ss3slot: Functions to convert SS3 output into FLQuant(s)

In iagomosqueira/ss3om: Tools for Conditioning Fisheries Operating Models Using Stock Synthesis 3

Functions to convert SS3 output into FLQuant(s)

Description

A series of auxiliary functions that convert one or more elements, typically of class data.frame. in the list returned by r4ss::SS_output into particular FLQuant or FLQuants objects.

Usage

ss3index(cpue, fleets)

ss3index.res(cpue, fleets)

ss3index.var(cpue, fleets)

ss3index.q(cpue, fleets)

ss3sel.pattern(selex, years, fleets, morphs, factor = "Asel2")

ss3wt(endgrowth, dmns, birthseas)

ss3mat(endgrowth, dmns, birthseas, option = 3)

ss3m(endgrowth, dmns, birthseas)

ss3n(n, dmns, birthseas)

ss3catch(catage, wtatage, dmns, birthseas, idx)

ss3mat30(endgrowth, dmns, spawnseas, option = 3)

ss3m30(endgrowth, dmns, birthseas)

ss3n30(n, dmns)

ss3catch30(catage, wtatage, dmns, birthseas, idx)

Arguments

cpue	A data frame obtained from SS_output$cpue.
fleets	Named vector of fleets (numeric) codes
selex	A data frame obtained from SS_output$ageselex.
years	Vector of years for which the index applies
morphs	Vector of morphs to use
endgrowth	A data frame obtained from SS_output$endgrowth.
dmns	dimnames of the output object, usually obatined using getDimnames.
birthseas	The birthseasons for this stock as a numeric vector.
n	A data frame obtained from SS_output$natage.
catage	A data frame obtained from SS_output$catage.
wtatage	A data frame obtained from SS_output$endgrowth but subset for birthseas and ⁠RetWt:_idx⁠.
idx	The fishing fleets, as in SS_output$fleet_ID[SS_output$IsFishFleet].

Details

• ss3index returns the index slot of each survey/CPUE fleet.

• ss3index.res returns the index.res slot of each survey/CPUE fleet.

• ss3index.var returns the index.var slot of each survey/CPUE fleet.

• ss3index.q returns the index.q slot of each survey/CPUE fleet.

• ss3sel.pattern returns the sel.pattern slot of each survey/CPUE fleet.

• ss3wt returns the stock.wt slot.

• ss3mat returns the mat slot.

• ss3m returns the m slot.

• ss3m returns the m slot.

• ss3catch currently returns the landings.n slot, equal to catch.n as discards are not being parsed.

• ss3mat30 returns the mat slot.

• ss3m returns the m slot.

• ss3n30 returns the stock.n slot.

• ss3catch currently returns the landings.n slot, equal to catch.n as discards are not being parsed.

Value

An FLQuant or FLQuants object, depending on the converted data structure

Author(s)

Iago Mosqueira, EC JRC D02

See Also

FLQuant readFLSss3

iagomosqueira/ss3om documentation built on Sept. 29, 2024, 2:07 p.m.