calcObsCatch: Calculate observed catch
In TESA-workshops/TESAsamSim: Closed-loop salmon simulator for 2021 TESA workshop

Description Usage Arguments Value Examples

This function adjusts realized catches by normally distributed observation error to simulate observed catches. For mixed stock fisheries a tau parameter representing multivariate logistic error is also incorporated to account for uncertainty in the stock assignment process.

calcObsCatch(
  catchVec,
  recVec,
  manUnit,
  tauCatch,
  stkID,
  catchObsErr,
  extinctThresh
)

`catchVec`	A numeric vector representing realized CU-specific catches (i.e. outcome uncertainty incorporated).
`recVec`	A numeric vector representing CU-specific recruits (RY).
`manUnit`	A character vector identifying the MU that each CU belongs to.
`tauCatch`	A numeric representing multivariate logistic error associated with assigning catch in mixed stock fisheries to the correct CU.
`stkID`	A character vector of CU names.
`catchObsErr`	A numeric representing log-nomrally distributed error in catch observations.
`extinctThresh`	A numeric representing the extinction threshold for the aggregate.

Returns a numeric vector of observed catch.

#Note that the function is intended to receive vectors rather than the DFs
#used in this example to increase efficiency.
head(exampleHCRList)

catch <- exampleHCRList$mixCatch
rec <- exampleHCRList$recRY
manUnit <- exampleHCRList$mu
stock <- exampleHCRList$stock
calcObsCatch(catch, rec, manUnit, tauCatch = 0.1, stock, catchObsErr = 0.2,
extinctThresh = 0.0001)