showGrowthFun: Creates a string or an expression for a specific growth...
In fishR-Core-Team/FSA: Simple Fisheries Stock Assessment Methods

showGrowthFun

R Documentation

Creates a string or an expression for a specific growth function.

Description

Creates a string or expression for a specific parameterization of the von Bertalanffy, Gompertz, Richards, logistic growth functions, as well as the Schnute and Schnute-Richards growth functions. Parameters may be replaced with values from a model fit. The string or expression can be added to plots as titles, annotations, etc. The string/expression can also be plotted to a blank plot with plot=TRUE to see the equation of the growth function.

Usage

showGrowthFun(
  type = c("von Bertalanffy", "Gompertz", "Richards", "logistic", "Schnute",
    "Schnute-Richards"),
  param = 1,
  pname = NULL,
  case = NULL,
  constvals = NULL,
  parse = FALSE,
  yvar = NULL,
  xvar = NULL,
  fit = NULL,
  digits = NULL,
  stackWhere = FALSE,
  plot = FALSE,
  ...
)

Arguments

`type`	A single string (i.e., one of “von Bertalanffy”, “Gompertz”, “logistic”, “Richards”, “Schnute”, “Schnute-Richards”) that indicates the type of growth function to show.
`param`	A single numeric that indicates the specific parameterization of the growth function. Will be ignored if `pname` is non-`NULL`. See details.
`pname`	A single character that indicates the specific parameterization of the growth function. If `NULL` then `param` will be used. See details.
`case`	A numeric that indicates the specific case of the Schnute function to use.
`constvals`	A NAMED numeric vector of constant values (either lengths or ages) to be used in some of the von Bertalanffy parameterizations. See details.
`parse`	A logical indicating whether a string (`FALSE`; default) or an expression (`TRUE`) should be returned.
`yvar`	A string that represents the right-hand-side (or y-variable) of the equation. Defaults to `NULL` such that a reasonable default for the model type will be chosen.
`xvar`	A string that represents the left-hand-side (or x) variable) of the equation. Defaults to `NULL` such that `t` will be used for models with ages and `Delta*t` will be used for models with tag-recapture data.
`fit`	An optional `nls` (or related) object from fitting data to the growth function. If `NULL` then a string/expression with symbols for parameters will be returned. If an `nls` object then values for the parameters will be extracted from `fit` and put in place of the parameters symbols.
`digits`	An optional numerical vector for which to round the parameter values. Only used if `fit` is not `NULL`. Digits must be in the same order as the order of parameters for the growth model as in `makeGrowthFun` and should include values for the model constants given in `constvals` (if so used).
`stackWhere`	A logical that indicates whether strings/expressions that use “where” to explain a constant or function that simplifies the expression of the equation should be shown in “inline” (`FALSE`; default) or “stacked” (`TRUE`). See examples.
`plot`	A logical for whether the expression should be shown on a “blank” plot. See examples.
`...`	Arguments for `plot`. In particular use `cex=` to make the expression larger and easier to read. See examples.

Value

A string or expression representing the equation of the growth function given in type and param/pname.

Examples

#===== The string (first) and expression (second) for default type="von Bertalanffy")
showGrowthFun()
showGrowthFun(parse=TRUE)
showGrowthFun(pname="Typical")

#===== Show on a plot, and then larger
showGrowthFun(plot=TRUE)
showGrowthFun(plot=TRUE,cex=2)

#===== Other growth functions
showGrowthFun(type="Richards",param=3,plot=TRUE,cex=1.5)
showGrowthFun(type="Schnute",case=2,plot=TRUE,cex=1.5)

#===== Growth functions which use "where" to define simplifying constants/functions
showGrowthFun(pname="Somers",plot=TRUE)
showGrowthFun(pname="Somers",stackWhere=TRUE,plot=TRUE,cex=1.25)

#===== Multiple expressions in one plot (need to use parse=TRUE here)
op <- par(mar=c(0.1,0.1,0.1,0.1))
plot(0,type="n",xlab="",ylab="",xlim=c(0,1),ylim=c(0,3),xaxt="n",yaxt="n")
text(0,2.5,"Original:",pos=4)
text(0.5,2.5,showGrowthFun(type="von Bertalanffy",pname="Original",parse=TRUE))
text(0,1.5,"Typical:",pos=4)
text(0.5,1.5,showGrowthFun(type="von Bertalanffy",pname="Typical",parse=TRUE))
text(0,0.5,"Francis:",pos=4)
text(0.5,0.5,showGrowthFun(type="von Bertalanffy",pname="Francis",parse=TRUE))
par(op)

#===== Put expression in title or otherwise on the plot
# Make a von Bertalanffy function
vb1 <- makeGrowthFun()
 # Get and save the expression of the von Bertalanffy growth function
tmp <- showGrowthFun(parse=TRUE)

# Make plot and put expression in plot title
ages <- 1:20
plot(vb1(ages,Linf=20,K=0.3,t0=-0.2)~ages,type="b",pch=19,ylab="Length",main=tmp)

# Put expression in plot body (as demo)
text(15,10,tmp)

#===== Fill expression with values from model fit
# Fit von Bertalanffy to GrowthData1 data
sv <- findGrowthStarts(tlV~age,data=GrowthData1)
rv <- nls(tlV~vb1(age,Linf,K,t0),data=GrowthData1,start=sv)

# Show expression with values
showGrowthFun(fit=rv,plot=TRUE)
# Same, but control decimals (Linf, K, and then t0 order as in vb1())
showGrowthFun(fit=rv,digits=c(1,5,3),plot=TRUE)
# Same, but change variables
showGrowthFun(fit=rv,yvar="Length",xvar="Age",plot=TRUE)

# Put on a plot
plot(tlV~age,data=GrowthData1,ylab="Length (mm)",xlab="Age (yrs)")
curve(vb1(x,Linf=coef(rv)),from=0,to=15,col="blue",lwd=2,add=TRUE)
text(10,150,showGrowthFun(fit=rv,parse=TRUE))

# Put on a ggplot (note parse=TRUE is outside showGrowthFun)
## Not run: 
library(ggplot2)
ggplot(data=GrowthData1,mapping=aes(y=tlV,x=age)) +
  geom_point() +
  stat_function(fun=vb1,args=list(Linf=coef(rv)),color="blue",linewidth=1) +
  annotate(geom="text",label=showGrowthFun(fit=rv),parse=TRUE,size=4,x=10,y=150) +
  labs(y="Length (mm)",x="Age (yrs)") +
  theme_bw()

## End(Not run)

fishR-Core-Team/FSA documentation built on June 14, 2025, 10:01 p.m.