An S4 class that contains assessment output. Created from a function of class
Name of the assessment model.
Name of Data object.
Logical. Whether the assessment model converged (defined by whether TMB returned a positive-definite covariance matrix for the model).
Estimate of exploitation at maximum sustainable yield.
Estimate of instantaneous fishing mortality rate at maximum sustainable yield.
Estimate of maximum sustainable yield.
Biomass at maximum sustainable yield.
Spawning stock biomass at maximum sustainable yield.
Vulnerable biomass at maximum sustainable yield.
Biomass at unfished equilibrium.
Recruitment at unfished equilibrium.
Abundance at unfished equilibrium.
Spawning stock biomass at unfished equilibrium.
Vulnerable biomass at unfished equilibrium.
Time series of exploitation.
Time series of relative exploitation.
Time series of instantaneous fishing mortality.
Time series of fishing mortality relative to MSY.
Time series of biomass.
Time series of biomass relative to MSY.
Time series of depletion.
Time series of spawning stock biomass.
Time series of spawning stock biomass relative to MSY.
Time series of spawning stock depletion.
Time series of vulnerable biomass.
Time series of vulnerable biomass relative to MSY.
Time series of vulnerable biomass depletion.
Time series of recruitment.
Time series of population abundance.
Time series of numbers-at-age matrix.
Observed catch-at-age matrix.
Predicted catch-at-age matrix.
A vector of estimated deviation parameters.
A description of the deviation parameters, e.g. "log recruitment deviations".
Negative log-likelihood. A vector for the total likelihood, integrated across random effects if applicable, components,
and penalty term (applied when
U > 0.975 in any year).
Standard error of UMSY estimate.
Standard error of FMSY estimate.
Standard error of MSY estimate.
Standard error of U/UMSY.
Standard error of F/FMSY.
Standard error of B/BMSY.
Standard error of B/B0.
Standard error of SSB/SSBMSY.
Standard error of SSB/SSB0.
Standard error of VB/VBMSY.
Standard error of VB/VB0.
A vector of standard errors of the deviation parameters.
A list containing the data and starting values of estimated parameters for the assessment.
A list containing components for forecasting:
per_recruit A data frame of SPR (spawning potential ratio) and YPR (yield-per-recruit), calculated for
a range of exploitation rate of 0 - 0.99 or instantaneous F from 0 - 2.5 FMSY.
catch_eq A function that calculates the catch for the next year (after the model terminal year) when an
apical F is provided.
A list with components returned from
A list with components from calling
A list (class sdreport) with parameter estimates and their standard errors, obtained from
A list of model output reported from the TMB executable, i.e.
obj$report(), and derived quantities (e.g. MSY).
A character string of data types required for the assessment.