Displaying 20 results from an estimated 3000 matches similar to: "From Distance Matrix to 2D coordinates"
2004 Feb 26
2
Multidimensional scaling and distance matrices
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
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 source code of "cmdscale" and
2001 Dec 13
2
k-means with euclidian distance but no coordinates
Hi,
I'm trying to build a thesaurus that will sensible values for rare words.
I suspect the best algorithm to use is k-means although I'm not sure about
that -- I would have preferred a k dimensional space with a binary cluster
in each dimension so a word can belong to 0..k clusters, but I digress...
I can measure the strength of correlation between words fairly easily by
counting
2012 Mar 23
1
Memory limits for MDSplot in randomForest package
Hello,
I am struggling to produce an MDS plot using the randomForest package
with a moderately large data set. My data set has one categorical
response variables, 7 predictor variables and just under 19000
observations. That means my proximity matrix is approximately 133000
by 133000 which is quite large. To train a random forest on this large
a dataset I have to use my institutions high
2011 May 18
3
Help with 2-D plot of k-mean clustering analysis
Hi, all
I would like to use R to perform k-means clustering on my data which
included 33 samples measured with ~1000 variables. I have already used
kmeans package for this analysis, and showed that there are 4 clusters in my
data. However, it's really difficult to plot this cluster in 2-D format
since the "huge" number of variables. One possible way is to project the
2002 Apr 19
4
Multidimensional scaling
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
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 morphological
variation can be
2005 Jun 28
1
enhanced multidimensional scaling?
Dear R list
Would anyone be able to tell me whether it is possible to do "enhanced
multidimensional scaling" (enhanced MDS) in R? In other words, something that
goes beyond "cmdscale" by iteratively improving the fit between observed
dissimilarities and inter-object distances, using the KYST algorithm
(Kruskal, 1964).
I have found several implementations of non-metric MDS
2011 Apr 02
3
Plotting MDS (multidimensional scaling)
Hi,
I just encountered what I thought was strange behavior in MDS. However, it
turned out that the mistake was mine. The lesson learned from my mistake is
that one should plot on a square pane when plotting results of an MDS. Not
doing so can be very misleading. Follow the example of an equilateral
triangle below to see what I mean. I hope this helps others to avoid this
kind of headache.
2007 Jun 14
2
Difference between prcomp and cmdscale
I'm looking for someone to explain the difference between these
procedures. The function prcomp() does principal components anaylsis,
and the function cmdscale() does classical multi-dimensional scaling
(also called principal coordinates analysis).
My confusion stems from the fact that they give very similar results:
my.d <- matrix(rnorm(50), ncol=5)
rownames(my.d) <-
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
2005 Jun 22
2
PCA and MDS
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
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
2013 Mar 24
3
Parallelizing GBM
Dear All,
I am far from being a guru about parallel programming.
Most of the time, I rely or randomForest for data mining large datasets.
I would like to give a try also to the gradient boosted methods in GBM,
but I have a need for parallelization.
I normally rely on gbm.fit for speed reasons, and I usually call it this
way
gbm_model <- gbm.fit(trainRF,prices_train,
offset = NULL,
misc =
2019 Jul 09
3
[R] Curl4, Quantmod, tseries and forecast
Hi Ralf,
I tried the following
> install.packages("RCurl")
which went OK, but then same story when I tried to install tseries.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK:
2013 Feb 09
3
Addressing Columns in a Data Frame
Dear All,
Probably a one liner, but I am banging my head against the floor.
Consider the following
DF <- data.frame(
x=1:10,
y=10:1,
z=rep(5,10),
a=11:20
)
mn<-names(DF)
but then I cannot retrieve a column by doing e.g,
DF$mn[2]
I tried to play with the quotes and so on, but so far with no avail.
Any suggestion is welcome.
Cheers
Lorenzo
2007 Jan 07
3
MDS in 3D
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
2009 Jul 20
3
Histograms on a log scale
Dear All,
I would like to be able to plot histograms/densities on a semi-log or
log-log scale.
I found several suggestions online
http://tolstoy.newcastle.edu.au/R/help/05/09/12044.html
https://stat.ethz.ch/pipermail/r-help/2002-June/022295.html
http://www.harding.edu/fmccown/R/#histograms
Now, consider the code snippet taken from
http://www.harding.edu/fmccown/R/#histograms
# Get a random
2007 Aug 08
2
Relocating Axis Label/Title --2
Apologies for the previous mail (I sent it off too early by mistake).
This is the correct example:
rm(list=ls())
D_mean<-seq(-5,5,length=100)
y<-exp(-D_mean^2/5)
pdf("my.pdf")
plot(D_mean,y,type="l",yaxt="n",lty=2,lwd=2,col="black",
ylab = list(expression(paste(dN/dlogD[agg]," ["*cm^-3*"]"))),
xlab = expression(paste(D[agg],"
2012 Nov 14
3
reversing distance matrix for original values
dear useRs,
i created a distance matrix, of certain voltage values. unfortunately, i lost the original values. i am only left with the distance matrix that i created from those values. i wanted to ask that is there a way in R to reverse distance matrix for the original values?
thanks in advance
eliza
[[alternative HTML version deleted]]