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Reproducing Plot 4a in Mokany et al (2022) #38
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This is the code the the gdm.plot function that creates the plot. You can customize as needed.
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@fitzLab-AL could you please clarify what the PSAMPLE vector is or comes from? I have the code working up to that point (ie., |
Have a look at the code for the |
I checked |
You asked about https://github.com/fitzLab-AL/gdm/blob/master/R/gdm.plot.R ctrl-F PSAMPLE and you will find it. |
Hello @fitzLab-AL and gdm users (also @rvalavi if you're inclined),
Is the code for reproducing plot 4a available? Section 1.7 of the supplementary materials (and online material - link below) includes code for reproducing plot 4b, but not 4a. A similar plot (to 4a) is one of many produced via
plot(gdm)
. I can reproduce that individual plot fromplot(gdm)
(in part) usingplot(gdm$ecological, gdm$observed)
. But I lack the line showing GDM-predicted dissimilarity.Having this code will also help clarify whether a data object from
predict(gdm, gdmTab)
is required to produce plot 4a; and thus further reveal the relationship between plots produced viaplot(gdm)
andplot(x, gdm.pred)
.My expectation is that other users have had this question. Thanks very much
[https://github.com/fitzLab-AL/gdm?tab=readme-ov-file#visualizing-multi-dimensional-biological-patterns]
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