| 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 |