calcObsCatch: Calculate observed catch

View source: R/calcObsCatch.R

calcObsCatchR Documentation

Calculate observed catch

Description

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.

Usage

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

Arguments

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.

Value

Returns a numeric vector of observed catch.

Examples

#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)

CamFreshwater/samSim documentation built on Sept. 25, 2023, 10:22 a.m.