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.

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

Author(s)

Q. Huynh

See Also

plot.RCModel RCM

SAMtool documentation built on Sept. 11, 2024, 8:07 p.m.