retrospective: Retrospective analysis

In multiSA: Multi-Stock Assessment

Retrospective analysis

Description

Perform a retrospective analysis, successive removals of most recent years of data to evaluate consistency in model estimates of biomass, recruitment, etc.

The summary method returns Mohn's rho and the plot method generates a markdown report.

Usage

retrospective(MSAassess, yret = 0:5, cores = 1)

## S3 method for class 'MSAretro'
plot(
  x,
  var = c("S_yst", "R_yst", "F_yst", "log_rdev_yst", "VB_ymft"),
  s = 1,
  f = 1,
  ...
)

## S3 method for class 'MSAretro'
summary(object, by = c("stock", "fleet"), ...)

## S3 method for class 'MSAretro'
report(
  object,
  filename = "retro",
  dir = tempdir(),
  open_file = TRUE,
  render_args = list(),
  ...
)

Arguments

MSAassess	MSAassess object
yret	Vector specifying the years (positive integers and include zero) to remove for the retrospective analysis
cores	Integer for the number of cores to use for parallel processing (snowfall package)
x, object	Output of retrospective function
var	Character to indicate the metric, the item in the MSAretro list to be plotted. See details below.
s	Integer for the stock index to plot
f	Integer for the fleet index to plot
...	Not used
by	Character indicating whether to calculate to Mohn's rho on stock or fleet-based time series
filename	Character string for the name of the markdown and HTML files.
dir	The directory in which the markdown and HTML files will be saved.
open_file	Logical, whether the HTML document is opened after it is rendered.
render_args	List of arguments to pass to rmarkdown::render().

Value

A MSAretro object containing a named lists of arrays generated by the retrospective analysis:

• S_yst Spawning output array ⁠[y, s, t]⁠ where t indexes the retrospective peel

• R_yst Recruitment array ⁠[y, s, t]⁠

• F_yst Apical fishing mortality ⁠[y, s, t]⁠

• VB_ymft Vulnerable biomass available to each fishery ⁠[y, m, f, t]⁠

plot generic for MSAretro returns individual figures using base graphics.

summary generic for MSAretro returns a matrix of Mohn's rho.

report generic for MSAretro invisibly returns the output of rmarkdown::render(): character of the path of the rendered HTML markdown report.

multiSA documentation built on March 21, 2026, 1:06 a.m.