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Calculate Mohn's rho values for select quantities

Source: R/SSmohnsrho.R
SSmohnsrho.Rd

Function calculates:

  1. a rho value for the ending year for each retrospective relative to the reference model as in Mohn (1999);

  2. a “Wood's Hole Mohn's rho”, which is a rho value averaged across all years for each retrospective relative to the reference model; and

  3. an Alaska Fisheries Science Center and Hurtado-Ferro et al. (2015) Mohn's rho, which is the average rho per retrospective “peel”.

Usage

SSmohnsrho(summaryoutput, endyrvec, startyr, verbose = TRUE)

Arguments

summaryoutput

List created by SSsummarize(). The expected order for the models are the full reference model, the retro -1, retro -2, and so forth. Order matters for the calculations.

endyrvec

Integer vector of years that should be used as the final year for each model in summaryoutput. The default, which happens if endyrvec is missing, is based on information in summaryoutput, i.e., summaryoutput[["endyrs"]][summaryoutput[["n"]]]: (summaryoutput[["endyrs"]][summaryoutput[["n"]]] - summaryoutput[["n"]] + 1). This parameter will be used to extract estimates of fishing mortality for each year in endyrvec and estimates of biomass-based quantities for each year in endyrvec + 1 because Stock Synthesis reports beginning of the year biomass, which we use here as a proxy for end of the year biomass.

startyr

Single year used to calculate the start year for the calculation of the Wood's Hole Mohn's rho value, which is computed across the range of years in the model. If this parameter is missing, the default is to use the startyr of the reference model.

verbose

A logical value specifying if output should be printed to the screen.

Value

A list with the following 12 entries:

  • "SSB"

  • "Rec"

  • "Bratio"

  • "F"

  • "WoodHole_SSB.all"

  • "WoodHole_Rec.all"

  • "WoodHole_Bratio.all"

  • "WoodHole_F.all"

  • "AFSC_Hurtado_SSB"

  • "AFSC_Hurtado_Rec"

  • "AFSC_Hurtado_F"

  • "AFSC_Hurtado_Bratio"

References

  • Hurtado-Ferro et al. 2015. Looking in the rear-view mirror: bias and retrospective patterns in integrated, age-structured stock assessment models. ICES J. Mar. Sci. 72(1), 99–110. https://doi.org/10.1093/icesjms/fsu198.

  • Mohn, R. 1999. The retrospective problem in sequential population analysis: an investigation using cod fishery and simulated data. ICES J. Mar. Sci. 56, 473–488. https://doi.org/10.1006/jmsc.1999.0481.

Author

Chantel R. Wetzel, Carey R. McGilliard, and Kelli F. Johnson