions |
| Gen | Multi-environmental trial |
| gen | Tetra-seed Pods |
| gibbs | Bayesian Mixed Model |
| gibbs2 | Bayesian Mixed Model |
| gmm | Genomic mixed model |
| GRM | Internal functions |
| gs | Internal functions |
| gwas | Empirical Bayes Genome Wide Association Mapping |
| gwas2 | Empirical Bayes Genome Wide Association Mapping |
| gwas3 | Empirical Bayes Genome Wide Association Mapping |
| gwasGE | Empirical Bayes Genome Wide Association Mapping |
| IMP | Internal functions |
| Import_data | Internal functions |
| inputRow | Internal functions |
| KMUP | Internal functions |
| KMUP2 | Internal functions |
| LD | Internal functions |
| markov | Internal functions |
| MCreml | Restricted Maximum Likelihood |
| met | Multi-environmental trial |
| meta3 | Empirical Bayes Genome Wide Association Mapping |
| mkr | Internal functions |
| mkr2X | Internal functions |
| ml | Bayesian Mixed Model |
| mrr | Internal functions |
| mrr2X | Internal functions |
| mrrFast | Internal functions |
| mrrV2 | Internal functions |
| MSX | Internal functions |
| NAM | Nested Association Mapping |
| NNcov | Internal functions |
| NNsrc | Internal functions |
| NOR | Internal functions |
| Obs | Multi-environmental trial |
| PedMat | Internal functions |
| PedMat2 | Internal functions |
| plot.fst | Fixation Index |
| plot.gibbs | Bayesian Mixed Model |
| plot.H2 | SNP heritability |
| plot.NAM | Manhattan plot for Association Studies |
| press | Internal functions |
| RcppExports | Internal functions |
| reference | SNP Quality Control |
| reml | Restricted Maximum Likelihood |
| SAMP | Internal functions |
| SAMP2 | Internal functions |
| snpH2 | SNP heritability |
| snpQC | SNP Quality Control |
| SPC | Internal functions |
| SPM | Internal functions |
| timesMatrix | Internal functions |
| timesVec | Internal functions |
| tpod | Tetra-seed Pods |
| wgr | Genome-wide prediction |
| y | Tetra-seed Pods |