matchID should allow to match founders with a specific ID within the population to be created by pedigreeCross. It works when founders are all on top of the pedigree, eg 1:n first individuals, but it won't work if there are founders (full/half) further down the pedigree. Those founders ID should be attributed directly when creating the founderpop which is not an option. The second option is to recode the pedigree accordingly with all founders as 1:n but problematic with sortPed() (linked to #6 (comment)).
Error can be reproduced by simply calling pedigreeCross with matchID set to TRUE.
founderPop = quickHaplo(nInd=5, nChr=1, segSites=10)
SP = SimParam$new(founderPop)
pop = newPop(founderPop, simParam=SP)
id = 1:10
mother = c(0,0,0,0,1,1,2,7,0,7)
father = c(0,0,0,0,3,3,4,5,6,6)
pop2 = pedigreeCross(pop, id, mother, father, simParam=SP, matchID = TRUE)
matchID should allow to match founders with a specific ID within the population to be created by pedigreeCross. It works when founders are all on top of the pedigree, eg 1:n first individuals, but it won't work if there are founders (full/half) further down the pedigree. Those founders ID should be attributed directly when creating the founderpop which is not an option. The second option is to recode the pedigree accordingly with all founders as 1:n but problematic with sortPed() (linked to #6 (comment)).
Error can be reproduced by simply calling pedigreeCross with matchID set to TRUE.