Re: [R] how to reduce stress value in isoMDS?

2008-09-04 Thread stephen sefick
no I mean maybe use a higher dimension solution- the other thing you may wish to check out is package vegan which has an mds function and very good viginettes, and is my favorite package for doing ordination analysis (metaMDS uses isoMDS). hope this helps On Wed, Sep 3, 2008 at 9:03 PM, 陈武

Re: [R] how to reduce stress value in isoMDS?

2008-09-03 Thread Prof Brian Ripley
There is still no call to isoMDS in your code, and nothing we can reproduce. It all depends on the dissimilarity matrix you have not given us: maybe there is no good 2D representation of it. Looks like you need to ask a local expert about what you are doing, for this is a statistical and

Re: [R] how to reduce stress value in isoMDS?

2008-09-03 Thread 陈武
haha...wrong code again, it's isoMDS not sammon in the 5th line. Thanks for Victor Lemes Landeiro's and Brian D. Ripley's advice. ÔÚ08-9-3£¬Prof Brian Ripley [EMAIL PROTECTED] дµÀ£º There is still no call to isoMDS in your code, and nothing we can reproduce. It all depends on the

Re: [R] how to reduce stress value in isoMDS?

2008-09-03 Thread stephen sefick
different dimensions? On Wed, Sep 3, 2008 at 8:13 AM, 陈武 [EMAIL PROTECTED] wrote: haha...wrong code again, it's isoMDS not sammon in the 5th line. Thanks for Victor Lemes Landeiro's and Brian D. Ripley's advice. ÔÚ08-9-3£¬Prof Brian Ripley [EMAIL PROTECTED] дµÀ£º There is still no call to

Re: [R] how to reduce stress value in isoMDS?

2008-09-03 Thread 陈武
No, the two dimensions are the same. It's a dissimilarity matrix in the txt file. data[x][x]=0 data[x][y]=data[y][x] and 0=data[x][y]=1. 2008/9/3, stephen sefick [EMAIL PROTECTED]: different dimensions? On Wed, Sep 3, 2008 at 8:13 AM, 陈武 [EMAIL PROTECTED] wrote: haha...wrong code

[R] how to reduce stress value in isoMDS?

2008-09-02 Thread 陈武
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,end=2008, frequency

Re: [R] how to reduce stress value in isoMDS?

2008-09-02 Thread 陈武
Sorry, wrong code. The right one here: library(MASS) cl-read.table(e:/data.txt,header=T,sep=,) row.names(cl)-colnames(cl) cm-as.matrix(cl) loc-sammon(cm) jpeg(filename=e:/plot.gif,width = 480, height = 480, units = px, pointsize = 12, quality = 75, bg = white, res = NA, restoreConsole = TRUE)