>>>>> "jh" == jim holtman <[EMAIL PROTECTED]>
>>>>> on Fri, 25 Jul 2008 12:34:49 -0400 writes:
>>>>> "jh" == jim holtman <[EMAIL PROTECTED]>
>>>>> on Fri, 25 Jul 2008 12:34:49 -0400 writes:
jh> Does this do what you want:
>> x <- matrix(1:25,5)
>> x
jh> [,1] [,2] [,3] [,4] [,5]
jh> [1,] 1 6 11 16 21
jh> [2,] 2 7 12 17 22
jh> [3,] 3 8 13 18 23
jh> [4,] 4 9 14 19 24
jh> [5,] 5 10 15 20 25
>> x[upper.tri(x)] <- NA
>> write.table(x, na="", row.names=FALSE, col.names=FALSE)
jh> 1
jh> 2 7
jh> 3 8 13
jh> 4 9 14 19
jh> 5 10 15 20 25
>>
Yes, but why not use the S / R objects / methods that were
exactly written for the purpose?
I strongly recommend to make your matrix into a "dist" object
(or a "dissimilarity" object -- the latter from package
'cluster', using function daisy(.)) !
> m <- matrix(1:25,5); m <- m + t(m); diag(m) <- 0
> (D <- as.dist(m))
1 2 3 4
2 8
3 14 20
4 20 26 32
5 26 32 38 44
Note that the above does *not* print the all-0 diagonal
and so saves printing space.
Martin Maechler, ETH Zurich
jh> On Fri, Jul 25, 2008 at 8:30 AM, pgseye <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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@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@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@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.
>>
jh> --
jh> Jim Holtman
jh> Cincinnati, OH
jh> +1 513 646 9390
jh> What is the problem you are trying to solve?
jh> ______________________________________________
jh> R-help@r-project.org mailing list
jh> https://stat.ethz.ch/mailman/listinfo/r-help
jh> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
jh> and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@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.
