Using napredict in prcomp
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.paquette at gmail.com Centre d'?tude de la for?t (CEF) Universit? du Qu?bec ? Montr?al www.cef-cfr.ca Projet TRIADE www.projettriade.ca alain.paquette at projettriade.ca
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