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

.

## Slots

`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`

Standard error of U/UMSY.

`SE_F_FMSY`

Standard error of F/FMSY.

`SE_B_BMSY`

Standard error of B/BMSY.

`SE_B_B0`

Standard error of B/B0.

`SE_SSB_SSBMSY`

Standard error of SSB/SSBMSY.

`SE_SSB_SSB0`

Standard error of SSB/SSB0.

`SE_VB_VBMSY`

Standard error of VB/VBMSY.

`SE_VB_VB0`

Standard error of VB/VB0.

`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.

`forecast`

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.

`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()`

.`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.

## Examples

```
# \donttest{
output <- DD_TMB(Data = MSEtool::SimulatedData)
class(output)
#> [1] "Assessment"
#> attr(,"package")
#> [1] "SAMtool"
# }
```