Assessment-class: Class-'Assessment'

In SAMtool: Stock Assessment Methods Toolkit

Class-Assessment

Description

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.

Author(s)

Q. Huynh

See Also

plot.Assessment summary.Assessment retrospective profile make_MP

Examples

output <- DD_TMB(Data = MSEtool::SimulatedData)
class(output)

SAMtool documentation built on Nov. 18, 2023, 9:07 a.m.