| leslie.sim2 {FSA} | R Documentation |
This function is used to simulate multiple results for the catch in multiple samples of fish in a depletion fishery. The user can control the number of removal events, initial population size, effort, catchability, survival, and recruitment for a hypothetical depletion fishery. The simulations, given a set of parameter values, are run multiple times and three plots are presented to allow explore the effects of changing parameters on the model.
leslie.sim2(rsmpls=100,ricker.mod=FALSE,...)
rsmpls |
a number for the number of simulations to run. |
ricker.mod |
A boolean value indicating whether to use the modification proposed by Ricker (=TRUE) or not (=FALSE, default). |
... |
Additional arguments to pass to plot. |
A slider object is created from which the parameters of the model can be changed. The number of removal events, initial population size, effort, and catchability are defined as usual with details in the FSA text. The remaining “parameter” choices on the slider are specific to modeling assumption violations. Each of these items is described below. The range of values allowed for each of the parameters were chosen to allow a wide variety of model values. However, it is highly likely that these ranges do not encompass every possible set of values that a user may wish to view.
The ‘q factor’ value is a constant that modifies the catchability coefficient for each subsequent sample. For example, if ‘q.factor’ is set to 0.8 then the catchability decreases by a constant multiplier of 0.8 for each sample. In other words, the catchability set with the catchability slider is multiplied by the vector c(1,0.8,0.8^2,0.8^3,...) to determine a catchability for each sample.
The ‘Survival’ value is a constant used as a proportion of fish alive at time t that surve to time t+1 or, if use.rand=TRUE, is the probability that a fish survives from time t to time t+1. The survival function is applied to the population after the catch at time t has alread been removed from the population.
The ‘Recruitment’ value is a constant used to determine the number of “new” fish to recruit to the population from time to time t+1. The number to recruit is equal to the recruitment portion of the extant number of fish alive at time t. For example, if 100 fish are alive at time t and the recruitment factor is 0.2 then 100*0.2=20 fish will be added to the population just before time t+1. The number of fish to recruit is computed after the catch at time t and any natural mortality at time t have been removed from the population.
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 is produced that is controlled by slider bars as described in the details. The dynamic graphic includes three graphs. The first is a histogram of the estimate of the initial population size (No) from all resamples with a red vertical line at the initial population size (provided by the user) and a green vertical line at the mean population estimate. The second is a histogram of the estimates of the catchability (q) with a red vertical line at the true catchability (provided by the user) and a green vertical line at the mean catchability estimate. The third graph is a scatterplot of the paired catchability and initial population size estimates with red lines showing the true values of the catchability and initial population size and green lines at the means of the respective estimates. The dynamics graphic is best displayed in a window that is about 3 times as wide as it is tall.
Derek H. Ogle, dogle@northland.edu