Visualise uncertainity in the terminal Fbar and SSB

Generates and visualises the two-dimensional confidence interval from a stock assessment based on a parametric bootstrapping exercise.

otolith(object, year=sam@range["maxyear"], plot=TRUE, show.points=FALSE, do.contours=TRUE, margin.plots=TRUE, show.estimate=TRUE,xlim="missing", ylim="missing",n=100, pch=".", alpha=0.05, show.grid=TRUE, n.grid=50, contour.args=list(),...)

Arguments

object

An FLSAM object upon which the stock assessment is based.

year

Year the otolith is based upon.

plot

Boolean. Whether the plot should be generated or whether or not.

show.points

Boolean. Show the individual point generated by the parametric bootstrap.

do.contours

Boolean. Generate contours showing the confidence intervals in the two dimensions.

margin.plots

Boolean. Generate horizontal and vertical plots to the sides of the main plot showing the 1-D confidence intervals.

show.estimate

Boolean. Show the point estimate generated by the assessment.

xlim, ylim

Two element numeric vectors giving the axis limits for the x- and y- axes respectively.

n

The number of individual parametric bootstrap values to generate.

pch

The symbol used to plot the individual points. See points for more information.

alpha

The confidence interval plotted in the margin plots. Defaults to 0.05 (95%).

show.grid

Boolean. Display a grid in the background.

n.grid

The density of the grid used to generate the two-dimensional uncertainty surface which the contours characterise. The default value of 50 works well for most applications, although it can be increased if the number of bootstrap estimates is also increased.

contour.args

A list of arguments suitable for use in the contour function controlling the formatting of the contour lines.

...

Other arguments suitable to be feed to the standard plot function.

Details

The function might become very slow when a large number of n is required while the variance-co-variance matrix is large.

Author

Mark Payne & Susan Lusseau

See also

sprintf, options

Examples

   #Load assessment objects
   data(NSH.sam)
   otolith(NSH.sam,year=2010,n=150)
#> Loading required package: MASS
#> 
#> Attaching package: ‘MASS’
#> The following object is masked from ‘package:FLCore’:
#> 
#>     mvrnorm
   otolith(NSH.sam,year=2010,n=1e4)


   otolith(NSH.sam,year=2010,n=1e4,show.points=TRUE)