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| HAPim-package | HAPim |
| allele.marq | alleles at markers |
| corresp | correspondance |
| data.test | data.test |
| depart.LD | starting values for the optimization of HAPimLD method |
| depart.LDL | starting values for the optimization of HAPimLDL method |
| descendant.pere | first and last indexes of each sire progeny |
| distance.marqueurs | distance of markers |
| distance.test | localisation of test positions |
| esp.freq.hap | expectation of extended haplotype frequencies |
| freq.all | allelic frequencies |
| haldanem1 | recombination rate |
| HAPim | HAPim |
| hapim.LD.add | HAPimLD method |
| hapim.LDL.add | HAPimLDL method |
| haplomax.add | HaploMax method in unrelated population |
| haplomax.HS.add | HaploMax method in half-sib family design |
| moyenne.pere | average of performances per sire |
| obj.haplomax.add | analysis of variance of the HaploMax method |
| obj.haplomax.HS.add | Analysis of variance of the HaploMmax method in half-sib family design |
| obj.LD.add | log-likelihood value of HAPimLD method under H1 |
| obj.LD.add.H0 | log-likelihood value of HAPimLD method under H0 |
| obj.LDL.add | log-likelihood value of the HAPimLDL method under H1 |
| obj.LDL.add.H0 | log-likelihood value of the HAPimLDL method under H0 |
| pi.hap | haplotype frequencies |
| pi.hap.NI | haplotype frequencies |
| poids.D | poids.D |
| proba.DL | conditional probabilities |
| proba.DL.diplotype | probabilities due to linkage disequilibrium |
| recode.hap | recoding of haplotypes |
| retrouve.all | haplotype reconstruction |
| structure.hap | Structure |
| vrais.LD.add | log likelihood of HAPIimLD method under H1 |
| vrais.LDL.add | log likelihood of HAPimLDL method under H1 |
| vrais.LDL.add.pere | intra-sire log likelihood of HAPimLDL method under H1. |