| create.mppData | Create a multi-parent population data object | 
| CV_partition | Cross validation partition | 
| design_connectivity | Connected parts of a MPP design | 
| EC_effect | Determine EC effects | 
| IBD.mppData | IBD coding for 'mppData' objects | 
| IBS.mppData | IBS coding for 'mppData' objects | 
| inc_mat_QTL | QTL incidence matrix | 
| mppData | Complete 'mppData' object | 
| mppData_add_pheno | Add new phenotypic values to a mppData object | 
| mppData_GE | Example 'mppData' object | 
| mppData_init | 'mppData' object with raw data | 
| mppData_mdf_pheno | Modify the phenotypic values of a mppData object | 
| mppGE_CIM | MPP GxE Composite Interval Mapping | 
| mppGE_proc | MPP GxE QTL analysis | 
| mppGE_SIM | MPP GxE Simple Interval Mapping | 
| mpp_back_elim | Backward elimination on QTL candidates | 
| mpp_CIM | MPP Composite Interval Mapping | 
| mpp_CV | MPP cross-validation | 
| mpp_forward | MPP QTL analysis using forward regression | 
| mpp_perm | QTL significance threshold by permutation | 
| mpp_proc | MPP QTL analysis | 
| mpp_SIM | MPP Simple Interval Mapping | 
| MQE_gen_effects | QTL genetic effects multi-QTL effect model | 
| MQE_proc | Multi-QTL effect MPP analysis | 
| parent_cluster.mppData | Parent clustering for 'mppData' objects | 
| par_clu | Parental clustering | 
| plot.QTLprof | plot QTL profile | 
| plot_allele_eff_GE | plot of genome wide QTL allelic effect significance | 
| plot_QxEC | plot QTLxEC effect | 
| print.summary.mppData | Print summary.mppData object | 
| print.summary.QeffRes | Print summary.QeffRes object | 
| print.summary.QR2Res | Print summary.QR2Res object | 
| QC.mppData | Quality control for 'mppData' objects | 
| QTL_effect_GE | MPP GxE QTL genetic effects | 
| QTL_effect_main_QEI | Main and QTL by environment interaction model | 
| QTL_effect_main_QxEC | Estimation of a model with main and QTL by environmental sensitivity terms | 
| QTL_forward | Forward regression QTL model | 
| QTL_gen_effects | QTL genetic effects | 
| QTL_pred_R2 | Predicted QTL global and partial R squared | 
| QTL_R2 | QTL global and partial R squared | 
| QTL_R2_GE | MPP GxE QTL R2 | 
| QTL_select | QTL candidates selection | 
| subset.mppData | Subset 'mppData' object | 
| summary.mppData | Summary of 'mppData' object | 
| summary.QeffRes | Summary of 'QeffRes' object | 
| summary.QR2Res | Summary of 'QR2Res' object | 
| USNAM_geno | Reduced genotype data maize US-NAM population | 
| USNAM_map | Reduced map maize US-NAM population | 
| USNAM_pheno | Reduced phenotype data from Maize US-NAM population |