Reproducing Plot 4a in Mokany et al (2022) about gdm HOT 5 CLOSED

This is the code the the gdm.plot function that creates the plot. You can customize as needed.

##plots the compositional dissimilarity spline plot
plot(x$ecological, x$observed, xlab="Predicted Ecological Distance", ylab="Observed Compositional Dissimilarity", type="n", ylim=c(0,1))
points(x$ecological, x$observed, pch=20, cex=0.25, col=plot.color)
overlayX <- seq( from=min(x$ecological), to=max(x$ecological), length=PSAMPLE )
overlayY <- 1 - exp( - overlayX )
lines( overlayX, overlayY, lwd=plot.linewidth )

from gdm.

You asked about PSAMPLE, which is defined in gdm.plot.

https://github.com/fitzLab-AL/gdm/blob/master/R/gdm.plot.R

ctrl-F PSAMPLE and you will find it.

from gdm.

@fitzLab-AL could you please clarify what the PSAMPLE vector is or comes from? I have the code working up to that point (ie., length=PSAMPLE). thanks

from gdm.

Have a look at the code for the gdm.plot function. It is in there. It is just an integer.

from gdm.

I checked plot.gdm and didn't see an argument for length. Or elsewhere in the gdm 1.6 package info. However, length() is in section 1.5 of Appendix S1 (Mokany et al 2022) and equivalent code on your website. The plot works okay with or without it. In the end, I matched it to the max(gdm$ecological) value for a useful visual. Thanks. I appreciate the assistance.

from gdm.