Re: [R] PCA with NA

2007-11-28 Thread Paul Hewson
Hilfe Subject: Re: [R] PCA with NA Hello, unfortunately I can not find the pcaMethods package. Birgit Am 26.11.2007 um 16:26 schrieb Kevin Wright: > The pcaMethods package offers a collection of different algorithms for > PCA, some of which (NIPALS and others) can be used on data that hav

Re: [R] PCA with NA

2007-11-28 Thread Birgit Lemcke
Hello, unfortunately I can not find the pcaMethods package. Birgit Am 26.11.2007 um 16:26 schrieb Kevin Wright: > The pcaMethods package offers a collection of different algorithms for > PCA, some of which (NIPALS and others) can be used on data that have > missing values. > > Kevin Wright > >

Re: [R] PCA with NA

2007-11-26 Thread Kevin Wright
The pcaMethods package offers a collection of different algorithms for PCA, some of which (NIPALS and others) can be used on data that have missing values. Kevin Wright On Nov 24, 2007 4:59 PM, Hartmut Oldenbürger <[EMAIL PROTECTED]> wrote: > Hi Birgit, and All > > Possibly you should not consid

Re: [R] PCA with NA

2007-11-24 Thread Hartmut Oldenbürger
Hi Birgit, and All Possibly you should not consider the case completed ;-) There is an important alternative to imputing means, or estimates from first or second order regression (Frane, Psychometrica, BMDP): partial-least-squares (Wold), which uses as much information from the data as possible t

Re: [R] PCA with NA

2007-11-23 Thread Birgit Lemcke
Thanks to all for your help. Only to complete this: The NA´s in my case mean that I have no information for this character in this species. These are not ecological data, so I have to deal somehow with the NA´s without replacing by zero. I think Thibauts help is very useful. Thanks a lot B

Re: [R] PCA with NA

2007-11-23 Thread Patrick Burns
The 'factor.model.stat' function (available in the public domain area of http://www.burns-stat.com) fits a principal components factor model to data that can have NAs. You might be able to copy what it does for your purposes. It does depend on there being some variables (columns) that have no missi

Re: [R] PCA with NA

2007-11-23 Thread Thibaut Jombart
Birgit Lemcke wrote: >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 analysi

Re: [R] PCA with NA

2007-11-23 Thread 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