calcObsCatch | R Documentation |
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)
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