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.LD.add            HAPimLD method
hapim.LDL.add           HAPimLDL method
haplomax.HS.add         HaploMax method in half-sib family design
haplomax.add            HaploMax method in unrelated population
moyenne.pere            average of performances per sire
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
obj.haplomax.HS.add     Analysis of variance of the HaploMmax method in
                        half-sib family design
obj.haplomax.add        analysis of variance of the HaploMax method
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.
