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 via faqs or
docs.
1) Are there existing functions for:
a) Bray-Curtis (polar) ordination?
b) non-metric multidimensional scaling (NMDS)?
c) canonical correlation analyses (CCA and DCA)?
d) TWINSPAN (doubtful...)?
2) If not, does anyone have these functions already?
3) I'm having difficulty figuring out how to dyn.load C object files in a
windows environment, which I admittedly know little about. I'm using the
Cygwin/Gnu compiler, no difficulty compiling or (I think) producing
.dll's, but I always get an error when I try to dyn.load the .dll's that
says a file is missing. Sorry, I can't reproduce the exact error mesg
from this machine, so let me know if it's critical-- nonetheless the mesg
is something to the effect that an important file is missing. I'm running
R 1.0, so if this is a version problem it'll go away when I update, any
day now.... As the text above suggests, I'm also not entirely certain
that I'm producing the .dll's correctly and the 1.0.0 win-faq is a bit
vague on
this point. Could someone familiar with this please post brief
instructions or reply directly? I didn't see anything in the (recent) help
archives.
Unfortunately, I will need to work this in a MSWindows environment in
order to coordinate with the University's computing platforms. I can post
code fragments, compiler output, and R output later if necessary, but I
thought it might be more useful to insure that I understand the process
fully before cluttering the list further.
Thanks!
--Mike C.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Michael A. Camann Voice: 707-826-3676
Assistant Professor of Zoology Fax: 707-826-3201
Institute for Forest Canopy Research Email: mac24 at axe.humboldt.edu
Department of Biology ifcr at axe.humboldt.edu
Humboldt State University
Arcata, CA 95521
URL:http://www.humboldt.edu/~mac24/camann.html
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On Mon, 21 Aug 2000, Michael Camann wrote:> 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 via faqs or > docs.Not the actual shipped docs, though!> 1) Are there existing functions for: > > a) Bray-Curtis (polar) ordination? > b) non-metric multidimensional scaling (NMDS)?sammon and isoMDS in package MASS> c) canonical correlation analyses (CCA and DCA)?cancor in package mva> d) TWINSPAN (doubtful...)? > > 2) If not, does anyone have these functions already? > > 3) I'm having difficulty figuring out how to dyn.load C object files in a > windows environment, which I admittedly know little about. I'm using the > Cygwin/Gnu compiler, no difficulty compiling or (I think) producing > .dll's, but I always get an error when I try to dyn.load the .dll's that > says a file is missing. Sorry, I can't reproduce the exact error mesg > from this machine, so let me know if it's critical-- nonetheless the mesg > is something to the effect that an important file is missing. I'm running > R 1.0, so if this is a version problem it'll go away when I update, any > day now.... As the text above suggests, I'm also not entirely certain > that I'm producing the .dll's correctly and the 1.0.0 win-faq is a bit vague on > this point.Well, how can we anticipate all your (the users') mistakes! You have not used the recommended compiler, nor told us anything about how you did this! The instructions are *not* in the `1.0.0 win-faq'!! Please update to 1.1.1 before doing anything else, as the availability of tools has changed in the last 6 months. Messages that important files are missing are critical! That's why our toolset provides pedump.exe for you to check dependencies. You may be able to solve this just by supplying the missing file.> Could someone familiar with this please post brief > instructions or reply directly? I didn't see anything in the (recent) help archives.Please read readme.packages which has the most detailed instructions, then follow them. If you are really using Cygwin/Gnu, yes an important file cygwin1.dll will be missing unless you used the -mno-cygwin flag and have one of the rare downloads in which it actually all works. That they are rare is why we do not recommend this combination. Advice: start again and follow the instructions to the letter. Then there is some chance we can help you if you can supply a useful problem report. That means getting version 2.95.2.1 of the mingw32 compiler and the tools at www.stats.ox.ac.uk/pub/Rtools .... It really is frustrating to spend time writing the instructions and keeping them up to date in a rapidly changing scene, and then to receive such a vague report about an old version (there have been three since). The FAQ has important information on preparing a problem report. -- 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 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
camann at babylon.cnrs.humboldt.edu said:> 1) Are there existing functions for: > a) Bray-Curtis (polar) ordination? > b) non-metric multidimensional scaling (NMDS)? > c) canonical correlation analyses (CCA and DCA)? > d) TWINSPAN (doubtful...)?There is not (yet:) a vegetation analysis package in R, and from the wording above I guess this is what was needed. A few notes: 1a) Would be trivial to write in its basic form (perhaps more complicated with enhancements ? la Bruce McCune), but is not worth of trying: You should let this method rest in peace. 1b) Venables & Ripley (mainly latter, I guess) have MDS packages in the MASS library. Some people claim that isoMDS is a bit too easily trapped into local optima, but I am not sure. sammon might be worth trying, since it is more local in its configuration whereas isoMDS is the old-fashioned global gradient space methods. However, you have to write up your similarity measures, since the standard choices in R are not the preferred in vegetation analysis. Another problem is that the detection of convergence to global optimum is a bit hard work in R, since there are no ready tools for this (although there are ready components for these tools). 1c) As you write `CCA', I guess you mean actually canonical *correspondence* analysis: Nothing like that is available in R, whereas canonical correlation analysis is in `cancor' (package `mva'). This `cancor' is a bit like RDA in vegetation ecology jargon, but I am afraid it regards most vegetation data sets as ill defined. 1c-d) DCA and TWINSPAN are not available. However, their "BSD style" licence would allow incorporation into R. I know of one person in GRASS (GIS) development team who is writing a pluggable module of TWINSPAN, and I hope he makes it so that it can be incorporated into R with minor modifications. It would not be too hard to modify these programs so that you can have them in R, but I am now too busy to try this (and the current version of my GNU Fortran compiler produces broken shared libraries, and I haven't seen the trouble of upgrading yet). I think that basically TWINSPAN and DCA are sick, and therefore I haven't given a high priority for these jobs. So I recommend warmly isoMDS and sammon, and as an alternative to TWINSPAN, the numerous cluster analysis methods. cheers, jari oksanen -- Jari Oksanen - Dept Ecol Env Sci, Univ Helsinki, 15140 Lahti Ph. +358 3 89220312, Fax -- 89220289, Mobile +358 40 5136529 jari.oksanen at helsinki.fi http://www.helsinki.fi/~jhoksane -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._