Nothing
plot.GroAgeMod <-
function(x, ...)
{
spec.name <- x$Properties$Species
sex <- x$Properties$Sex
model <- x$Model$Growth$Type
distr <- x$Model$Distribution$Distr
method <- x$Model$Method
options(warn=-1)
if(sex == "Males" | sex == "Females" | sex == "Pooled")
{
y <- x$Predictions[ do.call(order, list(x$Predictions$age)), ]
age <- y$age
obslen <- y$obslen
modlen <- y$predlen
resids <- y$resid
par(mfrow=c(2,2),oma=c(0,0,2,0),mar=c(4,4,2,2))
plot(x=age,y=obslen,pch=19,
xlab=paste("Age (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen,modlen)), main="", cex=0.75)
lines(x=age,y=modlen,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids,main="",xlab="Deviance Residuals",ylab="Frequency")
#
plot(x=age,y=resids,xlab=paste("Age (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#text(x=age,y=resids,lab=format(age),cex=0.75)
#
qqplot(x=obslen,y=modlen,
xlab=paste("Observed ",x$Properties$Length.Type, " Length (", x$Properties$Units.Length, ")", sep=""),
ylab=paste("Predicted ",x$Properties$Length.Type, " Length (", x$Properties$Units.Length, ")", sep=""),
pch=1)
abline(a=0,b=1,lwd=2)
mtext(side=3,outer=TRUE,text=paste(spec.name," - ", sex, " - ", model," - ", distr, sep=""))
}
else if(sex == "Both" | sex == "Total")
{
if(length(x$Predictions) == 3)
{
y <- vector("list",3)
y$Females <- x$Predictions$Females[ do.call(order, list(x$Predictions$Females$age)), ]
y$Males <- x$Predictions$Males[ do.call(order, list(x$Predictions$Males$age)), ]
y$Pooled <- x$Predictions$Pooled[ do.call(order, list(x$Predictions$Pooled$age)), ]
age.fem <- y$Females$age
obslen.fem <- y$Females$obslen
modlen.fem <- y$Females$predlen
resids.fem <- y$Females$resid
age.mal <- y$Males$age
obslen.mal <- y$Males$obslen
modlen.mal <- y$Males$predlen
resids.mal <- y$Males$resid
age.pld <- y$Pooled$age
obslen.pld <- y$Pooled$obslen
modlen.pld <- y$Pooled$predlen
resids.pld <- y$Pooled$resid
#
par(mfrow=c(3,3),oma=c(2,2,2,1), mar=c(4,4,2,2))
plot(x=age.fem,y=obslen.fem,pch=19,
xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Females (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.fem,modlen.fem)), main="", cex=0.75)
lines(x=age.fem,y=modlen.fem,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
plot(x=age.mal,y=obslen.mal,pch=19,
xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Males (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.mal,modlen.mal)), main="", cex=0.75)
lines(x=age.mal,y=modlen.mal,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
plot(x=age.pld,y=obslen.pld,pch=19,
xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Pooled (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.pld,modlen.pld)), main="", cex=0.75)
lines(x=age.pld,y=modlen.pld,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids.fem,main="",xlab="Deviance Residuals",ylab="Frequency Females")
#
hist(x=resids.mal,main="",xlab="Deviance Residuals",ylab="Frequency Males")
#
hist(x=resids.pld,main="",xlab="Deviance Residuals",ylab="Frequency Pooled")
#
plot(x=age.fem,y=resids.fem,xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#text(x=age,y=resids,lab=format(age),cex=0.75)
#
plot(x=age.mal,y=resids.mal,xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
plot(x=age.pld,y=resids.pld,xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
mtext(side=3,outer=TRUE,text=paste(spec.name," / ", model," / ", distr, " / ", method, sep=""))
}
else if(length(x$Predictions) == 2)
{
if(names(x$Predictions) == c("Females", "Males"))
{
y <- vector("list",2)
y$Females <- x$Predictions$Females[ do.call(order, list(x$Predictions$Females$age)), ]
