search for: isomds

Displaying 20 results from an estimated 89 matches for "isomds".

2006 Apr 19
3
isoMDS and 0 distances
Hi, I'm trying to do a non-metric multidimensional scaling using isoMDS. However, I have some '0' distances in my data, and I'm not sure how to deal with them. I'd rather not drop rows from the original data, as I am comparing several datasets (morphology and molecular data) for the same individuals, and it's interesting to see how much morpholo...
2004 Sep 08
8
isoMDS
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 background. I am working on a technique where individuals organize items based on how similar they perceive...
2007 Feb 13
4
isoMDS vs. other non-metric non-R routines
Dear useRs, last week I asked you about a problem related to isoMDS. It turned out that in my case isoMDS was trapped. Nonetheless, I still have some problems with other data sets. Therefore I would like to know if anyone here has experience with how well isoMDS performs in comparison to other non-metric MDS routines, like Minissa. I have the feeling that for...
2016 Apr 25
1
how to create initial configuraton for isoMDS
Hi, I'm trying to use isoMDS to project a directed graph to 2-dim vectors, but I got an error. #here is the code to create the graph using igraph package and run isoMDS on it. library(igraph) library(MASS) g<-make_graph(c(1,2, 2,3, 2,4, 3,4, 4,5, 5,6, 3,6, 1,6, 2,5),directed=TRUE) dist<-distances(g, mode="out"...
2004 Apr 12
1
question on isoMDS
Hello everyone, I have a question on isoMDS. My data set (of vegetation) with 210 samples is in this way: Rotfoehrenau Lavendelweidenau Silberweidenau .... 067_Breg.7 0 2 0 .... 071_Dona.4 0 2 6 .... ... I want to do an isoMD...
2008 Feb 20
1
Stress with MDS
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 "cmdscale" we get eigen values. What is the best way to choose optimal...
2008 Sep 04
2
isoMDS and dist
...tion plots and columns are various characteristics including ID# and elevation. I removed elevation and ID columns to avoid having those characteristics influence the distances between points which I calculated using the "dist" command. The resulting distance file was then used in isoMDS. What I want to know is whether I can reattach the ID and elevation onto the point location information given from isoMDS? or is it possible that the order given in the isoMDS output is not the same as the order of the original data used to calculate distances? Thanks, Carrie Pucko Universi...
2001 Oct 12
1
MASS: isoMDS and sammon
If tbl is an object of class 'dist', you can do this: a <- sammon(tbl, k=3) But you can't do this: b <- isoMDS(tbl, k=3) Wouldn't it be sensible to have identical interfaces to sammon() and isoMDS() ? I think all that would be needed is to change this: isoMDS <- function(d, y=cmdscale(d, 2), maxit=50, trace=TRUE) { ...into this: isoMDS <- function(d, y, k=2, maxit=50, trace=TRUE) {...
2007 Jun 01
1
Beginners Question
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) plot(x.mds$points, type="n") tex...
2009 Aug 30
1
about isoMDS method
Hi, For example: I built a half matrix "w" using a daisy(x, metric = c("euclidean")) http://www.nabble.com/file/p25211016/1.jpg And next I transformed this matrix "w" using isoMDS function, for example isoMDS(w, k=2) and as result I got: http://www.nabble.com/file/p25211016/2.jpg And now I have two questions: 1. If number in matrix w[2, 1] (= 0.41538462) match two points (below) in matrix created by isoMDS [1,1:2] and [2,1:2] ? http://www.nabble.com/file/p25211016/3.jpg...
2008 Sep 01
1
why isoMDS not found?
When I type "isoMDS()" in the R environment, a error shows up: no such function "isoMDS". Why? And what should I do to use isoMDS? Additionally, I cannot install add-on packages. Typing "Rcmd.exe INSTALL e:/VR_7.2-44.zip" results in "'perl' is neither command nor executable file.....
