plotCI: how to overlay plots of two variables - r

Question

I am trying to plot populations of predators and of prey over time, with confidence intervals. I can plot these two separately, how to plot on same graph?
#take mean, number, and create se of prey(d)
d.means=tapply(mydata$prey,mydata$week, mean)
d.n=tapply(mydata$prey,mydata$week, length)
d.se=tapply(mydata$prey,mydata$week, sd)/sqrt(d.n)
#plot with se using plotrix
plotCI(as.numeric(row.names(d.means)),d.means,d.se,ylim=c(0,400),pch=19,gap=0,xlab="Week",ylab="d, w population")
#take mean, number, and create se of predator(w)
w.means=tapply(mydata$pred,mydata$week, mean)
w.n=tapply(mydata$pred,mydata$week, length)
w.se=tapply(mydata$pred,mydata$week, sd)/sqrt(w.n)
#plot with se using plotrix
plotCI(as.numeric(row.names(w.means)),w.means,w.se,ylim=c(0,400),pch=19,gap=0,xlab="Week",ylab="d, w population")

Answer 1

After the first plot, use the code below before plotting the next plot:
par(new=T)
Make sure that you set the xlim and ylim to accommodate both plots. And you will need to use the options axes=F and ann=F.
These graphical features are discussed in detail in the ebook "R Fundamentals & Graphics". You might want to use it as a desk reference.

Answer 2

#take mean, number, and create se of prey(d)
d.means=tapply(mydata$prey,mydata$week, mean)
d.n=tapply(mydata$prey,mydata$week, length)
d.se=tapply(mydata$prey,mydata$week, sd)/sqrt(d.n)
#take mean, number, and create se of predator(w)
w.means=tapply(mydata$pred,mydata$week, mean)
w.n=tapply(mydata$pred,mydata$week, length)
w.se=tapply(mydata$pred,mydata$week, sd)/sqrt(w.n)
Here you have created all the variables you need but to plot them using ggplot you need them to be in a tall dataset with an variable indicating if they are predator or prey. I also added a time variable, I think yours would be week.
x=data.frame(means=c(w.means,d.means),
n=c(w.n,d.n),
se=c(w.se,d.se),
role=c(rep("pred",length(w.n)),rep("prey",length(d.n))),
time=c(1:length(w.n),1:length(d.n))
)
I don't know exactly what your data look like so here is a fake one I cooked up just to illustrate the format.
means n se role time
1 0.9874234 10 0.16200575 pred 1
2 1.4120207 12 0.08895026 pred 2
3 2.7352516 8 0.07991036 pred 3
4 1.1301248 11 0.05481813 prey 1
5 2.4810040 13 0.28682585 prey 2
6 3.1546947 9 0.22126054 prey 3
Once the data are in this nice format using ggplot is really pretty easy.
ggplot(x, aes(x=time, y=means, colour=role)) +
geom_errorbar(aes(ymin=means-se, ymax=means+se), width=.1) +
geom_line()
That gives this: