vbStartsDP: Uses dynamic plots to find reasonable starting values for a...

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

Description

Uses dynamic plots to find reasonable starting values for the parameters in a specific parameterization of the von Bertalanffy growth function.

Usage

vbStartsDP(
  formula,
  data = NULL,
  type = c("Typical", "typical", "Traditional", "traditional", "BevertonHolt",
    "Original", "original", "vonBertalanffy", "GQ", "GallucciQuinn", "Mooij", "Weisberg",
    "Schnute", "Francis", "Somers", "Somers2"),
  ages2use = NULL,
  methEV = c("means", "poly"),
  meth0 = c("yngAge", "poly"),
  ...
)

Arguments

formula	A formula of the form len~age.
data	A data frame that contains the variables in formula.
type	A string that indicates the parameterization of the von Bertalanffy model.
ages2use	A numerical vector of the two ages to be used in the Schnute or Francis paramaterizations. See vbStarts.
methEV	A string that indicates how the lengths of the two ages in the Schnute paramaterization or the three ages in the Francis paramaterization should be derived. See vbStarts.
meth0	A string that indicates how the t0 and L0 paramaters should be derived. See vbStarts.
...	Further arguments passed to the methods.

Details

Starting values can be obtained by plotting the data with the model superimposed but tied to slider bars that allow the parameters to be interactively changed. One can change the parameters until a reasonable fit is observed and then use those valeus as starting values. The initial parameters for the slider bars are the starting values constructed with vbStarts. It should be noted that the dynamic plot may show an error of “[tcl] can't get device image”, but the plot will correctly update if the slider bar is adjusted.

Value

None, but a dynamic plot is constructed.

IFAR Chapter

12-Individual Growth.

Note

The ‘original’ and ‘vonBertalanffy’ and the ‘typical’ and ‘BevertonHolt’ parameterizations are synonymous.

Author(s)

Derek H. Ogle, [e-mail]

References

Ogle, D.H. 2016. Introductory Fisheries Analyses with R. Chapman & Hall/CRC, Boca Raton, FL.

See references in vbFuns.

See Also

See vbStarts for related functionality.

Examples

## Dynamic Plots Method -- ONLY RUN IN INTERACTIVE MODE
if (interactive()) {
  require(FSA)
  data(SpotVA1)
  vbStartsDP(tl~age,data=SpotVA1)
  vbStartsDP(tl~age,data=SpotVA1,type="typical")
  vbStartsDP(tl~age,data=SpotVA1,type="Typical")
  vbStartsDP(tl~age,data=SpotVA1,type="traditional")
  vbStartsDP(tl~age,data=SpotVA1,type="Traditional")
  vbStartsDP(tl~age,data=SpotVA1,type="BevertonHolt")
  vbStartsDP(tl~age,data=SpotVA1,type="original")
  vbStartsDP(tl~age,data=SpotVA1,type="Original")
  vbStartsDP(tl~age,data=SpotVA1,type="vonBertalanffy")
  vbStartsDP(tl~age,data=SpotVA1,type="GQ")
  vbStartsDP(tl~age,data=SpotVA1,type="GallucciQuinn")
  vbStartsDP(tl~age,data=SpotVA1,type="Mooij")
  vbStartsDP(tl~age,data=SpotVA1,type="Weisberg")
  vbStartsDP(tl~age,data=SpotVA1,type="Francis",ages2use=c(0,5))
  vbStartsDP(tl~age,data=SpotVA1,type="Schnute",ages2use=c(0,5))
} 

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