similar to: Plotting MDS (multidimensional scaling)

Hi; I am working with the similarity matrix below and I would like to plot a two-dimensional MDS solution such as each point in the plot has a label. This is what I did: data <- read.table('c:/multivariate/mds/colour.txt',header=FALSE) similarity <- as.dist(data) distance <- 1-similarity result.nmds <- nmds(distance) plot(result.nmds) (nmds and plot.nmds as defined at

Hello, I now trying to solve this one : # Triangle Project Code. # Triangle analyzes the lengths of the sides of a triangle # (represented by a, b and c) and returns the type of triangle. # # It returns: # :equilateral if all sides are equal # :isosceles if exactly 2 sides are equal # :scalene if no sides are equal # # The tests for this method can be found in #

Dear All, I am in the somewhat unfortunate position of having to reproduce the results previously obtained from (non-metric?) MDS on a "kinship" matrix using Statistica. A kinship matrix measures affinity between groups, and has its maximum values on the diagonal. Apparently, starting with a nxn kinship matrix, all it was needed to do was to feed it to Statistica flagging that the

Hello I will be applying MDS (actually Isomap) to make a psychological "concept map" of the similarities between N concepts. I would like to scale to a large number of concepts, however, the resulting N*(N-1) pairwise similarities is prohibitive for a user survey. I'm thinking of giving people random subsets of the pairwise similarities. Does anyone have recommendations for this

Suppose I have three numbers p1, p2, p3 with 0 <= p1,p2,p3 <= 1 and p1+p2+p3=1, and a function f=f(p1,p2,p3) = f(p1,p2,1-p1-p2). How to draw a contour plot of f() on the p1+p2+p3=1 plane, that is, an equilateral triangle? Functions triplot(), triangle.plot(), and ternaryplot() give only scatterplots, AFAICS -- Robin Hankin Uncertainty Analyst National Oceanography Centre,

Hi all, I'm trying to perform an MDS of some data that I have. When I use cmdscale everything is fine and I get some interesting results however, the tends to be low. What I wnat to do is compare this with the Non-Metric MDS using isoMDS or sammon. However, when I try using these I get the following message. Error in isoMDS(x.dist) : zero or negative distance between objects 2 and 4

Hi, I am looking for the best multidimensional configuration for my data (47*47 distance matrix). I ve tried classical metric (cmdscale) and non metric MDS (isoMDS, nmds) but it is now difficult to choose the best solution because of the uncertainties in the definitions of the "stress" function. So, same problem, several questions : 1. Statistical consideration : With

Hi again Sorry, in looking again at sammon and isoMDS I see that they seem to do exactly what I want, except that they are non-metric, which means, as I understand it, that they relate the rank orders of the variables rather than the actual distances. Could I use these non-metric MDS packages even if my distances are metric? Thanks Karen -- Karen Kotschy Centre for Water in the Environment

Dear List, I'm trying to interpret the results of the Kruskal's Non-metric Multidimensional Scaling algorithm (isoMDS, MASS package). The 'goodness of fit' is reported as "The final stress achieved (in percent)". What does this mean exactly? I've tried to google for an answer but I've not come up with a definitive answer. Regards, Dieter -- Dieter Vanderelst

Hi, I need math function which is used in: isoMDS, Sammon and metaMDS method. Anybody know where I may find it? Any manual or webside? I would be very happy Thanks a lot ! -- View this message in context: http://n4.nabble.com/math-function-MDS-method-tp1008294p1008294.html Sent from the R help mailing list archive at Nabble.com.

Dear All, I am not familar with R. I want to use PCA (principal components analysis) and MDS (multidimensional scaling). Can someone tell me which R package I should use for PCA and MDS? I appreciate your help in advance. Ray

Hi, I have tried to develop multidimensional scaling for 3D space using PCA without success, yet;-) Is there some application ready in R? Cheers, Atte

A student of mine wants to use R to do some nonmetric multidimensional scaling. According to the R FAQ, there's a package called pcurve that computes multidimensional scaling solutions, but I was not able to locate it the contrib page (I am a Windows user with R version 1.4.1). Can anyone tell me whether it is possible to do nonmetric multidimensional scaling with R, and if so, how? John

What are the limitations on size of matrix for MDS functions? steve -- Steve Antos Priva-Technologies 847-640-9020 x3114 cell (540)409-1231 [[alternative HTML version deleted]]

i know cmdscale and isoMDS inR can do classical and non-metric MDS.but i want to konw if there is packages can carry on "individual differences scaling" and "multidimensional analysis og preference"?both method are important one,but i can not find any clue on how to do it using R. anyone can help? thank you!

I have a function for plotting soil texture that I am having a problem with. The function is: plot.psd <- function(sand, clay, ...) { conv.ter <- function(x, y) { x.con <- 100 - x - y*cos(1/3*pi) y.con <- y*sin(1/3*pi) data.frame(x=x.con, y=y.con) } plot(conv.ter(sand, clay), xlim = c(0,100), ylim = c(0,100*sin(1/3*pi)), axes = FALSE, xlab="",

Dear List: I have a question regarding an MDS procedure that I am accustomed to using. I have searched around the archives a bit and the help doc and still need a little assistance. The package isoMDS is what I need to perform the non-metric scaling, but I am working with similarity matrices, not dissimilarities. The question may end up being resolved simply. Here is a bit of substantive

Hi, I am trying to create 3 mds plots: one with axis 1 vs axis 2, one with axis 2 vs axis 3, and one with axis 1 vs axis 3. When inputting my code, I only end up with one diagram and when inputting mdsg.mds$dims, the program returns 2 for 2 dimensions. How can I create the other two plots? Any help would be greatly appreciated, Calla Carbone The table I use is number of each taxa on each

Dear all, I'm completely new to R and at first I must say that it is a great program! But I have a problem with the function isoMDS from the MASS package. I have this code which I load with source() from a file: x <- c(163.59514923926784, 150.01448475257115, ...... {here are some more values}) x.sort <- sort(x) x.dist <- dist(x.sort) library(MASS) x.mds <- isoMDS(x.dist)

Hi all, I am working on a filled contour plot which shows a triangular matrix data set (as shown below). Is there a possibilty to draw a triangular filled contour in a equilateral triangle (like a ternary plot)? Thanks in advance Johannes http://n4.nabble.com/file/n1557386/Bild3.png -- View this message in context: http://n4.nabble.com/Triangular-filled-contour-plot-tp1557386p1557386.html