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NMDS in Vegan: problems in stressplot, best solution
2 messages · Kumar Mainali, Gavin Simpson
On Fri, 2013-04-26 at 12:42 -0500, Kumar Mainali wrote:
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?
You can. What you can't do is use argument `dis` with an metaMDS object. If you use: stressplot(parth.mds, pch=1, p.col="gray", lwd=2, l.col="red") you'll see it works just fine. We'll see about providing a better error message if you do what the documentation asks you not to.
If I have 100 iterations for metaMDS, then when I plot the result, does it give me result from best solution?
The best solution it encountered in the 100 random starts, yes.
How do I know that.
It is implied in point 4. of the Details section of ?metaMDS.
Can you plot the Stress by Iteration number?
Not in a graphical plot. The stresses for each iteration are printed to the console at each iteration. Note these "iterations" are random starts, each of which has iterations of the algorithm. HTH G
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
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