retrospective_AM: retrospective_AM (retrospective of Assessment model in MSE)

In SAMtool: Stock Assessment Methods Toolkit

retrospective_AM (retrospective of Assessment model in MSE)

Description

Plots the true retrospective of an assessment model during the closed-loop simulation. A series of time series estimates of SSB, F, and VB are plotted over the course of the MSE are plotted against the operating model (true) values (in black).

Usage

retrospective_AM(MSE, MP, sim = 1, plot_legend = FALSE)

Arguments

MSE	An object of class MSEtool::MSE.
MP	Character. The name of the management procedure created by make_MP() containing the assessment model.
sim	Integer between 1 and MSE@nsim. The simulation number for which the retrospectives will be plotted.
plot_legend	Logical. Whether to plot legend to reference year of assessment in the MSE.

Details

For assessment models that utilize annual exploitation rates (u), the instantaneous fishing mortality rates are obtained as F = -log(1 - u).

Value

A series of figures for SSB, depletion, fishing mortality, and vulnerable biomass (VB) estimated in the MP over the course of the closed-loop simulation against the values generated in the operating model (both historical and projected).

Note

This function only plots retrospectives from a single simulation in the MSE. Results from one figure may not be indicative of general assessment behavior and performance overall.

Author(s)

Q. Huynh

See Also

diagnostic

Examples

SP_40_10 <- make_MP(SP, HCR_MSY, diagnostic = "full")
OM <- MSEtool::testOM; OM@proyears <- 20
myMSE <- MSEtool::runMSE(OM = OM, MPs = "SP_40_10")
retrospective_AM(myMSE, MP = "SP_40_10", sim = 1)

# How to get all the estimates
library(dplyr)
assess_estimates <- lapply(1:myMSE@nMPs, function(m) {
  lapply(1:myMSE@nsim, function(x) {
    myMSE@PPD[[m]]@Misc[[x]]$Assessment_report %>% 
      mutate(MP = myMSE@MPs[m], Simulation = x)
  }) %>% bind_rows()
}) %>% bind_rows()

SAMtool documentation built on Sept. 11, 2024, 8:07 p.m.