growthResid: Plot residuals of growth model fitted to tag data

In fishmethods: Fishery Science Methods and Models

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

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.

Value

output

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

Author(s)

Janos Hoenig Virginia Institute of Marine Science May 2013 [e-mail]

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)

fishmethods documentation built on April 27, 2023, 9:10 a.m.