Sorry for not translating, misspackaging (MASS) and not reading
properly (zerodist).
I would like to implement the weighting in distance()
foo <- function(x, method, ...)
as.dist(distance(x = x, method = method,
weights=vectorname))
This seems to work but it would be much more elegant if I could call
the weighting in metaMDS.
Is that the right way:
foo <- function(x, method,weights, ...)
as.dist(distance(x = x, method = method,
weights=weights))
metaMDS(train, distance = "mixed", distfun = foo,
weights=vectorname)
Thanks again for help.
Birgit
And again
Am 15.05.2008 um 13:41 schrieb Gavin Simpson:
On Thu, 2008-05-15 at 13:13 +0200, Birgit Lemcke wrote:
Hello R-user community!
I am running R 2.7.0 on a Power Book (Tiger). (I am still R and
statistics beginner)
Presently I try to run the function metaMDS (vegan) using an existing
dissimilarity-matrix.
The help for metaMDS explicitly says that you can't do this; that is
what the error message says. (which would have been better if
translated
into English so I didn't have to resort to reading the sources to see
what the error meant).
As I would like to start with this matrix I thought I could just give
the matrix using the x= -argument
Test<-metaMDS(x=Dist.Gower)
Fehler in inherits(comm, "dist") : Argument "comm" fehlt (ohne
Standardwert)
But obviously that is not the way it works.
It is not immediately obvious to the new user how to get this to work
where the distance function is not vegdist. (Jari or I should possibly
look to see if we can get metaMDS to work when a dissimilarity
matrix is
present - although writing a simple wrapper that works is quite
easy, so
maybe we just need an example?) This is compounded by the fact
that, by
design, analogue:::distance returns the full dissimilarity matrix (I
should look to rectify that!)
A solution is the following wrapper:
foo <- function(x, method, ...)
as.dist(distance(x = x, method = method))
which creates a new local wrapper to distance that includes an
explicit
call to as.dist().
We then call metaMDS like so, using the simple example dataset 'train'
from ?distance:
train <- data.frame(matrix(abs(runif(200)), ncol = 10))
rownames(train) <- LETTERS[1:20]
colnames(train) <- as.character(1:10)
metaMDS(train, distance = "mixed", distfun = foo)
So you see it works now.
The second problem is that it seems that I have zero distance value
between some objects what causes a problem in isoMDS (vegan)
Test<-isoMDS(Dist.GowerTest) Fehler in isoMDS(Dist.GowerTest)
: zero or negative distance between objects 240 and 241
isoMDS is in package MASS, *not* vegan (credit where credit is due!)
metaMDSdist contains argument 'zerodist' to handle this situation. If
you do zerodist = "add", a small amount will be added to 0
dissimilarities. metaMDS passes arguments to metaMDSdist so you could
do:
metaMDS(train, distance = "mixed", distfun = foo, zerodist = "add")
Although be careful to understand the implications of doing this!
HTH
G
Sorry might be that I am just to stupid to understand the
documentation, but could somebody help me anyway.
Thanks in advance
B.
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
175 Jahre UZH
«staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.»
MNF-Jubiläumsevent für gross und klein.
19. April 2008, 10.00 Uhr bis 02.00 Uhr
Campus Irchel, Winterthurerstrasse 190, 8057 Zürich
Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-
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and provide commented, minimal, self-contained, reproducible code.
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
175 Jahre UZH
«staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.»
MNF-Jubiläumsevent für gross und klein.
19. April 2008, 10.00 Uhr bis 02.00 Uhr
Campus Irchel, Winterthurerstrasse 190, 8057 Zürich
Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
