R help - Jul 2004 - questions about principle component analysis (princomp)

Hi, I am a new R user and am currently using princomp to conduct a PCA. 
I have read the help(princomp) and still do not quite understand 
everything in the help. Basically I want to get the covariance matrix, 
and eigenvector/eigenvalues (loadings()?) so that I can find the 
principle components. Thanks!

Yunfeng
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Research Associate, Ph.D
Department of Molecular Biology, MB-5
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037
Tel. (858) 784-2204
Fax. (858) 784-2860
Emal: yunfeng at scripps.edu
Web: http://www.scripps.edu/~yunfeng
###################################

Yunfeng Hu wrote:
> Hi, I am a new R user and am currently using princomp to conduct a PCA. 
> I have read the help(princomp) and still do not quite understand 
> everything in the help. Basically I want to get the covariance matrix, 
> and eigenvector/eigenvalues (loadings()?) so that I can find the 
> principle components. Thanks!
Hello,

you may start with the examples at the bottom of the help page to get 
more understanding. Here is a modified version of that example:

  data(USArrests)
  pc<- princomp(USArrests)

  summary(pc)
  loadings(pc)

  plot(pc)
  biplot(pc)

# some other useful methods mentioned on the help page:

  cov(USArrests)          # covariance matrix
  eigen(cov(USArrests))   # eigenvalues/vector

# and a way to show, what things are stored in pc

  str(pc)

# so they can be extracted as shown on the help page.

# Please note, that the scaled version (correlation matrix)
# would be more appropriate there, e.g.

  pc<- princomp(USArrests, cor=TRUE)
  summary(pc)
  cor(USArrests)
  eigen(cor(USArrests))


Hope it helps

Thomas P.

Thank you, Thomas. It is very helpful. I will dig more into the man 
page but for now I get what I want.

Yunfeng
On Jul 21, 2004, at 11:29 PM, Thomas Petzoldt wrote:
> Yunfeng Hu wrote:
>> Hi, I am a new R user and am currently using princomp to conduct a 
>> PCA. I have read the help(princomp) and still do not quite understand 
>> everything in the help. Basically I want to get the covariance 
>> matrix, and eigenvector/eigenvalues (loadings()?) so that I can find 
>> the principle components. Thanks!
>
> Hello,
>
> you may start with the examples at the bottom of the help page to get 
> more understanding. Here is a modified version of that example:
>
>  data(USArrests)
>  pc<- princomp(USArrests)
>
>  summary(pc)
>  loadings(pc)
>
>  plot(pc)
>  biplot(pc)
>
> # some other useful methods mentioned on the help page:
>
>  cov(USArrests)          # covariance matrix
>  eigen(cov(USArrests))   # eigenvalues/vector
>
> # and a way to show, what things are stored in pc
>
>  str(pc)
>
> # so they can be extracted as shown on the help page.
>
> # Please note, that the scaled version (correlation matrix)
> # would be more appropriate there, e.g.
>
>  pc<- princomp(USArrests, cor=TRUE)
>  summary(pc)
>  cor(USArrests)
>  eigen(cor(USArrests))
>
>
> Hope it helps
>
> Thomas P.
>
>
###################################
Research Associate, Ph.D
Department of Molecular Biology, MB-5
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037
Tel. (858) 784-2204
Fax. (858) 784-2860
Emal: yunfeng at scripps.edu
Web: http://www.scripps.edu/~yunfeng
###################################