2003 Apr 14
1
isoMDS and stress
Hi all, I try to calculate the stress of a configuration using the formula in the isoMDS help, but I don't have the same result than the stress returned by isoMDS : > library(mva) > library(MASS) > data(swiss) > swiss.x <- as.matrix(swiss[,-1]) > swiss.dist <- dist(swiss.x) > swiss.mds <- isoMDS(swiss.dist) initial value 2.979731 iter 5 value 2.43148...
2014 Nov 06
1
limit of cmdscale function
Hi We have a few questions regarding the use of the "isoMDS" function. When we run "isoMDS" function using 60,000 x 60,000 data matrix, we get the following error message: ------------------------------------ cmdscale(d, k) : invalid value of 'n' Calls: isoMDS -> cmdscale ------------------------------------ We checked the sour...
2001 Dec 18
2
isoMDS: core dump (PR#1221)
I'm not sure this belong here... Package: MASS Version: 6.2-8 I get a core dump when I call isoMDS with an incorrect argument for y. With d as an object of class "dist": > isoMDS(d,2) Program received signal SIGSEGV, Segmentation fault. 0x40229e43 in VR_mds_init_data () at MASS.c:157 --please do not edit the information below-- Version: platform = i586-pc-linux-gnu arch...
2006 Oct 21
1
Problems running IsoMDS using vegdist with pres-abs data and two sites with zero distance
...fish dataset with 28 sites and 18 species. When trying to follow the Vegan manual to run nmds from distance measures calculated by the vegdist function it turns out that I have two sites (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an error message saying that: Error in isoMDS(vare.dis) : zero or negative distance between objects 14 and 15 i.e. the two sites with the same fish species. I can run the decorana function with "sensible" results so the dataset seems to be ok. My next step would be to compare the...
2003 Mar 25
0
isoMDS results
...to reproduce the results, please contact me directly to get the data. (First mail, rejected:) > Attached there is a 149*149 dissimilarity matrix; it is a file obtained by > save(dm,file="dissim.Rsav"). OK, here is my question: I worry about the reproducability of the results of isoMDS. I try > set.seed(5678) > mdslinux <- isoMDS(dm,k=4) initial value 31.071976 final value 31.071976 converged > R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status...
2008 Sep 03
1
how to reduce stress value in isoMDS?
I apply isoMDS to my data, but the result turns out to be bad as the stress value stays around 31! Yeah, 31 ,not 3.1... I don't know if I ignore something before recall isoMDS. My code as follow: m <- read.table("e:/tsdata.txt",header=T,sep=",") article_number <- ts(m, start = 2004,...
2009 Feb 10
2
Problem installing MASS-Package
Dear R-Help-Team, I tried to use isoMDS-Function of the MASS-Package: Message: Fehler: konnte Funktion "isoMDS" nicht finden (error: could not find function "isoMDS") so I tried to install the package MASS: > utils:::menuInstallPkgs() versuche URL 'http://cran.rakanu.com/bin/windows/contrib/2.8/VR_7.2-45.zip...
2000 Feb 29
0
Reading the documentation (was isoMDS error message!!!)
...[Mail to your address is undeliverable!!!] > I do this > > > valumod<-read.table("valu-medie.txt",header=T) > > library(mass) > > library(mva) > > valumod.x <- as.matrix(valumod) > > valumod.dist<-dist(valumod.x) > > valumod.mds <- isoMDS(valumod.dist) > Error in isoMDS(valumod.dist) : zero or negative distance between objects 2 and 4 It means that rows 2 and 4 of valumod.x are identical. > Where is the error? isoMDS is from package MASS, and there is an example of this, the reason for it and the workaround on page 334 of...
2010 May 25
2
Calculation time of isoMDS and the optimal number of dimensions
Dear all, I'm running a set of nonparametric MDS analyses, using a wrapper for isoMDS, on a 800x800 distance matrix. I noticed that setting the parameter k to larger numbers seriously increases the calculation time. Actually, with k=10 it calculates already longer than for k=2 and k=5 together. It's now calculating for 6 hours, and counting... There is quite a difference betwee...