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

From: pgseye <prseye_at_gmail.com>
Date: Fri, 25 Jul 2008 20:07:51 -0700 (PDT)

Great, thanks for that Jim,

It does what I need it do do.

Regards,

Paul

jholtman wrote:
>
> Does this do what you want:
>

>> x <- matrix(1:25,5)
>> x

> [,1] [,2] [,3] [,4] [,5]
> [1,] 1 6 11 16 21
> [2,] 2 7 12 17 22
> [3,] 3 8 13 18 23
> [4,] 4 9 14 19 24
> [5,] 5 10 15 20 25
>> x[upper.tri(x)] <- NA
>> write.table(x, na="", row.names=FALSE, col.names=FALSE)

> 1
> 2 7
> 3 8 13
> 4 9 14 19
> 5 10 15 20 25
>>

>
>
> On Fri, Jul 25, 2008 at 8:30 AM, pgseye <prseye@gmail.com> wrote:
>>
>> 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
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://www.nabble.com/Write-lower-half-of-distance-matrix-only-tp18649556p18649556.html
>>>> Sent from the R help mailing list archive at Nabble.com.
>>>>
>>>> ______________________________________________
>>>> 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.
>>>>
>>>
>>>
>>>
>>> --
>>> 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.
>>>
>>>
>>
>> --
>> View this message in context:
>> http://www.nabble.com/Write-lower-half-of-distance-matrix-only-tp18649556p18650794.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> 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.
>>

>
>
>
> --
> 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.
>
>
-- 
View this message in context: http://www.nabble.com/Write-lower-half-of-distance-matrix-only-tp18649556p18662636.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
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.
Received on Sat 26 Jul 2008 - 06:44:49 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Sat 26 Jul 2008 - 07:32:13 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive