Functions to convert SS3 output into FLQuant(s)

Source: R/ss3slots.R, R/ss3slots30.R

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.

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].

Value

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

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.

See also

FLQuant readFLSss3

Author

Iago Mosqueira, EC JRC D02