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 Birgit Am 23.11.2007 um 17:26 schrieb 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 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 >> [EMAIL PROTECTED] >> >> ______________________________________________ >> 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. >> >> >> >> > Hi, > > in centred PCA, missing data should be replaced by the mean of > available data. > Let X be your analyzed matrix (variables in columns). > > ## > X = matrix(runif(300),ncol=10) > idx = sample(1:nrow(X),5) > X[idx,] = NA > sum(is.na(X)) > [1] 95 > > library(ade4) > dudi.pca(X,center=TRUE,scale=FALSE) > Erreur dans dudi.pca(X, center = TRUE, scale = FALSE) : na entries > in table > ## > > Now we replace missing values : > > ## > f1 <- function(vec) { > m <- mean(vec, na.rm = TRUE) > vec[is.na(vec)] <- m > return(vec) > } > > Y = apply(X,2,f1) > > pcaY = dudi.pca(Y,center=TRUE,scale=FALSE,nf=2,scannf=FALSE) > > s.label(pcaY$li) > sunflowerplot(pcaY$li[idx,1:2], add=TRUE) > ## > > All missing values are placed at the non-informative point, i.e. at > the origin. > > Regards, > > Thibaut. > > -- > ###################################### > Thibaut JOMBART > CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive > Universite Lyon 1 > 43 bd du 11 novembre 1918 > 69622 Villeurbanne Cedex > Tél. : 04.72.43.29.35 > Fax : 04.72.43.13.88 > [EMAIL PROTECTED] > http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en > http://pbil.univ-lyon1.fr/software/adegenet/ Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] ______________________________________________ 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.
