plot.CatDynMod: Examination of Results from Fitting Catch Dynamic Models

In CatDyn: Fishery Stock Assessment by Catch Dynamics Models

Description

After model fit and prediction, examine model results on a graphical display.

Usage

## S3 method for class 'CatDynMod'
plot(x, leg.pos, Biom.tstep, Cat.tstep, Biom.xpos, Biom.ypos,
                         Cat.xpos, Cat.ypos,
                         diagnostics.panels = 2, top.lab = TRUE, ...)

Arguments

x	An object of class CatDynMod.
leg.pos	The position of the legend in the top left panel. Passed to legend().
Biom.tstep	Integer. The number of time steps over which to average the population biomass counting from the end of the season backwards.
Cat.tstep	Integer. The number of time steps over which to add the catch counting from the end of the season backwards.
Biom.xpos	Numeric. The position of the biomass estimate on the x-axis of the first panel of the plot in relative units.
Biom.ypos	Numeric. The position of the biomass estimate on the y-axis of the first panel of the plot in relative units.
Cat.xpos	Numeric. The position of the catch value on the x-axis of the first panel of the plot in relative units.
Cat.ypos	Numeric. The position of the catch value on the y-axis of the first panel of the plot in relative units.
diagnostics.panels	Integer. Whether to plot just one panel with the data and model prediction (diagnostics.panels = 0), or add three more panels for diagnostics based on deviance residual of the same size as the data-prediction panel (diagnostics.panels = 1), or to make the deviance residual panels smaller (diagnostics.panels = 2, the default).
top.lab	Logical. Whether to put a top label describing choices of model type, likelihood, and numerical method. Defaults to TRUE.
...	Further arguments to pass to plot(), hist().

Details

If the average population biomass over the whole season is to be posted then an integer equal to the number of time steps in the season shall be entered for the Biom.tstep argument.

Value

A four panel plot of data, model predictions, and residual analysis.

Note

The target symbols on the bottom of the tope left panel are the timings of any perturbations set by the user.

In transit fisheries, entry target symbols are in red and exit target symbols are in blue.

Author(s)

Ruben H. Roa-Ureta (ORCID ID 0000-0002-9620-5224)

References

Roa-Ureta, R. H. 2012. ICES Journal of Marine Science 69(8):1403-1415.

Examples

#See examples for CatDynFit().

Example output

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 Fishery Stock Assessment by Catch Dynamics Models
 CatDyn version 1.1-1 (built on 2018-12-18) is now loaded
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CatDyn documentation built on May 2, 2019, 4:21 a.m.