y$Males <- x$Predictions$Males[ do.call(order, list(x$Predictions$Males$age)), ]
age.fem <- y$Females$age
obslen.fem <- y$Females$obslen
modlen.fem <- y$Females$predlen
resids.fem <- y$Females$resid
age.mal <- y$Males$age
obslen.mal <- y$Males$obslen
modlen.mal <- y$Males$predlen
resids.mal <- y$Males$resid
par(mfrow=c(3,2),oma=c(2,2,2,1), mar=c(4,4,2,2))
plot(x=age.fem,y=obslen.fem,pch=19,
xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Females (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.fem,modlen.fem)), main="", cex=0.75)
lines(x=age.fem,y=modlen.fem,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
plot(x=age.mal,y=obslen.mal,pch=19,
xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Males (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.mal,modlen.mal)), main="", cex=0.75)
lines(x=age.mal,y=modlen.mal,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids.fem,main="",xlab="Deviance Residuals",ylab="Frequency Females")
#
hist(x=resids.mal,main="",xlab="Deviance Residuals",ylab="Frequency Males")
#
plot(x=age.fem,y=resids.fem,xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#text(x=age,y=resids,lab=format(age),cex=0.75)
#
plot(x=age.mal,y=resids.mal,xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
mtext(side=3,outer=TRUE,text=paste(spec.name," / ", model," / ", distr, " / ", method, sep=""))
}
else if(names(x$Predictions) == c("Females", "Pooled"))
{
y <- vector("list",2)
y$Females <- x$Predictions$Females[ do.call(order, list(x$Predictions$Females$age)), ]
y$Pooled <- x$Predictions$Pooled[ do.call(order, list(x$Predictions$Pooled$age)), ]
age.fem <- y$Females$age
obslen.fem <- y$Females$obslen
modlen.fem <- y$Females$predlen
resids.fem <- y$Females$resid
age.pld <- y$Pooled$age
obslen.pld <- y$Pooled$obslen
modlen.pld <- y$Pooled$predlen
resids.pld <- y$Pooled$resid
par(mfrow=c(3,2),oma=c(2,2,2,1), mar=c(4,4,2,2))
plot(x=age.fem,y=obslen.fem,pch=19,
xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Females (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.fem,modlen.fem)), main="", cex=0.75)
lines(x=age.fem,y=modlen.fem,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
plot(x=age.pld,y=obslen.pld,pch=19,
xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Pooled (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.pld,modlen.pld)), main="", cex=0.75)
lines(x=age.pld,y=modlen.pld,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids.fem,main="",xlab="Deviance Residuals",ylab="Frequency Females")
#
hist(x=resids.pld,main="",xlab="Deviance Residuals",ylab="Frequency Pooled")
#
plot(x=age.fem,y=resids.fem,xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
plot(x=age.pld,y=resids.pld,xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
mtext(side=3,outer=TRUE,text=paste(spec.name," / ", model," / ", distr, " / ", method, sep=""))
}
else if(names(x$Predictions) == c("Males", "Pooled"))
{
y <- vector("list",2)
y$Males <- x$Predictions$Males[ do.call(order, list(x$Predictions$Males$age)), ]
y$Pooled <- x$Predictions$Pooled[ do.call(order, list(x$Predictions$Pooled$age)), ]
age.mal <- y$Males$age
obslen.mal <- y$Males$obslen
modlen.mal <- y$Males$predlen
resids.mal <- y$Males$resid
age.pld <- y$Pooled$age
obslen.pld <- y$Pooled$obslen
modlen.pld <- y$Pooled$predlen
resids.pld <- y$Pooled$resid
par(mfrow=c(3,2),oma=c(2,2,2,1), mar=c(4,4,2,2))
#
plot(x=age.mal,y=obslen.mal,pch=19,
xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Males (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.mal,modlen.mal)), main="", cex=0.75)
lines(x=age.mal,y=modlen.mal,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
