| stock.recruit.sim {FSA} | R Documentation |
Plots hypothetical number of recruits versus stock size for four parameterizations of the Beverton-Holt and two parameterizations of the Ricker stock-recruit models. Slider bars are used to alter the parameters of each model.
stock.recruit.sim(R=NULL,S=NULL,type=c("BevertonHolt","Ricker"),
param=1,max.R=1000,max.S=500)
R |
An optional vector containing observed numbers of recruits. See details. |
S |
An optional vector containing observed numbers of spawning stock. See details. |
type |
A string indicating which stock-recruitment family of models to use. See details. |
param |
A numeric indicating which parameterization of the model in type to use. See details. |
max.R |
A numeric indicating the maximum recruitment to use for scaling the y-axis. |
max.S |
A numeric indicating the maximum spawning stock to use for scaling the x-axis. |
This function is best used for exploring the “shape” of the model for various choices of a single parameter while holding the other parameters constant. Multiple parameters can be changed in the simulations but the results are more difficult to interpret. For model exploration the R and S arguments should be left set at NULL.
This function can be used to visually “fit” a stock-recruit model to a set of observed stock and recruitment sizes in order to determine reasonable starting values for the non-linear least-squares fit of the stock-recruit model. Observed data are plotted by including the vector of observed recruits in the R argument and the vector of observed stock sizes in the S argument.
The type argument is used to choose either the "BevertonHolt" or "Ricker" models. Different parameterizations of these two models are chosen with the param= argument. There are four paramaterizations of the Beverton-HOld model (where S=stock and R=recruits):
param="1" | R = frac{S}{a+bS} |
param="2" | R = frac{aS}{b+S} |
param="3" | R = frac{aS}{1+bS} |
param="4" | R = frac{aS}{1+frac{a}{b}S} |
and two parameterizations of the Ricker model
param="1" | R = aSe^{-bS} |
param="2" | R = Se^{a(1-frac{S}{b})} |
Once the function is submitted a dialog box will appear in which the user can change values of the ‘a’ and ‘b’ parameters specific to the stock-recruit model. The meanings of each parameter are discussed in the FSA text.
The slider object has a tendency to “disappear” when focus is put on the plot. The slider object can be brought back to the foreground by finding the object listed on the Windows toolbar. The slider object should be “exit”ed when finished exploring a model.
None. However a dynamic graphic connected to slider bar controls is produced.
Derek H. Ogle, dogle@northland.edu
## Not run: ## These examples cannot be run by examples() but should work in an interactive R session # Example 1 -- Defaults - Beverton-Holt, first parameterization ## Not run: stock.recruit.sim() # Example 2 -- Ricker model first parameterization ## Not run: stock.recruit.sim(type="Ricker") ## Not run: data(CodNorwegian) ## Not run: attach(CodNorwegian) # Example 3 -- Ricker model first parameterization with Norwegian Cod data ## Not run: stock.recruit.sim(R=recruits,S=stock,type="Ricker",param=1)