Package 'ss3om'

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)

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nameGrid

Description

Creates folder names from a 'grid' df of scenarios

Usage

nameGrid(df, dir, from = 1)

Arguments

df	Model grid data.frame
dir	Folder name
from	Starting number

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A function to read the CPUE series from an SS3 run into an FLIndex object

Description

A function to read the CPUE series from an SS3 run into an FLIndex object

Usage

readFLIBss3(
  dir,
  fleets,
  birthseas = out$birthseas,
  repfile = "Report.sso",
  compfile = "CompReport.sso",
  ...
)

Arguments

dir	Directory containing the SS3 output files
birthseas	The birthseasons for this stock as a numeric vector.
...	Any other argument to be passed to r4ss::SS_output

Value

An object of class FLStock

Author(s)

Iago Mosqueira, EC JRC

References

Methot RD Jr, Wetzel CR (2013) Stock Synthesis: A biological and statistical framework for fish stock assessment and fishery management. Fisheries Research 142: 86-99.

See Also

FLComp

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A function to read the stock-recruit relationships from an SS3 run into an FLSR object

Description

A function to read the stock-recruit relationships from an SS3 run into an FLSR object

Usage

readFLSRss3(
  dir,
  birthseas = out$birthseas,
  repfile = "Report.sso",
  compfile = "CompReport.sso",
  ...
)

Arguments

dir	Directory containing the SS3 output files
birthseas	The birthseasons for this stock as a numeric vector.
...	Any other argument to be passed to r4ss::SS_output

Value

An object of class FLStock

Author(s)

Iago Mosqueira, EC JRC

References

Methot RD Jr, Wetzel CR (2013) Stock Synthesis: A biological and statistical framework for fish stock assessment and fishery management. Fisheries Research 142: 86-99.

See Also

FLComp

---

A function to read SS3 results as an FLStock object

Description

Results of a run of the Stock Synthesis sofware, SS3 (Methot & Wetzel, 2013), can be loaded into an object of class FLStock. The code makes use of the r4ss::SS_output function to obtain a list from Report.sso. The following elements of that list are used to generate the necessary information for the slots in FLStock: "catage", "natage", "ageselex", "endgrowth", "catch_units", "nsexes", "nseasons", "nareas", "IsFishFleet", "fleet_ID", "FleetNames", "spawnseas", "inputs" and "SS_version".

Usage

readFLSss3(
  dir,
  repfile = "Report.sso",
  compfile = "CompReport.sso",
  wtatage = out$wtatage_switch,
  ...
)

Arguments

dir	Directory holding the SS3 output files
...	Any other argument to be passed to r4ss::SS_output
birthseas	Birth seasons for this stock, defaults to spawnseas
name	Name of the output object to fil the name slot
desc	Description of the output object to fill the desc slot

Value

An object of class ⁠\link{FLStock}⁠

Author(s)

The FLR Team

References

Methot RD Jr, Wetzel CR (2013) Stock Synthesis: A biological and statistical framework for fish stock assessment and fishery management. Fisheries Research 142: 86-99.

See Also

FLComp

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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

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