Ok, thanks, that helps. What about running the same code on a bit of a different set of data, ex.; korma<- read.csv(text=" GR T C M B 1 0 0 0 1 2 0 1 0 0 3 1 1 0 1 4 1 0 1 1 5 0 0 0 1 6 1 0 1 1... ",sep="",row.names=1,header=TRUE)
str(korma) dist(korma) korma.dist<- dist(korma) korma.mds <- isoMDS(korma.dist) #Error in isoMDS(korma.dist) : zero or negative distance between objects 1 and 5 # What do I need to do to my data to avoid the error message? On Sun, Sep 1, 2013 at 3:03 AM, Berend Hasselman <[email protected]> wrote: > > On 01-09-2013, at 00:30, Simona Augyte <[email protected]> wrote: > > > I'm trying to run a very simple non-metric multidimensional scaling code > on > > a 8x5 character matrix. > > gr T C M B > > arcor 6 4 6 5 > > corfo 24 21 23 24 > > corma 25 15 26 17 > > crust 3 2 6 5 > > fil 15 12 15 15 > > fol 11 9 6 8 > > leat 10 11 13 13 > > seag 2 2 2 2 > > > > My code is as follows; > > coma<-read.csv("coma.csv",header=TRUE) > > coma.x<-as.matrix(coma) > > coma.dist <- dist(coma.x) # right here I get a warning message -> In > > dist(coma.x) : NAs introduced by coercion > > > > WHAT DOES THAT MEAN??? the table has values and there are not NAs. Could > > this be a by product of the way I inserted the data? > > > > Yes. > Your table contains characters and not numbers. > > Tell read.csv that the first column contains row names (assuming that that > is indeed the case). > > coma<- read.csv(text=" > gr T C M B > arcor 6 4 6 5 > corfo 24 21 23 24 > corma 25 15 26 17 > crust 3 2 6 5 > fil 15 12 15 15 > fol 11 9 6 8 > leat 10 11 13 13 > seag 2 2 2 2 > ",sep="",row.names=1,header=TRUE) > > coma > str(coma) > dist(coma) > > Berend > > > > Please help. > > > > -- > > > > Simona Augyte, MS > > PhD student > > Ecology and Evolutionary Biology > > University of Connecticut > > cell 707-832-7007 > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > [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. > > -- Simona Augyte, MS PhD student Ecology and Evolutionary Biology University of Connecticut cell 707-832-7007 [[alternative HTML version deleted]] ______________________________________________ [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.
