adjustAlaska: (SPFI) Sum SEAK CWT data

In MichaelFolkes/ctctools: Analytical tools For The Pacific Salmon Commission's Chinook Technical Committee.

Description

CWT data in SEAK fishery 4 (AK JLO T) is revised to equal sum of fishery 4+6 (AK FALL T). This is a summation that is unique to SPFI estimation for SEAK only. If estimating for SEAK, then the hrj database variables: NomCat# (VB variable:cwtcatch), AEQCat# (VB variable:aeqcwtcat), and AEQTot# (VB variable:aeqcwttotmort) for fishery 4 are revised to equal sum of fishery 4+6. The basis of this summation is not documented. Up to 2017 the SEAK catch data file has been limited to 5 strata. These are the fishery definitions:

fishery	gear	fishery	fishery	fishery	fishery	fishery
index		type	country	name	region	psc
4	T	P	US	AK JLO T	AK	AABM
6	T	P	US	AK FALL T	AK	AABM

Usage

adjustAlaska(x, data.catch)

Arguments

x	A data frame, representation of the CWT data. Equivalent to a subset of the hrj data frame where data.type=="NomCat"
data.catch	A list with structure equivalent to the output from the function readCatchData.

Value

The function returns a data frame representation of the CWT data, in same format as the first input argument.

Examples

## Not run: 
#user needs to define catch file:
data.catch <- readCatchData(...)
#this assumes hrj.df has been read in and transformed to long format:
cwtcatch <- hrj.df[hrj.df$data.type=="NomCat"
                   & hrj.df$fishery.index %in% 1:6
                   & hrj.df$Stock.Number %in% C(1,9,10,15,17,20),]
cwtcatch <- adjustAlaska(x = cwtcatch, data.catch = data.catch)

## End(Not run)

MichaelFolkes/ctctools documentation built on May 7, 2019, 4:56 p.m.