growthModelSim: Dynamics plots to explore typical fisheries growth models.

In droglenc/FSAsim: Simulate Data for Fisheries Stock Assessment Methods

Description

Plots hypothetical size-at-age for one of seven possible parameterizations of the von Bertalanffy, three possible parameterizations of the Gompertz, and the Schnute growth models. Slider bars are used to dynamically alter the parameters of each model.

Usage

growthModelSim(
  type = c("vbTypical", "vbOriginal", "vbGQ", "vbGallucciQuinn", "vbMooij",
    "vbWeisberg", "vbSchnute", "vbTypicalW", "vbOriginalW", "Gompertz1", "Gompertz2",
    "Gompertz3", "Schnute"),
  max.len = 500,
  max.wt = 500
)

Arguments

type	A single character string that indicates which growth model to use. See details.
max.len	A single numeric that indicates the maximum length to use in the simulations.
max.wt	A single numeric that indicates the maximum weight to use in the simulations (only used of type= "vbTypicalW" or "vbOriginalW".

Details

This function can be used to explore the “shape” of the growth models for various choices of the parameters. In this usage the x and y arguments should be (left) set at NULL. This function can also be used to visually “fit” a growth model to a set of observed lengths and ages. This usage may be used to provide reasonable starting values for the parameters when fitting the growth model to the data with non-linear least-squares. The observed data are plotted by including a formula of the form length~age in x and a data frame from which to draw the variables in the formula in the data arguments.

The type argument is used to choose a type of growth model and must be one of the following (the models can be seen with growthFunShow described in growthModels:

"vbTypical"	The "typical" Beverton-Holt parameterized von Bertalanffy model.
"vbOriginal"	The original parameterization from von Bertalanffy.
"vbMooij"	The Mooij et al (1999) paramaterization of the von Bertalanffy model.
"vbGQ"	The Gallucci & Quinn (1979) parameterization of the von Bertalanffy model.
"vbWeisberg"	The Weisberg et al. (2010) parameterization of the von Bertalanffy model.
"vbSchnute"	The Schnute-like paramaterization of the von Bertalanffy model.
"vbTypicalW"	The "typical" Beverton-Holt parameterized von Bertalanffy model, but for weights rather than lengths (thus, includes one more parameter).
"vbOriginalW"	The original parameterization from von Bertalanffy, but for weights rather than lengths (thus, includes one more parameter).
"Gompertz1"	The "first" parameterization of the Gompertz model.
"Gompertz2"	The "second" parameterization of the Gompertz model.
"Gompertz3"	The "third" parameterization of the Gompertz model.
"schnute"	The Schnute(1981) four-parameter general growth model.

Value

None. However a dynamic graphic connected to slider bar controls in which the user can change the maximum age over which the growth model is evaluated and change the parameters specific to the chosen growth model.

Author(s)

Derek H. Ogle, [e-mail]

References

Francis, R.I.C.C. 1988. Are growth parameters estimated from tagging and age-length data comparable? Canadian Journal of Fisheries and Aquatic Sciences, 45:936-942.

Gallucci, V.F. and T.J. Quinn II. 1979. Reparameterizing, fitting, and testing a simple growth model. Transactions of the American Fisheries Society, 108:14-25.

Mooij, W.M., J.M. Van Rooij, and S. Wijnhoven. 1999. Analysis and comparison of fish growth from small samples of length-at-age data: Detection of sequal dimorphism in Eurasian perch as an example. Transactions of the American Fisheries Society 128:483-490.

Schnute, J. 1981. A versatile growth model with statistically stable parameters. Canadian Journal of Fisheries & Aquatic Sciences, 38:1128-1140.

Schnute, J. and D. Fournier. 1980. A new approach to length-frequency analysis: Growth structure. Canadian Journal of Fisheries and Aquatic Sciences, 37:1337-1351.

Weisberg, S., G.R. Spangler, and L. S. Richmond. 2010. Mixed effects models for fish growth. Canadian Journal of Fisheries And Aquatic Sciences 67:269-277.

See Also

See model equations with growthFunShow described in growthModels. See similar functionality for von Bertalanffy models in vbStarts.

Examples

## ONLY RUN IN INTERACTIVE MODE
if (interactive()) {

# Explore growth models (no data) -- use the defaults
growthModelSim()

# Schnute parameterization of the von Bertalanffy model
growthModelSim(type="vbSchnute")

## Explore growth models superimposed on length-at-age data
# get Smallmouth Bass data from FSA package
data(SMBassWB)

# interactively "fit" the typical paramaterization of the von Bertalanffy model to the data
growthModelSim(lencap~agecap,data=SMBassWB)

# interactively "fit" the second paramaterization of the Gompertz model to the data
growthModelSim(lencap~agecap,data=SMBassWB,type="Gompertz2")

} ## END IF INTERACTIVE MODE

droglenc/FSAsim documentation built on Feb. 15, 2020, 11:20 p.m.