Hello,
I can draw a basic stress plot for NMDS with the following code in package
Vegan.
> stressplot(parth.mds, parth.dis)
When I try to specify the line and point types, it gives me error message.
> stressplot(parth.mds, parth.dis, pch=1, p.col="gray", lwd=2, l.col="red")
Error in plot.xy(xy, type, ...) : invalid plot type
In the above code, if I removed line type, it does give me the plot only of
points with my choice of type.
> stressplot(parth.mds, parth.dis, pch=1, p.col="gray")
Why cannot I define both line and point at the same time?
If I have 100 iterations for metaMDS, then when I plot the result, does it
give me result from best solution? How do I know that. Can you plot the
Stress by Iteration number?
parth.mds <- metaMDS(WorldPRSenv, distance = "bray", k = 2, trymax = 100,
engine = c("monoMDS", "isoMDS"),
autotransform =TRUE, wascores = TRUE, expand = TRUE, trace = 2)
plot(parth.mds, type = "p")
Thanks in advance,
Kumar
--
Section of Integrative Biology
University of Texas at Austin
Austin, Texas 78712, USA
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