extractSS: Extracts derived quantities from SS output

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

Extracts derived quantities from SS output

Description

A number of derived quantities are available in the Report.sso file, and are useful for checking that the generated FLR objects lead to the same values. These functions are called on the list returned by readOutputss3 or r4ss::SS_output, and extract the yearly values from the following rows in the derived_quants data.frame:

Usage

extractSSB(out)

extractRec(out)

extractFbar(out)

extractZatage(out)

extractDevs(out)

Arguments

out	A list as returned by r4ss::SS_output.

Details

• extractSSB: SSB_y for y between startyr and endyr.

• extractRec: Recr_y for y between startyr and endyr.

• extractFbar: F_y for y between startyr and endyr.

• extractZatage: Z_ay for y between startyr and endyr and ages but last.

For 2 sex models (nsexes), extractRec will return a two-unit FLQuant, with the Recr_y values split according to the recruitment sex ratio. This is extracted from recruitment_dist[[1]][, "Frac/sex"].

The value returned by extractFbar is the actual mean F over the age range, and the value in derived_quants is corrected according to F_report_basis for models where F reporting basis is F/FMSY.

Value

An FLQuant object of the requested quantity.

Examples

out <- readOutputss3(system.file("ext-data", "herring", package="ss3om"))

extractSSB(out)

extractFbar(out)

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