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.
retrospective(MSAassess, yret = 0:5, cores = 1)# S3 method for MSAretro
plot(
x,
var = c("S_yst", "R_yst", "F_yst", "log_rdev_yst", "VB_ymft"),
s = 1,
f = 1,
...
)
# S3 method for MSAretro
summary(object, by = c("stock", "fleet"), ...)
# S3 method for MSAretro
report(
object,
filename = "retro",
dir = tempdir(),
open_file = TRUE,
render_args = list(),
...
)
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.
MSAassess object
Vector specifying the years (positive integers and include zero) to remove for the retrospective analysis
Integer for the number of cores to use for parallel processing (snowfall package)
Output of retrospective function
Character to indicate the metric, the item in the MSAretro list to be plotted. See details below.
Integer for the stock index to plot
Integer for the fleet index to plot
Not used
Character indicating whether to calculate to Mohn's rho on stock or fleet-based time series
Character string for the name of the markdown and HTML files.
The directory in which the markdown and HTML files will be saved.
Logical, whether the HTML document is opened after it is rendered.
List of arguments to pass to rmarkdown::render().