Re: [R] Write lower half of distance matrix only

From: pgseye <prseye_at_gmail.com>
Date: Fri, 25 Jul 2008 05:30:46 -0700 (PDT)

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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>>
>> ______________________________________________
>> R-help_at_r-project.org mailing list
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>> PLEASE do read the posting guide
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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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Received on Fri 25 Jul 2008 - 13:01:58 GMT

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