matel.rtest accepts both Euclidean and non Euclidean matrices. If both
distance matrices are Euclidean, then a faster algorithm is used to
speed up the permutation procedure.
You can also use mantel.randtest which is exactly similar to rtest but
faster as computation are in C.
Sarah Goslee wrote:
Hi,
For the Mantel test, your matrices do not need to be Euclidean, but they
do need to be symmetric. You could write a similar test that does not
require a symmetric matrix, though.
Sarah
On Tue, Mar 3, 2009 at 11:40 AM, Koen Hufkens <koen.hufk...@ua.ac.be> wrote:
Hi List,
I would like to compare two (confusion) matrices. I ended up with the ade4
mantel.rtest function as my best option. However it seems that my data is
non-euclidean in nature (is.euclid gives a FALSE). I attached both matrices
at the end of the document.
Are there any tools to transform these matrices into an euclidean form so I
can use mantel.rtest with confidence.
Other suggestions are also welcome.
Kind regards,
Koen
--
matrix 1
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
1 0 60 5 0 9 3 3 0 18 1 1
2 30 0 12 0 2 45 1 0 5 4 1
3 8 32 0 1 19 5 4 0 27 1 3
4 0 0 3 0 67 1 3 0 0 0 25
5 12 3 13 26 0 12 27 0 3 2 2
6 1 72 1 0 4 0 11 0 0 10 1
7 3 2 9 0 45 40 0 0 0 0 0
8 13 3 0 0 0 1 0 0 10 0 72
9 24 26 34 0 6 2 0 2 0 2 4
10 2 21 1 0 1 67 0 0 1 0 6
11 2 2 28 11 10 10 0 22 3 13 0
matrix 2
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
1 0 66 0 10 9 5 0 3 7 0 0
2 43 0 0 14 2 32 0 1 5 3 0
3 11 32 4 0 19 10 1 7 13 2 0
4 0 0 0 0 0 0 0 0 0 0 0
5 11 6 4 18 0 15 18 22 4 1 0
6 2 40 3 3 12 0 1 24 1 14 0
7 4 5 0 8 32 49 2 0 0 0 0
8 0 0 0 0 0 0 0 0 0 0 0
9 19 23 2 42 8 2 0 0 0 3 1
10 1 16 3 3 3 73 0 0 2 0 0
11 2 4 0 20 15 10 15 0 10 7 17
--
Stéphane DRAY (d...@biomserv.univ-lyon1.fr )
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
Tel: 33 4 72 43 27 57 Fax: 33 4 72 43 13 88
http://pbil.univ-lyon1.fr/members/dray/
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