Displaying 20 results from an estimated 700 matches similar to: "I: results from sammon()"
2005 Apr 20
4
results from sammon()
Dear all,
I'm trying to get a two dimensional embedding of some data using different
meythods, among which princomp(), cmds(), sammon() and isoMDS(). I have a
problem with sammon() because the coordinates I get are all equal to NA.
What does it mean? Why the method fails in finding the coordinates? Can I do
anything to get some meaningful results?
Thank you very much
Domenico
2001 Nov 01
1
Erratic behaviour of sammon()
I'm not sure this list is the right place for this thing.
I noticed some erratic behaviour in sammon(). Running sammon on
two nearly identical sets of data results in very different
results. Below is an example. I create an initial configuration
with cmdscale() and store it into 'vec1'. I write this to file,
and read it back in again to 'vec2'. According to cor() on the
three
2004 Jun 14
1
error running sammon
Hello,
I am inputing a 17 x 17 symetric matrix to sammon. The matrix is a co-occurance matrix with no missing data. If this is at all relevant, running hclust on this matrix works.
> samx <- sammon(q23axproduct)
I receive the following error:
Error in sammon(q23axproduct) : initial configuration must be complete
In addition: Warning messages:
1: some of the first 2 eigenvalues are
2006 Jan 30
1
Varying results of sammon(), for the same data set
Hello,
I have a data set on which I run the sammon algorithm as follows:
library(MASS)
data = read.table('problemforr.dat')
y = cmdscale(data, add=TRUE)
s = sammon(data, y$points)
(In case it should be relevant, I make the data available at
http://idi.ntnu.no/~edsberg/problemforr.dat)
With R 2.2.1 on Debian Sid I always get one of two solutions (stress
1.74288 after 10 iterations or
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 <-
2005 Oct 10
1
details about lm()
Dear all,
I'd like to get a linear regression of some data, and impose that the line
goes through a given point P. I've tried to use the lm() method in the
package "stats", but I wasn't able to specify the coordinates of the point
P. Maybe I should use another method?
I also have another question: How does lm() choose the point through which
the output straight line goes in
2002 Jul 30
3
Error running sammon() in multiv package
When I try to run the "sammon" function of the multiv package, I always get
this error message:
Error in as.vector(dist(a)) : couldn't find function "dist"
It happens even with example(sammon). I am running R 1.5.0 on Win98 and I
have still installed R 1.4.1 but it doesn't work on the old R version with
the older multiv package either. Is there a problem with the
2010 May 28
0
error in sammon (duplicates in configuration)
Dear members of R-mailing list,
I am using Sammon's Non-Linear Mapping in R as implemented in MASS
package. I have two distance matrices (attached with the mail).
For the first (/5HT_MACCS_dist.dat/) /sammon()/ works fine but for the
second (/5HT_TGT_dist.dat/), I get an error message "configuration has
duplicates". I checked both the matrices for duplicate values using/
2005 Sep 20
1
Shy Suggestion?
The R-exts manual says about 'Suggests' field in package DESCRIPTION:
"The optional `Suggests' field uses the same syntax as `Depends' and
lists packages that are not necessarily needed."
However, this seems to be a suggestion you cannot refuse. If you suggest
packages:
(a line from DESCRIPTION):
Suggests: MASS, ellipse, rgl, mgcv, akima, lattice
This is what happens:
2005 May 04
1
MacOS X: update.packages(type="mac.binary") fails (PR#7834)
Dear Mr Moderator, please let me through. I want to reply to my own
thread. I once subscribed to this list, but then my subscription was not
accepted.
