R help - Jun 2010 - Accessing the elements of summary(prcomp(USArrests))

Hello again,

I was hoping one of you could help me with this problem. Consider the sample
data from R:
> summary(prcomp(USArrests))
Importance of components:
                          PC1     PC2    PC3     PC4
Standard deviation     83.732 14.2124 6.4894 2.48279
Proportion of Variance  0.966  0.0278 0.0058 0.00085
Cumulative Proportion   0.966  0.9933 0.9991 1.00000

How do I access the information contained within this summary? For instance,
let's say I wanted to make a graph based on the second row ("Proportion
of Variance").

Please rest assured this is not a homework assignment. I'm just a relatively
novice R user trying to do stuff that's often over my head.

Thanks in advance,
-----------------------------------
Josh Banta, Ph.D
Center for Genomics and Systems Biology
New York University
100 Washington Square East
New York, NY 10003
Tel: (212) 998-8465
http://plantevolutionaryecology.org


      
	[[alternative HTML version deleted]]

Josh B wrote:
> Hello again,
> 
> I was hoping one of you could help me with this problem. Consider the
> sample data from R:
> 
>> summary(prcomp(USArrests))
> Importance of components: PC1     PC2    PC3     PC4 Standard
> deviation     83.732 14.2124 6.4894 2.48279 Proportion of Variance
> 0.966  0.0278 0.0058 0.00085 Cumulative Proportion   0.966  0.9933
> 0.9991 1.00000
> 
> How do I access the information contained within this summary? For
> instance, let's say I wanted to make a graph based on the second row
> ("Proportion of Variance").
> 
The easiest way is to use the ?str function to see how an object is put 
together.

So, assign the results of the summary to a variable

x <- summary(prcomp(USArrests))

then

str(x)

will lead you to :

plot(x$importance[2, ], type = "l")

Hints:

(i) List the function by stats:::summary.prcomp . You will see that 
the table is component 'importance' of the list result. So take a look 
at summary(prcomp(USArrests))$importance[2, ]

(ii) This looks a lot like screeplot().

(iii) prcomp(USArrests) is inappropriate, as the help file for 
prcomp stresses.

On Wed, 16 Jun 2010, Josh B wrote:
> Hello again,
>
> I was hoping one of you could help me with this problem. Consider the
sample data from R:
>
>> summary(prcomp(USArrests))
> Importance of components:
>                          PC1     PC2    PC3     PC4
> Standard deviation     83.732 14.2124 6.4894 2.48279
> Proportion of Variance  0.966  0.0278 0.0058 0.00085
> Cumulative Proportion   0.966  0.9933 0.9991 1.00000
>
> How do I access the information contained within this summary? For
instance, let's say I wanted to make a graph based on the second row
("Proportion of Variance").
>
> Please rest assured this is not a homework assignment. I'm just a
relatively novice R user trying to do stuff that's often over my head.
>
> Thanks in advance,
> -----------------------------------
> Josh Banta, Ph.D
> Center for Genomics and Systems Biology
> New York University
> 100 Washington Square East
> New York, NY 10003
> Tel: (212) 998-8465
> http://plantevolutionaryecology.org
>
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595