Description Slots Author(s) See Also Examples

An S4 class that contains assessment output. Created from a function of class `Assess`

.

`Model`

Name of the assessment model.

`Name`

Name of Data object.

`conv`

Logical. Whether the assessment model converged (defined by whether TMB returned a positive-definite covariance matrix for the model).

`UMSY`

Estimate of exploitation at maximum sustainable yield.

`FMSY`

Estimate of instantaneous fishing mortality rate at maximum sustainable yield.

`MSY`

Estimate of maximum sustainable yield.

`BMSY`

Biomass at maximum sustainable yield.

`SSBMSY`

Spawning stock biomass at maximum sustainable yield.

`VBMSY`

Vulnerable biomass at maximum sustainable yield.

`B0`

Biomass at unfished equilibrium.

`R0`

Recruitment at unfished equilibrium.

`N0`

Abundance at unfished equilibrium.

`SSB0`

Spawning stock biomass at unfished equilibrium.

`VB0`

Vulnerable biomass at unfished equilibrium.

`h`

Steepness.

`U`

Time series of exploitation.

`U_UMSY`

Time series of relative exploitation.

`FMort`

Time series of instantaneous fishing mortality.

`F_FMSY`

Time series of fishing mortality relative to MSY.

`B`

Time series of biomass.

`B_BMSY`

Time series of biomass relative to MSY.

`B_B0`

Time series of depletion.

`SSB`

Time series of spawning stock biomass.

`SSB_SSBMSY`

Time series of spawning stock biomass relative to MSY.

`SSB_SSB0`

Time series of spawning stock depletion.

`VB`

Time series of vulnerable biomass.

`VB_VBMSY`

Time series of vulnerable biomass relative to MSY.

`VB_VB0`

Time series of vulnerable biomass depletion.

`R`

Time series of recruitment.

`N`

Time series of population abundance.

`N_at_age`

Time series of numbers-at-age matrix.

`Selectivity`

Selectivity-at-age matrix.

`Obs_Catch`

Observed catch.

`Obs_Index`

Observed index.

`Obs_C_at_age`

Observed catch-at-age matrix.

`Catch`

Predicted catch.

`Index`

Predicted index.

`C_at_age`

Predicted catch-at-age matrix.

`Dev`

A vector of estimated deviation parameters.

`Dev_type`

A description of the deviation parameters, e.g. "log recruitment deviations".

`NLL`

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).`SE_UMSY`

Standard error of UMSY estimate.

`SE_FMSY`

Standard error of FMSY estimate.

`SE_MSY`

Standard error of MSY estimate.

`SE_U_UMSY_final`

Standard error of U/UMSY in the terminal year.

`SE_F_FMSY_final`

Standard error of F/FMSY in the terminal year.

`SE_B_BMSY_final`

Standard error of B/BMSY in the terminal year.

`SE_B_B0_final`

Standard error of B/B0 in the terminal year.

`SE_SSB_SSBMSY_final`

Standard error of SSB/SSBMSY in the terminal year.

`SE_SSB_SSB0_final`

Standard error of SSB/SSB0 in the terminal year.

`SE_VB_VBMSY_final`

Standard error of VB/VBMSY in the terminal year.

`SE_VB_VB0_final`

Standard error of VB/VB0 in the terminal year.

`SE_Dev`

A vector of standard errors of the deviation parameters.

`info`

A list containing the data and starting values of estimated parameters for the assessment.

`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`

.`TMB_report`

A list of model output reported from the TMB executable, i.e.

`obj$report()`

, and derived quantities (e.g. MSY).`dependencies`

A character string of data types required for the assessment.

Q. Huynh

plot.Assessment summary.Assessment retrospective profile make_MP

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