plot(x=age.pld,y=obslen.pld,pch=19,
xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Pooled (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.pld,modlen.pld)), main="", cex=0.75)
lines(x=age.pld,y=modlen.pld,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids.mal,main="",xlab="Deviance Residuals",ylab="Frequency Males")
#
hist(x=resids.pld,main="",xlab="Deviance Residuals",ylab="Frequency Pooled")
#
plot(x=age.mal,y=resids.mal,xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
plot(x=age.pld,y=resids.pld,xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
mtext(side=3,outer=TRUE,text=paste(spec.name," / ", model," / ", distr, " / ", method, sep=""))
}
}
else if(length(x$Predictions) == 1)
{
if(names(x$Predictions) == "Females")
{
y <- vector("list",1)
y$Females <- x$Predictions$Females[ do.call(order, list(x$Predictions$Females$age)), ]
age.fem <- y$Females$age
obslen.fem <- y$Females$obslen
modlen.fem <- y$Females$predlen
resids.fem <- y$Females$resid
par(mfrow=c(3,1),oma=c(2,2,2,1), mar=c(4,4,2,2))
plot(x=age.fem,y=obslen.fem,pch=19,
xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Females (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.fem,modlen.fem)), main="", cex=0.75)
lines(x=age.fem,y=modlen.fem,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids.fem,main="",xlab="Deviance Residuals",ylab="Frequency Females")
#
plot(x=age.fem,y=resids.fem,xlab=paste("Age Females (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
mtext(side=3,outer=TRUE,text=paste(spec.name," / ", model," / ", distr, " / ", method, sep=""))
}
else if(names(x$Predictions) == "Males")
{
y <- vector("list",1)
y$Males <- x$Predictions$Males[ do.call(order, list(x$Predictions$Males$age)), ]
age.mal <- y$Males$age
obslen.mal <- y$Males$obslen
modlen.mal <- y$Males$predlen
resids.mal <- y$Males$resid
par(mfrow=c(3,1),oma=c(2,2,2,1), mar=c(4,4,2,2))
#
plot(x=age.mal,y=obslen.mal,pch=19,
xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Males (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.mal,modlen.mal)), main="", cex=0.75)
lines(x=age.mal,y=modlen.mal,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids.mal,main="",xlab="Deviance Residuals",ylab="Frequency Males")
#
plot(x=age.mal,y=resids.mal,xlab=paste("Age Males (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
mtext(side=3,outer=TRUE,text=paste(spec.name," / ", model," / ", distr, " / ", method, sep=""))
}
else if(names(x$Predictions) == "Pooled")
{
y <- vector("list",1)
y$Pooled <- x$Predictions$Pooled[ do.call(order, list(x$Predictions$Pooled$age)), ]
age.pld <- y$Pooled$age
obslen.pld <- y$Pooled$obslen
modlen.pld <- y$Pooled$predlen
resids.pld <- y$Pooled$resid
par(mfrow=c(3,1),oma=c(2,2,2,1), mar=c(4,4,2,2))
plot(x=age.pld,y=obslen.pld,pch=19,
xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab=paste(x$Properties$Length.Type, " Length Pooled (", x$Properties$Units.Length, ")", sep=""),
ylim=c(0,max(obslen.pld,modlen.pld)), main="", cex=0.75)
lines(x=age.pld,y=modlen.pld,col="black",lwd=2)
legend("bottomright",c("Observed Length", "Predicted Length"), bty="n", pch=c(19, NA), lty=c(0, 1), lwd=c(0,2), col=c("black", "black"))
#
hist(x=resids.pld,main="",xlab="Deviance Residuals",ylab="Frequency Pooled")
#
plot(x=age.pld,y=resids.pld,xlab=paste("Age Pooled (", x$Properties$Units.Age, ")", sep=""),
ylab="Deviance Residuals",pch=1)
abline(h=0,lwd=2)
#
mtext(side=3,outer=TRUE,text=paste(spec.name," / ", model," / ", distr, " / ", method, sep=""))
}
}
}
}
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