Thanks for the answer.
Yes indeed, napredict only puts NAs in the right places (ie where
na.action was used). Anyway I realize that I'm much better off dealing
with the missing values prior to the PCA, and R offers many options for
that.
Thanks
Alain
Prof Brian Ripley a écrit :
On Tue, 10 Mar 2009, Alain Paquette wrote:
Hello all,
I wish to compute site scores using PCA (prcomp) on a matrix with
missing values, for example:
Drain Slope OrgL
a 4 1 NA
b 2.5 39 6
c 6 8 45
d 3 9 12
e 3 16 4
...
Where a,b... are sites.
The command
pca<-prcomp(~ Drain + Slope + OrgL, data = t, center = TRUE, scale =
TRUE,
na.action=na.exclude)
works great, and from
pca$x
I can get site scores, e.g.
PC1 PC2 PC3
a NA NA NA
b -2.10475208 -2.315128625 -0.885197753
c 5.01177388 -1.778786252 -0.193285051
d 0.28638602 0.298315086 0.386113799
e -0.58861254 0.089498632 -0.434951813
...
Easy enough...
But how do I use the "napredict" argument? Is it intended as an
argument to be used in the prcomp line (as suggested in ?prcomp), or
is it to be used by itself, to replace NAs in the above site score
matrix (which is what I really want to do).
I don't see an 'napredict' argument. The help says
x: if 'retx' is true the value of the rotated data (the centred
(and scaled if requested) data multiplied by the 'rotation'
matrix) is returned. Hence, 'cov(x)' is the diagonal matrix
'diag(sdev^2)'. For the formula method, 'napredict' is
applied to handle the treatment of values omitted by the
'na.action'.
'napredict' is a function (so please look up its help), and it says R
applies it, not that you need to. It is napredict which gives you the
NAs in the correct places.
Thank you,
Alain
--
Alain Paquette, Ph.D.
alain.paque...@gmail.com
Centre d'étude de la forêt (CEF)
Université du Québec à Montréal
www.cef-cfr.ca
Projet TRIADE
www.projettriade.ca
alain.paque...@projettriade.ca
______________________________________________
R-help@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.
--
Alain Paquette, Ph.D.
alain.paque...@gmail.com
Centre d'étude de la forêt (CEF)
Université du Québec à Montréal
www.cef-cfr.ca
Projet TRIADE
www.projettriade.ca
alain.paque...@projettriade.ca
______________________________________________
R-help@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.
