[R] PCA with NA

[ONKELINX, Thierry]

Dear Birgit,

You need to think about why you have that many NA's. In case of vegetation data, it is very common to have only a few species present in a site. So how would you record the abundance of a species that is absent? NA or 0 (zero)? One could argument that it needs to be NA because you can't measure the abundance of the species that is absent. But others could argument that a missing species has by definition zero abundance.
In my opinion it's best to use 0 (zero) for absent species and NA for present species but with missing information on the abundance.

HTH,

Thierry


----------------------------------------------------------------------------
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx op inbo.be 
www.inbo.be 

Do not put your faith in what statistics say until you have carefully considered what they do not say.  ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney

-----Oorspronkelijk bericht-----
Van: r-help-bounces op r-project.org [mailto:r-help-bounces op r-project.org] Namens Birgit Lemcke
Verzonden: vrijdag 23 november 2007 16:43
Aan: R Hilfe
Onderwerp: [R] PCA with NA


Dear all,
(Mac OS X 10.4.11, R 2.6.0)
I have a quantitative dataset with a lot of Na´s in it. So many, that it is not possible to delete all rows with NA´s and also not possible, to delete all variables with NA´s.
Is there a function for a principal component analysis, that can deal with so many NA´s.

Thanks in advance

Birgit


Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
birgit.lemcke op systbot.uzh.ch

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