Displaying 20 results from an estimated 2000 matches similar to: "various ordinations"
2000 Aug 28
0
R: various ordinations
-----Messaggio originale-----
Da: Michael Camann <camann at babylon.cnrs.humboldt.edu>
A: r-help at stat.math.ethz.ch <r-help at stat.math.ethz.ch>
Data: marted? 22 agosto 2000 21.02
Oggetto: [R] various ordinations
>Colleagues,
>
>I'm developing a library of functions for community ecology analyses and
>have a couple of questions that I've not been able to answer
2002 Jul 24
0
[R] Free Software Application for UNIX/Linux and Microsoft Windows
Dear Michael Camann,
My concern was after having a hetero-computing environment for many years, I
found that I had to keep an old version of Microsoft Windows based
applications to be able to interact with my constituents. This at times can
become very expensive. I have had to limit my budget on the UNIX/Linux
platform to compensate for Microsoft Windows based applications.
With Open Office
2002 Jul 24
0
[R] Free Software Application for UNIX/Linux and Microsoft Windows (PR#1827)
Dear Michael Camann,
My concern was after having a hetero-computing environment for many years, I
found that I had to keep an old version of Microsoft Windows based
applications to be able to interact with my constituents. This at times can
become very expensive. I have had to limit my budget on the UNIX/Linux
platform to compensate for Microsoft Windows based applications.
With Open Office
2001 Feb 16
12
canonical correspondence analysis
Is there an R function that does canonical correspondence analysis. Can
it be done using the VR function corresp()?
If not, how hard it be to write R code to do it? I am a population
biologist with long but patchy programming experience in C, Smalltalk,
Java and other languages.
Thanks,
Patrick Foley
patfoley at csus.edu
1999 Aug 02
2
zero replacement
AARRGGHH! Sometimes it's the simple things that are particularly frustrating,
especially late at night....
Can anyone suggest a simple means for replacing all of the zero values in a
matrix with NANs? I ended up writing an awk script to massage the input file,
which works, of course, but is rather an inelegant blunt instrument. I'd
prefer an R operation. I'm certain that
2000 Feb 22
1
identify() output doesn't print
Hope this isn't a faq, but....
I'm using R 0.99 for Windows under Win98. When I label points in a scatterplot
with identify(), the labels appear as expected on the graphics device, but do
not print when I select the printer icon. The scatter plot itself prints just
fine-- only the output from identfy() is missing. Can anyone offer any hints?
--Mike C.
2002 Feb 15
1
exact inference tests
R-community--
Is there a contributed package (or does anyone have code otherwise) for
exact inference tests and resampling statistics ala' StatExact? I've
perused the package descriptions on CRAN and didn't see anything, but
since several contain many functions, I thought perhaps I'd ask.
--Mike C.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Michael
2002 Jun 09
1
rw-patched destiny
R-devel team--
Will the patches that Brian Ripley has posted be rolled into the main
R-win distribution on CRAN? I ask because I'm going to be using R in one
of my ecology courses during fall semester, and although I'll probably
give the students a CD with R and a variety of other tools bundled onto
it, I'll also tell them where to upgrade and look for additional
packages and other
2001 Nov 13
1
rarefaction variance
Here's a question for ecologists on the r-help list-- I'm addressing this
to ecologists in particular because they're most likely to be familiar
with the equation in question but I'll be happy to discuss the problem
with anyone who's willing to take a whack at it.
I'm trying to write a function to calculate the large sample variance of
species richness estimates by
2002 Jun 02
2
R 1.5.0 printing problems on Win98?
Colleagues--
I'm having a problem upgrading to R 1.5.0 on a Windows 98 computer. The
windows() graphics device seems to behave strangely. A call to windows()
opens an active graphics device, as does a call to a plotting function,
e.e. plot(1:5,1:5). So far so good. When I click on the Printer icon
(with the graphics device active) nothing happens. Likewise when I use
win.print() from the
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 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 <-
2003 Mar 27
5
Plot of Canonical Correlation Analysis
Dear all,
I didn't find any graphical solution in the package "mva" to plot the
canonical scores from a CCA (canonical correlation analysis).
Does anybody knows how to plot or has anybody already programmed :
- the map of the canonical scores,
- the graph of the canonical weights,
- the correlation circle i.e. the canonical loadings ?
Thank you for help ...
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
2005 Jun 28
2
enhanced MDS
Hi again
Sorry, in looking again at sammon and isoMDS I see that they seem to do
exactly what I want, except that they are non-metric, which means, as I
understand it, that they relate the rank orders of the variables rather than
the actual distances.
Could I use these non-metric MDS packages even if my distances are metric?
Thanks
Karen
--
Karen Kotschy
Centre for Water in the Environment
2008 Apr 18
2
Correspondence and detrended correspondence analysis
Hi,
I hope someone knows the answer to this or has a real good reference about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package.
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 large data sets with a high
2010 Jan 06
1
math function - MDS method
Hi,
I need math function which is used in: isoMDS, Sammon and metaMDS method.
Anybody know where I may find it? Any manual or webside?
I would be very happy
Thanks a lot !
--
View this message in context: http://n4.nabble.com/math-function-MDS-method-tp1008294p1008294.html
Sent from the R help mailing list archive at Nabble.com.
2004 Mar 26
2
Fwd: MDS problems [ajtee@ajtee.uklinux.net]
Hi all,
I'm trying to perform an MDS of some data that I have. When I use
cmdscale everything is fine and I get some interesting results however,
the tends to be low.
What I wnat to do is compare this with the Non-Metric MDS using isoMDS
or sammon. However, when I try using these I get the following message.
Error in isoMDS(x.dist) : zero or negative distance between objects 2
and 4
2008 Sep 04
2
isoMDS and dist
I am starting with a matrix in which rows are vegetation 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