Hi all,

I attended the Proteus workshop in spring 2017 and was given the code for multi-season occupancy analyses in R-Presence. I am trying to plot local extinction as per reviewer's request for a manuscript revision.

In the code, we were showed how to plot occupancy (in this case initial occupancy) but there was no example code on how to plot localized extinction or colonization. I have no issue plotting occupancy (psi) and adding confidence intervals to the plot, but I am a bit lost when it comes to plotting localized extinction.

The code for occupancy looks like this

# plot estimated occupancy vs elevation

plot(x=mydata$unitcov$outcrop,y=m1$real$psi$est,

ylim=c(0,1), pch=16,

xlab="Distance to Outcrops",

ylab="Estimated occupancy probability")

col=mydata$unitcov$outcrop,

li=m1$real$psi$lower_0.95,

ui=m1$real$psi$upper_0.95,

sfrac=0,gap=0)

How would I adapt this for localized extinction? I have hit a wall, I am sure I am overthinking all of this but any help would be much appreciated it.