[R] MDS, line of best fit, and id of variables

[Bert Gunter]

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" <kagbones at 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 <dcarlson at 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-bounces at r-project.org] On Behalf Of Kirsten
> > Green
> > Sent: Tuesday, October 18, 2016 12:28 PM
> > To: r-help at 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*
> > kagbones at gmail.com
> > 916-712-5193
> > ______________________________________________
> > R-help at 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*
> kagbones at gmail.com
> 916-712-5193
>
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>
> ______________________________________________
> R-help at 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.

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