fishmethods (version 1.9-0)

growthResid: Plot residuals of growth model fitted to tag data

Description

Plot residuals (observed - expected growth increments) vs relative age at the time of tagging and versus time at liberty.

Usage

growthResid(K, Linf, dat, lentag, lenrec, timelib, graph =1,  main = "Residuals of growth increments", cex.lab=1.5, cex.axis=1.5, cex.main=1, xlab1="Relative age, yr", xlab2="Time at liberty, yr", ylab="Observed - expected increment", xlim1=NULL, xlim2=NULL, ylim=NULL, col=1, 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

lentag

alternative way to pass data to function

lenrec

alternative way to pass data to function

timelib

alternative way to pass data to function

graph

which graph to plot - 1: residuals versus Relative age, 2: residuals versus time-at-liberty

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

xlab1

a title for the x axis 1

xlab2

a title for the x axis 2

ylab

a title for the y axis

xlim1

lower and upper limits of x axis 1 e.g., c(0,100)

xlim2

lower and upper limits of x axis 2 e.g., c(0,100)

ylim

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

col

color of points in plot

returnvec

logical - if TRUE, function returns a dataframe with the computed age at tagging and the residual (obs - pred increment)

returnlimits

logical - if TRUE, function returns the x and y limits for the plot

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, computed age and residuals. If returnlimits=TRUE, x and y limits for plot

Details

Function plots residuals (observed - expected growth increments) vs relative age at the time of tagging and vs time at liberty from VB growth model fitted to tagging data. Relative age is calculated by inverting the von Bertalanffy growth curve.

Examples

 data(bonito)
 temp<-bonito[c(bonito$T2-bonito$T1)>0,]
 growthResid(0.19,97.5,lentag=temp$L1, lenrec=temp$L2,timelib=c(temp$T2-temp$T1),graph=1)