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.
