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Retrospective analysis

Source: R/retrospective.R
retrospective.Rd

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.MSAretro returns individual figures using base graphics.

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

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