how to reduce stress value in isoMDS?
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, ?? <geminiwhu at gmail.com> wrote:
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 <ssefick at gmail.com>:
different dimensions? On Wed, Sep 3, 2008 at 8:13 AM, ?? <geminiwhu at gmail.com> 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. ??08-9-3??Prof Brian Ripley <ripley at stats.ox.ac.uk> ??????
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 not an R question. On Wed, 3 Sep 2008, ???? wrote: 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)
plot(loc$points,type="p")
text(loc$points,rownames(cl),cex=1,pos=1,offset=1)
dev.off()
And "e:/data.txt" contains a 40*40 dissimilarity matrix. Thanks for
you
advices!
2008/9/3, ???? <geminiwhu at gmail.com>:
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 = 1
,names=colnames(m))
jpeg(filename="e:/tsmap.gif",width = 480, height = 480, units = "px",
pointsize = 12, quality = 75, bg = "white", res = NA, restoreConsole
=
TRUE)
plot(article_number, plot.type="single",
lty=c(1,1,1,1,1),col=c(1,2,3,4,5),las=1)
max<-range(m)
x<-c(2004,2004,2004,2004,2004)
y<-c(max[2]*0.96,max[2]*0.9199999999999999,max[2]*0.88,max[2]*0.84,max[2]*0.7999999999999999)
points(x,y,col=c(1,2,3,4,5),pch=15)
text(x,y,colnames(m),pos=4,offset=0.4)
dev.off()
A 40*40 matrix in "e:/tsdata.txt". How should I do to improve the
effect?
Thank you!
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-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis