Hi all,

I'm executing some multivariate exploratory annalysis, with vegan and MASS
packages.

Some problems are not solved for me at this moment. I have read all past
discussions over MDS problems.

In my studies occurs a situation that some samples are equal each other, and
this results in zero dissimilarities.

I tryed with no success, use the stepacross function. So, in this case I
changed one of these zero dissimilarities values for a minimum (1e-5). Some
of these modifications are different than "stepacross" or same isoMDS(x.dist
+ 1e-5)  (proposed by Jari oksanen to 'lie' to isoMDS? When I delete a
sample I do not loose some weight?

Changing one of those zero dissimilarities and using zerodist = "add" option
of metaMDS, it passed the current error (zero or negative distance between
objects).

Someone could explain the function posted by Gavin Simpson (Jan 12, 2010;
05:45pm Re: Non-metric multidimensional scaling (NMDS) help). I didn't get
some result.

If there is a good reason, and you want to include all samples, then
>
you'll need to come up with a means for handling them. metaMDSdist allow
>
you to add a small value to the zero dissimilarities. The details are in
> the code, but effectively all zero distances are replaced by half the
> smallest non zero distance. You could do a similar replacement yourself
> if you feel this is warranted and/or justified.
>
> minDij <- min(Dij[Dij > 0) / 2
> Dij[Dij <= 0] <- minDij
>
> Will do this replacement if Dij is your matrix (replace Dij with
> whatever the name of your matrix is). Then supply the new matrix to
> metaMDS. "
>


When I use unique function as #x.dist <- dist(unique(X))
this cutted some of my samples that I do not know. I can't see my variables
in the plot. Some help?

Cheers, Arnaldo.


epi<- read.table("epi.txt", h=TRUE,row.names=1)

library('vegan')
library('MASS')

epi.<- as.matrix(epi)

dissim1<- vegdist(epi., method="jaccard", binary=TRUE)
dissim1.mds<-metaMDS(dissim1,k=2)

plot(dissim1.mds,type="n")
text(dissim1.mds, labels=as.character(row.names(epi)))

#epi
sample    sp1    sp2    sp3    sp4    sp5    sp6    sp7    sp8    sp9
sp10    sp11    sp12    sp13    sp14    sp15    sp16    sp17    sp18    sp19
1E    1    0    1    0    0    0    0    0    0    0    0    0    0    0
0    0    0    0    0
2E    0    0    1    0    1    0    0    0    0    0    0    0    0    0
0    0    0    0    0
3E    1    0    1    0    0    0    0    0    0    0    0    0    0    0
0    0    0    0    0
4E    1    0    1    0    1    0    0    0    0    0    0    0    0    0
0    0    0    0    0
5E    1    0    0    0    0    0    0    0    0    0    0    0    0    0
0    0    0    0    0
6E    1    0    0    0    0    0    0    0    0    0    0    0    0    0
0    0    0    0    0
7M    1    0    1    0    0    0    1    0    0    0    0    0    0    0
0    0    0    0    0
8E    1    0    0    0    0    0    1    0    0    0    0    0    0    0
0    0    0    0    0
11E    1    0    0    0    1    0    1    0    0    0    0    0    0    0
0    0    0    0    0
12E    0    0    0    0    0    1    0    0    0    0    0    0    0    0
0    0    0    0    0
13E    0    0    0    0    0    0    1    0    0    0    1    1    0    0
0    0    0    0    0
14E    0    0    1    0    0    0    0    0    0    0    0    1    0    0
0    0    0    0    0
15E    1    0    0    0    0    0    1    0    0    0    0    0    1    0
0    0    0    0    0
17E    0    0    0    0    1    0    1    0    1    0    0    0    0    0
0    0    0    0    0
18E    0    0    0    0    0    0    1    0    0    0    0    0    0    0
0    0    0    0    0
20E    1    0    0    0    1    0    0    0    0    0    0    0    0    0
0    0    0    0    0
21E    1    0    0    0    0    0    0    0    0    0    0    0    0    1
0    0    0    0    0
22E    1    0    0    0    1    0    0    0    1    0    0    0    0    0
0    0    0    0    0
23E    1    0    1    1    1    0    0    0    0    0    0    0    0    0
0    0    0    0    0
27E    1    0    0    1    1    0    0    0    0    0    0    0    0    0
0    0    0    0    0
28E    1    0    0    0    1    0    1    1    0    0    1    0    0    0
0    0    0    0    0
30E    1    1    0    0    1    0    0    0    0    0    0    0    0    0
0    0    0    0    0
31E    0    0    0    0    0    0    0    0    0    0    0    0    0    0
1    0    0    0    0
32E    1    0    0    0    0    0    0    0    1    0    0    0    0    0
0    0    0    0    0
9E    0    0    0    0    0    1    1    1    1    1    0    0    0    0
0    0    1    0    0
10E    0    0    1    0    0    1    1    0    1    1    1    0    0    0
0    1    0    1    1

------
Arnaldo D`Amaral Pereira Granja Russo
Instituto Ambiental Boto Flipper
www.institutobotoflipper.com.br

	[[alternative HTML version deleted]]

