From: jim holtman <jholtman_at_gmail.com>

Date: Fri, 25 Jul 2008 12:34:49 -0400

*> 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

*>
*

Date: Fri, 25 Jul 2008 12:34:49 -0400

Does this do what you want:

[,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

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_at_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.Received on Fri 25 Jul 2008 - 16:38:17 GMT

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