[R] Principle Component Analysis

[Prof Brian Ripley]

You've omitted the command to create testscores.prc, so it's hard to tell.
However, R is not a *clone* of S-PLUS, and there are some differences.
In particular, the print and summary methods for princomp are different.

BTW, it's Principal CA.


On Fri, 17 Aug 2001, Shawn Way wrote:

> I have the manual for S+ 6 and I'm trying to use R for the Principle
> Component Analysis example and I'm getting a few interesting answers...
>
> The log is as follows:
>
> R : Copyright 2001, The R Development Core Team
> Version 1.3.0  (2001-06-22)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type `license()' or `licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type `contributors()' for more information.
>
> Type `demo()' for some demos, `help()' for on-line help, or
> `help.start()' for a HTML browser interface to help.
> Type `q()' to quit R.
>
>
> > library(mva)
> > data <- read.table("h:/test.txt",header=T,sep="")
> > data
>    diffgeom complex algebra reals statistics
> 1        36      58      43    36         37
> 2        62      54      50    46         52
> 3        31      42      41    40         29
> 4        76      78      69    66         81
> 5        46      56      52    56         40
> 6        12      42      38    38         28
> 7        39      46      51    54         41
> 8        30      51      54    52         32
> 9        22      32      43    28         22
> 10        9      40      47    30         24
> 11       32      49      54    37         52
> 12       40      62      51    40         49
> 13       64      75      70    66         63
> 14       36      38      58    62         62
> 15       24      46      44    55         49
> 16       50      50      54    52         51
> 17       42      42      52    38         50
> 18        2      35      32    22         16
> 19       56      53      42    40         32
> 20       59      72      70    66         62
> 21       28      50      50    42         63
> 22       19      46      49    40         30
> 23       36      56      56    54         52
> 24       54      57      59    62         58
> 25       14      35      38    29         20
> > summary(testscores.prc)
> Importance of components:
>                            Comp.1     Comp.2     Comp.3     Comp.4
> Comp.5
> Standard deviation     28.4896795 9.03547104 6.60095491 6.13358179
> 3.72335754
> Proportion of Variance  0.8212222 0.08260135 0.04408584 0.03806395
> 0.01402668
> Cumulative Proportion   0.8212222 0.90382353 0.94790936 0.98597332
> 1.00000000
> > summary(testscores.prc,loadings=T)
> Importance of components:
>                            Comp.1     Comp.2     Comp.3     Comp.4
> Comp.5
> Standard deviation     28.4896795 9.03547104 6.60095491 6.13358179
> 3.72335754
> Proportion of Variance  0.8212222 0.08260135 0.04408584 0.03806395
> 0.01402668
> Cumulative Proportion   0.8212222 0.90382353 0.94790936 0.98597332
> 1.00000000
>
> Loadings:
>            Comp.1 Comp.2 Comp.3 Comp.4 Comp.5
> diffgeom   -0.598 -0.675  0.185  0.386
> complex    -0.361 -0.245 -0.249 -0.829 -0.247
> algebra    -0.302  0.214 -0.211 -0.135  0.894
> reals      -0.389  0.338 -0.700  0.375 -0.321
> statistics -0.519  0.570  0.607        -0.179
> > print(testscores.prc,loadings=T)
> Call:
> princomp(x = data)
>
> Standard deviations:
>    Comp.1    Comp.2    Comp.3    Comp.4    Comp.5
> 28.489680  9.035471  6.600955  6.133582  3.723358
>
>  5  variables and  25 observations.
>
>
>
> Any thoughts as to what I'm doing wrong??
>

-- 
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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