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MSEtool (version 2.0.1)

SRA-class: Class-SRA

Description

An S4 class for the output from SRA_scope.

Arguments

Slots

OM

An updated operating model, class '>OM.

SSB

A matrix of estimated spawning biomass with OM@nsim rows and OM@nyears+1 columns.

NAA

An array for the predicted numbers at age with dimension OM@nsim, OM@nyears+1, and OM@maxage.

CAA

An array for the predicted catch at age with dimension OM@nsim, OM@nyears, OM@maxage, and nfleet.

CAL

An array for the predicted catch at length with dimension OM@nsim, OM@nyears, length bins, and nfleet.

conv

A logical vector of length OM@nsim indicating convergence of the SRA scoping model in the i-th simulation.

Misc

A list of length OM@nsim with more output from the fitted SRA scoping model. Within each simulation, items of interest include:

  • B - total biomass - vector of length nyears+1

  • E0 - annual unfished spawning biomass - vector of length nyears

  • E0_SR - unfished spawning biomass for the stock-recruit relationship - numeric

  • Arec - alpha parameter of the stock-recruit relationship - numeric

  • Brec - beta parameter of the stock-recruit relationship - numeric

  • R - recruitment - vector of length nyears+1

  • R_early - recruitment for the cohorts in first year of the model - vector maxage-1

  • VB - vulnerable biomass - matrix of nyears x nfleet

  • N - abundance at age - matrix of nyears+1 x maxage

  • F - apical fishing mortality - matrix of nyears x nfleet

  • F_at_age - fishing mortality at age - array of nyears x maxage x nfleet

  • F_equilibrium - equilibrium fishing mortality prior to first year - vector of length nfleet

  • M - natural mortality - matrix of nyears x maxage

  • Z - total mortality - matrix of nyears x maxage

  • q - survey catchability - vector of length nsurvey

  • s_vul - survey selectivity at age - array of dim nyears+1, maxage, nsurvey

  • s_vul_len - corresponding survey selectivity at length - matrix of nbins x nsurvey

  • Ipred - predicted index values - matrix of nyears x nsurvey

  • s_CAApred - predicted survey catch at age - array of dim nyears, maxage, nsurvey

  • vul - fleet selectivity at age - array of dim nyears+1, maxage, nfleet (or nsel_block)

  • vul_len - corresponding fleet selectivity at length - matrix of nbins x nfleet (or nsel_block)

  • s_CALpred - predicted survey catch at length - array of dim nyears, nbins, nsurvey

  • MLpred - predicted mean length - matrix of nyears x nfleet

  • MWpred - predicted mean weight - matrix of nyears x nfleet

  • CAApred - predicted catch at age - array of nyears, maxage, nfleet

  • CALpred - predicted catch at length - array of nyears, nbins, nfleet

  • Cpred - predicted catch in weight - matrix of nyears x nfleet

  • CN - predicted catch in numbers - matrix of nyears x nfleet

  • nll - Total objective function of the model - numeric

mean_fit

A list of output from fit to mean values of life history parameters in the operating model. The named list consists of:

  • obj - a list with components returned from MakeADFun.

  • opt - a list with components from calling nlminb to obj.

  • SD - a list (class sdreport) with parameter estimates and their standard errors, obtained from sdreport.

  • report - a list of model output reported from the TMB executable, i.e. obj$report(). See Misc.

data

A list of the data inputs for the SRA scoping model.

config

A data frame describing configuration of the SRA scoping model (not currently used).

See Also

plot.SRA SRA_scope