Error in F_flbeia

[marchtaylor]

In F_flbeia, there appears to be an error in how fishing mortality is calculated for stocks with a single age dimension. It appears to show that F = catch/biomass, but I believe the function is actually calculating catch.n / stockBiomass:

FLBEIA/R/Results_Summary.R

Lines 70 to 75 in 3936481

	if(na == 1){
	# Catch:
	catch <- apply(catchStock(obj$fleets, stk),c(2,4,6), sum)[,years,drop = TRUE] # [ny,ns,it]
	B <- (obj$biols[[stk]]@n*obj$biols[[stk]]@wt)[,years,,,drop= TRUE] # [ny,ns, it] , 1st season biomass
	res[stk,,,] <- (catch/B)
	}

The fix should possibly be to use numbers (catch.n / stock.n), which I believe is preferable to total weight (catch/stock). In the case of biomass dynamics stocks, we use mean weights = 1.0 and numbers equal the total weight of the stock and catch. Thus, harvest weight based on weight or numbers would be equivalent. However, with Nephrops, mean weights are different for landings and discards, and harvest rates should be based on numbers.

Likewise, I believe the perfectObs function would benefit from using numbers as the basis for harvest rate calculation - currently catch/stockBiomass:

FLBEIA/R/MP_1a_Observation_Model.R

Lines 124 to 126 in 3936481

	if(na == 1){
	harvest(res)[] <- (res@catch)/(res@stock.n*res@stock.wt)
	units(res@harvest) <- 'hr'