I am here again ... :)
So, to try having a comparison of the real goodness of my metaMDS data I
tried to perform a DCA (with same input table)
Then please forgive me if I do somethign wrong with it... That's my R code:
decorana(sqrtABCD, iweigh=0, ira=0) - DCA.1
DCA.1
Call:
decorana(veg =
Okey, I understood...
I have a matrix of 40 rows (samples) and 29 columns (species). In the
ordination graph the data divide in two clades ( as i supposed they must
to)... and that's my best solution for reduce the Stress...
metaMDS(sqrtABCD, distance = bray, k = 23, trymax = 50, autotransform
On 2/12/09 19:55 PM, Gian Maria Niccolò Benucci gian.benu...@gmail.com
wrote:
Okey, I understood...
I have a matrix of 40 rows (samples) and 29 columns (species). In the
ordination graph the data divide in two clades ( as i supposed they must
to)... and that's my best solution for reduce the
On 2/12/09 19:55 PM, Gian Maria Niccolò Benucci gian.benu...@gmail.com
wrote:
... I supposed, that If we use as many dimensions as there are variables,
then we can perfectly reproduce the observed distance matrix. Isn't it?
Gian, Not quite so. I think it would be useful to consult a good book,
Jari,
Yes, you right, I am sorry I didn't say that I was talking about Euclidean
measure of distance in that passage, I know that other distance are
different, and finally I understood the non-linear regression stuff, now is
much more clear!
If you have some good book titles I would appreciate a
Hi Hi there,
I am trying to use funcion metaMDS (vegan pakage) for Community Ecology
data, but I find no way to calculate the expressed variance of the first 2
axis? is there a way to do that?
Thanks a lot in advance,
Gian
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hi gian,
no, there is no such way. A MDS can´t express explained variance.
However, the stress value is the overall measure of quality of fit of
your MDS to the data. There are various measures of stress, but loosely
speaking you can regard the stress as a percentage of variation NOT
Hi!
According to Clarke and Warwick (Clarke, K. R. and Warwick, R. M. 2001.
Change in marine communities: an approach to statistical analysis and
interpretation. PRIMER-E, Plymouth) you could consider the following
rough rule-of-thumb:
stress 0.05: excellent representation; stress 0.1: good
Dear all,
What about a r2 statistic in this case? I have seen some people using the r2
of the relationship (a matrix regression) between te original distance and
the final distance obtained with the NMDS.
This r2 is not similar to the stress measure, as we can see above:
library(vegan)
Maria Dulce Subida mdsub...@icman.csic.es
writes:
Nevertheless you should take into account that the stress usually
increases with increasing quantity of data.
I think this is the key point. The stress will always increase with
increasing data, as it is harder to capture the information
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