fishmethods (version 1.9-0)

growthTraject: Plot growth trajectories obtained from tagging data

Description

Age and length coordinates for the time of tagging and time of recapture are plotted as line segments overlayed on the von Bertalannfy growth curve

Usage

growthTraject(K, Linf, dat, lentag, lenrec, timelib, subsets=NULL,   main = "Growth trajectories & fitted curve", cex.lab=1.5, cex.axis=1.5, cex.main=1, xlab="Relative age, yr", ylab="Length, cm", xlim=NULL, ylim=NULL,ltytraject=1, lwdtraject=1, coltraject=1, ltyvonB=1, lwdvonB=2, colvonB="red",  returnvec=FALSE, returnlimits=FALSE, warn=TRUE, ...)

Arguments

K

parameter of the von Bertalanffy growth equation

Linf

parameter of the von Bertalanffy growth equation

dat

dataframe containing length at tagging, length at recapture and time at liberty. These must be named lentag, lenrec and timelib or else column 1 must contain the length at tagging, column 2 must contain length at recapture and column 3 must contain time at liberty OR the variables must be named lentag, lenrec and timelib

lentag

alternative way to pass data to function

lenrec

alternative way to pass data to function

timelib

alternative way to pass data to function

subsets

factor or integer variable specifying subsets of the data to be plotted with separate colors or line types

main

an overall title for the plot

cex.lab

The magnification to be used for x and y labels relative to the current setting of cex

cex.axis

The magnification to be used for axis annotation relative to the current setting of cex

cex.main

The magnification to be used for main titles relative to the current setting of cex

xlab

a title for the x axis

ylab

a title for the y axis

xlim

lower and upper limits of x axis e.g., c(0,100)

ylim

lower and upper limits of y axis e.g., c(0,100)

ltytraject

line type for the growth trajectories

lwdtraject

line width for the growth trajectories

coltraject

line color for the growth trajectories

ltyvonB

line type for the fitted von Bertalanffy growth curve

lwdvonB

line width for the fitted von Bertalanffy growth curve

colvonB

line color for the fitted von B. curve

returnvec

logical for whether the coordinates of the line segments should be returned)

returnlimits

logical for whether the x-axis and y-axis limits should be returned

warn

logical - if TRUE, function issues a warning if names of variables in dat do not match the 3 names expected.

...

other arguments to pass to plot

Value

output

if returnvec = TRUE, coordinates of the line segments are returned. If returnlimits=TRUE, x and y limits for plot are returned

Details

The relative age at tagging is computed from the inverted von Bertalannfy growth equation (i.e., age expressed as a function of length); the age at recapture is taken to be the age at tagging plus the time at liberty. Then the (age, length) coordinates for the time of tagging and time of recapture are plotted as a line segment. Additional parameters control the format of the plot as follows. A call to plot() sets up the axes. Then a call to arrows() draws the line segments. Finally, a call to curve() adds the von Bertalanffy growth curve. Specifying additional graphical parameters is permissable but these will be passed only to plot().

Examples

 data(bonito)
 temp<-bonito[c(bonito$T2-bonito$T1)>0,]
 growthTraject(0.19,97.5,lentag=temp$L1, lenrec=temp$L2,timelib=c(temp$T2-temp$T1))