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

>

--

%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

Dr. Gavin Simpson [t] +44 (0)20 7679 0522

ECRC, UCL Geography, [f] +44 (0)20 7679 0565

Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk

Gower Street, London [w]

http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w]

http://www.freshwaters.org.uk%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

______________________________________________

[hidden email] mailing list

https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide

http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.