RCModel-class: Class-'RCModel'

In SAMtool: Stock Assessment Methods Toolkit

Class-RCModel

Description

An S4 class for the output from RCM.

Slots

OM

An updated operating model, class MSEtool::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.

report

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

Misc

Slot for miscellaneous information for the user. Currently unused.

Author(s)

Q. Huynh

See Also

plot.RCModel RCM

SAMtool documentation built on April 4, 2025, 2:15 a.m.