Now to the business:
The final failure came from missing .install.macbinary() function. I
grepped R-patched sourcesand the only instance of .install.macbinary()
was the call to the function in R-
patched/src/library/utils/R/packages2.R (stupid
2001 Oct 02
1
Graceful exit from fortran. (fwd)
rolf at math.unb.ca said:
> If I say something like
> if(x .gt. 42.d0) stop
> then indeed everything stops, i.e. R falls over. I'd ***like*** to be
> able to print out an informative error message (which I guess could be
> done -
In Fortran:
subroutine foo(..., ier)
integer ier
ier=0
...
if (x .gt. 42.d0) then
ier=1
return
endif
2001 Mar 05
1
Canberra dist and double zeros
Canberra distance is defined in function `dist' (standard library `mva') as
sum(|x_i - y_i| / |x_i + y_i|)
Obviously this is undefined for cases where both x_i and y_i are zeros. Since
double zeros are common in many data sets, this is a nuisance. In our field
(from which the distance is coming), it is customary to remove double zeros:
contribution to distance is zero when both x_i
2001 Mar 05
1
Canberra dist and double zeros
Canberra distance is defined in function `dist' (standard library `mva') as
sum(|x_i - y_i| / |x_i + y_i|)
Obviously this is undefined for cases where both x_i and y_i are zeros. Since
double zeros are common in many data sets, this is a nuisance. In our field
(from which the distance is coming), it is customary to remove double zeros:
contribution to distance is zero when both x_i
2005 Aug 31
1
Why should package.skeleton() fail R CMD check?
I find it a bit peculiar that a package skeleton created with a utils
function package.skeleton() fails subsequent R CMD check. I do
understand that the function is intended to produce only a skeleton that
should be edited by the package author. I think that it would be
justified to say that the skeleton *should* fail the test. However, I
have two arguments against intentional failure:
* When you
2007 May 15
0
step in Sweave
Dear peRsons,
I have a Sweave document which demonstrates the usage of step()
function. With current R version 2.5.0 the step() function was changed
so that the heading of trace=TRUE output for each model is printed using
command message():
if (trace)
message("\nStep: AIC=", format(round(bAIC, 2)),
"\n",
2007 May 09
1
step() in sink() and Sweave()
Dear developers,
I just noticed that step() function currently prints the current model
using message(), but the resulting model using print(). The relevant
commands within the step() body are:
if (trace) message("Start: AIC=", format(round(bAIC, 2)), "\n",
cut.string(deparse(as.vector(formula(fit)))), "\n")
(with example() output:)
Start: AIC=190.69
2002 Nov 12
2
Wandering usr values in par(no.readonly=TRUW) (PR#2283)
--==_Exmh_1801894504P
Content-Type: text/plain; charset=us-ascii
Dear R folks,
Initially I had a plotting routine using logarithmic y-axes that failed after
repeated calls if I tried to restore the graphical parameters (which I wanted to
do because I used `layout' within the routine. I tried to isolate the problem
and found out that the following code with logarithmic axis is sufficient for
2004 Apr 16
2
Masked help page
Hi list,
not really a problem to solve but a strange unwanted behavior (at least I
do not like it):
I'm loading
library(multiv)
to use sammon.
Later I load
library(MASS)
which tells me that sammon is masked now, because
there is also a MASS version of sammon.
Since I believe that the MASS version is at least as good as the multiv
version, I would also use the MASS version, but
help(sammon)
2002 Oct 30
4
Sweave in packages
Dear R folks,
One of the fantastic new tools in R is `Sweave'. I have tested it so much that I
know it works and produces fine documentation, and with (GNU) Emacs/ESS it is
nice to work with, too. I started to have a look at including some Swoven (is
that a strong verb?) documentation with my R package, but it seems that there is
no model to copy among those packages that I have installed in
2003 Oct 07
0
NaN values returned by cmdscale
Hello all,
I'm using R1.7.1 on Linux, generating sammon-optimized MDS plots from
distance matrices. This is a calculation I run routinely, often on
sample sets of up to 100 samples. This time, with three samples, the
sammon function returned an error (shown below), which I tracked down to
the cmdscale function it uses to find a starting configuration. In
short, cmdscale is returning NaN