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
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.hufkens at 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 >-- Sarah Goslee http://www.functionaldiversity.org
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.hufkens at 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 >> >> > > >-- St?phane DRAY (dray at 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/