Describe the bug
If I simulate a trait and add names (e.g. "DailyGain") and then subsequently call pull- and setMarkerHaplo (or Geno) on a Pop class, the trait names are removed, but only for genetic values. They are still present for the phenotypes.
Steps To Reproduce
# Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)
SP <- SimParam$new(founderPop)
SP$addTraitA(nQtlPerChr = 10, mean = 0, var = 1, name = "trait1")
SP$setVarE(varE = 1)
basePop <- newPop(founderPop)
basePop@gv
basePop@pheno
# Extract haplotypes for marker "1_1"
H = pullMarkerHaplo(basePop, markers="1_1")
# Set the first haplotype to 1
H[1,1] = 1L
# Set marker haplotypes
basePop = setMarkerHaplo(basePop, haplo=H)
basePop@gv
basePop@pheno
Expected behavior
I'm guessing that the function recalculates the gv (but not the pheno) due to the changed genotype - but the names should be kept.
Thanks for catching this. Yes, this genetic values are recalculated incase a change hits alters the QTL genotype. It looks like I didn't handle trait names appropriately when this happens.
Describe the bug If I simulate a trait and add names (e.g. "DailyGain") and then subsequently call
pull-
andsetMarkerHaplo
(or Geno) on aPop
class, the trait names are removed, but only for genetic values. They are still present for the phenotypes.Steps To Reproduce
Expected behavior I'm guessing that the function recalculates the gv (but not the pheno) due to the changed genotype - but the names should be kept.