You need to spend time with an R tutorial or two. Your error is due to ignorance of basic R data structures.
Bert On Oct 18, 2016 10:48 PM, "Kirsten Green" <kagbo...@gmail.com> wrote: > David, > > I have run the str() function and all my data is int (integer). So I am > trying to change it to numeric using: > str(mortdata) > class(mortdata) > is.numeric(mortdata) > mortdata.num <- as.numeric(data.frame(mortdata)) > > But I keep getting an error: > mortdata.num <- as.numeric(data.frame( > mortdata)) > Error: (list) object cannot be coerced to type 'double > > On Tue, Oct 18, 2016 at 1:23 PM, David L Carlson <dcarl...@tamu.edu> > wrote: > > > What do you get with str(mortdata)? The error message indicates that at > > least one of the variables is not numeric and the second suggests it is a > > factor. You said the values were coded binomially, but they must be > > numeric, e.g. 0, 1 and not "Present" "Absent" or something like that. If > > they are all factors, something like > > > > mortdata1 <- sapply(mortdata, as.numeric)-1 > > > > would convert factor levels of 1 and 2 to 0 and 1. > > ------------------------------------- > > David L Carlson > > Department of Anthropology > > Texas A&M University > > College Station, TX 77840-4352 > > > > -----Original Message----- > > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Kirsten > > Green > > Sent: Tuesday, October 18, 2016 12:28 PM > > To: r-help@r-project.org > > Subject: [R] MDS, line of best fit, and id of variables > > > > Hi, > > > > I have created a dataset that includes 28 rows (burials) and 27 columns > > (variables) that are coded binomially. I have gotten metaMDS to run in > the > > pst but now can't seem to get it run at all. > > Error message: > > > mortdata.mds <- metaMDS(mortdata) > > Error in FUN(X[[i]], ...) : > > only defined on a data frame with all numeric variables > > In addition: Warning message: > > In Ops.factor(left, right) : ‘<’ not meaningful for factors > > > > I'd like to create a 3D MDS plot and add the line of best fit for the 3 > > dimensions (3 variables). I am also trying to figure out, or understand, > > which variables are causing the variation. > > > > I ran PCA and it told me that with 3 variables approximately 50% of the > > data variation is explained. So I assumed that meant that running MDS in > 3 > > dimensions would show me 3 variables causing the variation but I can't > get > > that to work. > > > > Here is my code so far (i've also attached it to the email): > > > > mortdata<-read.csv("Table5.5.csv", header=TRUE) > > mortdata > > row.names(mortdata) <- mortdata[,1] > > mortdata <- mortdata[,-1] > > mortdata > > > > mortdata.mds <- metaMDS(mortdata) > > mortdata.mds.alt <- metaMDS(mortdata, distance="euclidean", k=3, > trymax=50, > > autotransform=FALSE, noshare=FALSE) > > > > > > *object = mortdata.mds.alt > > > > names(mortdata.mds.alt) > > > > mortdata.mds.alt > > summary(mortdata.mds.alt) > > > > *stress plot > > stressplot(mortdata.mds.alt) > > > > x <- mortdata.mds.alt$species > > y <- mortdata.mds.alt$points > > na.exclude(mortdata.mds.alt) > > vScoresScale <- scale(, center = TRUE, scale = TRUE) > > > > > > plot(mortdata.mds.alt) > > plot(mortdata.mds.alt, type="t") > > > > *multiple linear regression model > > lm(formula = x ~ y) > > abline(lm(x ~ y), col="red") > > > > > > *scatterplot3D > > library(scatterplot3d) > > attach(mortdata.mds.alt) > > scatterplot3d(mortdata.mds.alt, x="sampleScores", y="variableScores", > > main="3D Scatterplot") > > > > Any help would be greatly appreciated. I can also send the dataset if > that > > helps. > > > > -- > > *Kirsten Green* > > kagbo...@gmail.com > > 916-712-5193 > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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. > > > > > > -- > *Kirsten Green* > kagbo...@gmail.com > 916-712-5193 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
