Silvia Lomascolo wrote: > It was suggested that the 'NAs introduced by coercion' message might be > warning me that my data are not what they should be. I checked this using > str(PeaksMatrix), as suggested, and the data seem to be what I thought they > were: > > 'data.frame': 335 obs. of 127 variables: > $ Code : Factor w/ 335 levels "A1MR","A1MU",..: 1 2 3 4 5 6 7 8 9 10 ... > $ P3.70 : num 0 0 0 0 0 0 0 0 0 0 ... > $ P3.97 : num 0 0 0 0 0 0 0 0 0 0 ... > $ P4.29 : num 0 0 0 0 0 0 0 0 0 0 ... > $ P4.90 : num 0 0 0 0 0 0 0 0 0 0 ... > $ P6.30 : num 0 0 0 0 0 0 0 0 0 0 ... > $ P6.45 : num 7.73 0 0 0 0 0 4.03 0 0 0 ... > $ P6.55 : num 0 0 0 0 0 0 0 0 0 0 ... > > ... > > I do have 335 observations, 127 variables that are named P3.70, 3.97, P4.29, > etc.. This was a relief, but I still don't know whether the distance matrix > is what it should be. I tried 'str(dist.PxMx)', which is the name of my > distance matrix, but I get something that has not much meaning to me, an > unexperienced R user: > > Class 'dist' atomic [1:55945] 329.6 194.9 130.1 70.7 116.9 ... > ..- attr(*, "Size")= int 335 > ..- attr(*, "Labels")= chr [1:335] "1" "2" "3" "4" ... > ..- attr(*, "Diag")= logi FALSE > ..- attr(*, "Upper")= logi FALSE > ..- attr(*, "method")= chr "euclidean" > ..- attr(*, "call")= language dist(x = PeaksMatrix, method = "euclidean", > diag = FALSE, upper = FALSE, p = 2) > > Any more suggestions, please? > > > Actually, you seem to have 126 variables plus a factor called "Code", which has non-numeric levels. I think you probably want to lose that one before calculating distances. > Silvia Lomascolo wrote: > >> I work with Windows and use R version 2.4.1. I am JUST starting to learn >> this program... >> >> I get this warning message 'NAs introduced by coercion' while trying to >> build a distance matrix (to be analyzed with NMDS later) from a 336 x 100 >> data matrix. The original matrix has lots of zeros and no missing values, >> but I don't think this should matter. >> >> I searched this forum and people have suggested that the warning should be >> ignored but when I try to print the distance matrix I only get the row >> numbers (the matrix seems to be 'empty') and I'm not being able to judge >> whether the matrix worked or not. >> >> To get the distance matrix I wrote: >> dist.PxMx <- dist (PeaksMatrix, method='euclidean', diag=FALSE, >> upper=FALSE) >> >> I tried including the p argument (included in the help for dist()) and >> leaving it out, but that didn't seem to change anything. I think that's >> required for one distance measure though, not for euclidean dist. >> >> Should I really ignore this warning? If so, why am I not being able to see >> the distance matrix? >> >> > >
-- O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 ______________________________________________ [email protected] 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.
