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Class-RCModel

Source: R/define_S4_class_RCModel.R
RCModel-class.Rd

An S4 class for the output from RCM.

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+1.

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 RCM in the i-th simulation.

Misc

A list of length OM@nsim with more output from the fitted RCM. Within each simulation, a named list containing items of interest include:

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

  • EPR0 - annual unfished spawners per recruit - vector of length nyears

  • ageM - age of 50% maturity - integer

  • EPR0_SR - unfished spawners per recruit for the stock-recruit relationship (mean EPR0 over the first ageM years) - numeric

  • R0 - unfished recruitment for the stock-recruit relationship - numeric

  • h - steepness for the stock-recruit relationship - numeric

  • Arec - stock-recruit alpha parameter - numeric

  • Brec - stock-recruit beta parameter - numeric

  • E0_SR - unfished spawning biomass for the stock-recruit relationship (product of EPR0_SR and R0) - numeric

  • CR_SR - compensation ratio, the product of Arec and EPR0_SR - numeric

  • E0 - annual unfished spawning biomass (intersection of stock-recruit relationship and unfished spawners per recruit) - vector of length nyears

  • R0_annual - annual unfished recruitment (annual ratio of E0 and EPR0) - vector of length nyears

  • h_annual - annual steepness (calculated from EPR0 and Arec) - vector of length nyears

  • CR - annual compensation ratio, the product of alpha and annual unfished spawners per recruit (EPR0) - vector of length nyears

  • R - recruitment - vector of length nyears+1

  • R_early - recruitment for the cohorts in first year of the model - vector n_age-1 (where n_age = maxage + 1)

  • VB - vulnerable biomass - matrix of nyears x nfleet

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

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

  • F_at_age - fishing mortality at age - matrix of nyears x n_age

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

  • M - natural mortality - matrix of nyears x n_age

  • Z - total mortality - matrix of nyears x n_age

  • q - index catchability - vector of length nsurvey

  • ivul - index selectivity at age - array of dim nyears+1, n_age, nsurvey

  • ivul_len - corresponding index selectivity at length - matrix of nbins x nsurvey

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

  • IAApred - predicted index catch at age - array of dim nyears, n_age, nsurvey

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

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

  • IALpred - predicted index 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, n_age, 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

  • dynamic_SSB0 - the dynamic unfished spawning biomass calcaluated by projecting the historical model with zero catches - vector of length nyears+1

  • SPR_eq - equilibrium spawning potential ratio calculated from annual F-at-age - vector of length nyears

  • SPR_dyn - dynamic (transitional) spawning potential ratio calculated from cumulative survival of cohorts - vector of length nyears

  • nll - total objective function of the model - numeric

  • nll_fleet - objective function values for each annual data point(s) from fleets - array of nyears x nfleet x 5 (for Catch, equilibrium catch, CAA, CAL, and mean size)

  • nll_index - objective function values for each annual data point(s) in the index - array of nyears x nsurvey x 3 (for Index, IAA, and IAL)

  • prior - penalty value added to the objective function from priors - numeric

  • penalty - additional penalty values added to the objective function due to high F - numeric

  • conv - whether the model converged (whether a positive-definite Hessian was obtained) - logical

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 TMB::MakeADFun().

  • opt - a list with components from calling stats::nlminb() to obj.

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

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

data

A RCMdata object containing data inputs for the RCM.

config

A list describing configuration of the RCM:

  • drop_sim - a vector of simulations that were dropped for the output

See also

plot.RCModel RCM

Author

Q. Huynh