[R] Write lower half of distance matrix only
pgseye
prseye at gmail.com
Fri Jul 25 14:30:46 CEST 2008
Thanks Jim,
The morphometry software I mentioned outputs distance matrices in the
format:
0.0000
7.1598 0.0000
8.7241 8.3506 0.0000
9.5217 7.2457 2.5642 0.0000
I would have liked to write to a file the same type of matrix in R, to
ensure the same data format. Mantel for Windows is optimally setup to take
this type of matrix.
Thanks
jholtman wrote:
>
> How do you want the lower half written out? can you give us an
> example of the input matrix and then what you would expect to see on
> the output. Is it still a matrix with the upper half set to zero/NA?
> Do you want it as a vector? What is the other program expecting as
> input?
>
> You need to provide more information so that we can provide suggestions.
>
> On Fri, Jul 25, 2008 at 7:03 AM, pgseye <prseye at gmail.com> wrote:
>>
>> Hi,
>>
>> I'm very new to R. I want to know if there is any way to write only the
>> lower half of a distance matrix created in R to a csv file for example.
>> I
>> get the 'cannot coerce class "dist" into a data.frame' message when I
>> try.
>> I have used as.matrix and can write to a file this way, but as a full
>> matrix.
>>
>> The reason I only want the lower half is that I've been doing some Mantel
>> correlations with distance matrices (of Procrustes distances) generated
>> by
>> other (geometric morphometric) software that are in this format. However,
>> I'm needing to use an alternative such as R to calculate distance
>> matrices
>> of Fourier coefficients which the other software can't do. So far, the
>> Mantel correlations calculated from these two matrices (with R and also
>> another software (Mantel for Windows)) are slightly different (when they
>> should be exactly the same) and I'm wondering whether it's because the
>> input
>> format is different (ie one full, one half).
>>
>> Thanks,
>>
>> Paul
>>
>>
>> --
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>>
>> ______________________________________________
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>>
>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem you are trying to solve?
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
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