Nevermind on this questions, I was able to solve the issue by using as.dist() instead of dist().
Thanks, Kerrio On Mon, Dec 30, 2013 at 2:38 PM, Kerrio Brown <kerriobr...@gmail.com> wrote: > Hi, > > I'm trying to understand what are the appropriate input for the dist() > function ( > http://stat.ethz.ch/R-manual/R-patched/library/stats/html/dist.html) > > If I run the dist() function on a matrix, is it correct to have > *distance*values in the original matrix? > > The original values in my matrix are the actual Euclidean distances I want > to feed into a multi-dimensional scaling algorithm (MDS). My concern is > that the dist() function is going treat the original values as something > other than distances. For instance, two data points of 0.9 may be > considered exactly similar, even though 0.9 is supposed to mean a large > difference between variables. > > For the original values below: > > John JakeWilliam John10.10.9 Jake0.11 0.9 William0.90.91 > > John and Jake are very close (0.1) > William and John are very distant (0.9) > William and Jake are very distant (0.9) > > But the plotted distances do not reflect anything close to these original > distance values. > > Here is my script using the csv data copied above as MyData.csv (dist > function in red): > > #Read data > > MyData <- read.csv("MyData.csv", header = TRUE) > > MyMatrix <- as.matrix(MyData) > > > #Compute/translate(?) distances > > d <- dist(MyMatrix) > > fit <- cmdscale(d,eig=TRUE, k=2) > > > > # plot solution > > x <- fit$points[,1] > > y <- fit$points[,2] > > plot(x, y, xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", > type="n") > > text(x, y, labels = names(MyData), cex=.7) > > > One option would be to skip using the dist() function, but I can't seem to > get the data in the right format for cmdscale, which has to look like this: > > > > JohnJakeWilliam John > > > Jake0.1 > > William0.9 0.9 > > > Thank you for any clarification you can provide! > > -Kerrio > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org 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.
