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How to change a coefficient matrix into a semi-matrix?
5 messages · Zongshan, Li, Gavin Simpson, Jari Oksanen
On Sun, 2009-08-30 at 22:26 +0800, Zongshan, Li wrote:
Dear all of r-sig-ecology:
I have a coefficient matrix produced by Phylocom, for example:
plot1 plot2 plot3 plot4 plot5
plot1 245.76 258.94 252.88 254.23 249.19
plot2 258.94 269.58 264.39 265.55 261.85
plot3 252.88 264.39 259.87 260.42 256.30
plot4 254.23 265.55 260.42 262.75 257.44
plot5 249.19 261.85 256.30 257.44 254.01
I want to do the hierarchical cluster analysis in R with the funtion:
hclust, but the format of input data of hclust is semi-matrix, for
example:
plot1 plot2 plot3 plot4
plot2 258.94
plot3 252.88 264.39
plot4 254.23 265.55 260.42
plot5 249.19 261.85 256.30 257.44
Is there some function in R to change a matrix into the format of
semi-matrix?
See as.dist? to go from the full matrix format to an object of class 'dist' as required by hclust. HTH G
Thanks a lot! Best regards to all of you! Zongshan, Lizsli_st at rcees.ac.cn 2009-08-30 ------------------- Zongshan, Li Research Center for Eco-Environmental Sciences, Chinese Academy of Science P. O. Box 2871 18 Shuangqing Road, Haidian District, Beijing, 100085 Peoples Republic of China Tel:0086-10-13699145748 Fax:0086-10-62923549 Email:zsli_st at rcees.ac.cn [[alternative HTML version deleted]]
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On 30/08/2009 17:26, "Zongshan, Li" <zsli_st at rcees.ac.cn> wrote:
Dear all of r-sig-ecology:
I have a coefficient matrix produced by Phylocom, for example:
plot1 plot2 plot3 plot4 plot5
plot1 245.76 258.94 252.88 254.23 249.19
plot2 258.94 269.58 264.39 265.55 261.85
plot3 252.88 264.39 259.87 260.42 256.30
plot4 254.23 265.55 260.42 262.75 257.44
plot5 249.19 261.85 256.30 257.44 254.01
I want to do the hierarchical cluster analysis in R with the funtion: hclust,
but the format of input data of hclust is semi-matrix, for example:
plot1 plot2 plot3 plot4
plot2 258.94
plot3 252.88 264.39
plot4 254.23 265.55 260.42
plot5 249.19 261.85 256.30 257.44
Is there some function in R to change a matrix into the format of semi-matrix?
Thanks a lot! Best regards to all of you!
Zongshan, Gav already told you about 'as.dist'. Here some more news: check the 'picante' package which is Phylocom in R. cheers, jari oksanen
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