Assessment-class: Class-'Assessment'
In tcarruth/MSEtool: Management Strategy Evaluation Toolkit

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.