[R] Comparing two matrices

Stéphane Dray
Wed, 04 Mar 2009 09:13:52 -0000

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