When do we consider a bee as a queen?

[janaobsteter]

I think we agreed that a bee can only be in the queen slot if it's mated --> otherwise it should be in the virginQueens slot. This raises a couple of questions / issues:

• why do we then have a function isQueen() and isQueenMated()?
  -isQueen() and isQueenMated() can show a different thing. For example:

#' founderGenomes <- quickHaplo(nInd = 20, nChr = 1, segSites = 100)
#' SP <- SimParamBee$new(founderGenomes)
#' basePop <- createVirginQueens(founderGenomes)
#'
#' drones <- createDrones(x = basePop[1], nInd = 100)
#'
#' # If input is a Pop class of virgin queen(s)
#' virginQueen1 <- basePop[2]
#' isQueen(virginQueen1)
#' (matedQueen1 <- cross(
#'   x = virginQueen1,
#'   fathers = drones[1:5]
#' ))
#' 
#' isQueen(virginQueen1)
#' isQueenMated(virginQueen1)

returns

> isQueen(virginQueen1)
[1] TRUE
> isQueenMated(virginQueen1)
[1] FALSE

[gregorgorjanc]

isQueen is based on isCaste

SIMplyBee/SIMplyBee/R/Functions_L0_auxilary.R

Line 603 in e88eaef

isQueen <- function(x, simParamBee = NULL) {

, which checks the caste of an individual in SimParamBee object.

So, when you mated the virgin queen above, the cross function changed the caste for the individual in the SimParamBee object and now both the matedQueen1 and virginQueen1 contain the same individual whose ID is linked to the ID in the SimParamBee and associated caste, which has been set to queen.

Does this make sense?

[janaobsteter]

Yes, I do understand why it happens, it is just super confusing. A queen shouldn't be a queen if not mated - hence I don't know whether one of the functions is redundant? And second, I think we should avoid such confusing examples - we can assign the queen back to itself?

[gregorgorjanc]

Good point. I think this reflect evolution of the code. Initially we did not have isCaste/isQueen/…. We only had isQueenMated and we used it in other functions. So, I guess we should remove the isQueenMated in favour of isQueen. Can you check where we use it? Best to open an issue so we track this properly. Also, we should make sure that cross doesn’t change caste of a failed mating (say mating with 0 fathers)!!!!

[gregorgorjanc]

@janaobsteter is this resolved so we mark the discussion as answered?

[janaobsteter]

In SIMplyBee, the bee is a queen only when she's mated.