SAMtool (version 1.8.1)

retrospective_AM: 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)

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).

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.

Author

Q. Huynh

Details

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

See Also

diagnostic

Examples

# \donttest{
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) {
    report <- myMSE@PPD[[m]]@Misc[[x]]$Assessment_report
    if (is.null(report)) {
      return(data.frame())
    } else {
      mutate(report, MP = myMSE@MPs[m], Simulation = x)
    }
  }) %>% bind_rows()
}) %>% bind_rows()
# }