Displaying 20 results from an estimated 3000 matches similar to: "metaMDS"
2009 Oct 06
1
previous.best in metaMDS
Dear R-community, dear Jari Oksanen!
I use metaMDS (package vegan) to calculate NMDS.
In a lot of papers I read that it is recommended to use previous best solutions as a new starting configuration to get better results and to avoid local minima.
On the help page I found that a previous.best-command is already implemented in metaMDS:
metaMDS(comm, distance = "bray", ...,plot = FALSE,
2008 Apr 11
1
Vegan plotting- color help
I have looked all over the internet for being able to color sites
differently in a plot of an MDS (metaMDS)- I would like to color the
different sites in the ordination plot (plot or ordiplot). I have set
the matrix up so that my site code is 1 .... 296 (first column). is
there a way to make 1-23 blue, 24-40 red etc.
thanks
Stephen
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2012 Jul 27
1
labeling loading vectors in vegan
Hello,
I am using vegan to do an NMDS plot and I would like to suppress the labels
for the loading vectors. Is this possible? Alternatively, how can I avoid
overlap?
Many thanks for the help.
Example code:
#perform NMDS using metaMDS() function
spe.nmds<-metaMDS(data, distance='bray',k=2 , engine = "isoMDS",
autotransform=F, trymax=1000)
#calculate the loading (i.e.,
2011 Aug 09
2
reflecting a PCA biplot
Hi Listers,
I am trying to reflect a PCA biplot in the x-axis (i.e. PC1) but am not
having much success. In theory I believe all I need to do is multiply the
site and species scores for the PC1 by -1, which would effectively flip the
biplot.
I am creating a blank plot using the plot command and accessing the results
from a call to rda. I then use the calls to scores to obtain separate site
and
2009 Oct 14
2
metaMDS NMDS: use of alternative distances?
Dear r-helpers!
How can I integrate other distances (in the form of a dist object) into function metaMDS? The problem: metaMDS needs the original data.frame for the calculation and only the default distances of function vegdist are allowed.
Any suggestions are greatly appreciated!
Thank you,
Kim
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2007 Aug 24
1
Adding new points to a metaMDS ordination ("vegan" pkg)
Hi, I've been using R for a while now but I've got a problem with
metaMDS (in the vegan package) that I can't quite figure out.
I have a set of proportion data (from 0-1, rows sum to 1) that I apply
metaMDS to using the command:
nMDS.set=metaMDS(sqrt(test.set),distance="euclidean",k=3,zerodist="add",autotransform=FALSE)
I am using a squared-chord distance
2011 May 10
3
metaMDS and envfit: Help reading output
Hello R experts,
I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were identified and counted. I ran metaMDS on this data
2008 May 15
1
metaMDS using Dissimilarity matrix
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.
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") :
2006 Nov 10
2
Problems with metaMDS from vegan
Hello all,
I recently used the Vegan library quite extensively (in the context of
text similarity assessment) on an Ubuntu 6.06 LTS system with R version
2.2.1 (2005-12-20 r36812). The Vegan lib is version 1.6-10.
I hit on a problem yesterday, though, when trying to install R and Vegan
on two further computers - one Windows XP and one further Ubuntu 6.06
machine, taking either R version 2.4.0
2011 Aug 10
1
Plotting Ellipses and Points of Matching Colors in an Ordination
Hello, R-Help -
I am trying to plot the results of an ordination from package vegan. The
tricky part for me right now is getting the colors of the ellipses denoting
the 95% confidence intervals of the group centroids to match the colors of
the points for those same groups.
>From and earlier post, I saw the code to make a plot of the ordination using
different colors for my different groups.
2009 May 27
1
vegan metaMDS question
The design decision in metaMDS says that it uses:
Minchin, P.R. (1987) An evaluation of relative robustness of
techniques for ecological ordinations. Vegetatio 71, 145-156.
This is the paper that I found by the same name. Is this the correct reference?
Minchin, Peter R.1987. An Evaluation of the Relative Robustness of
Techniques for Ecological Ordination. Vegetatio. Vol. 69, No. 1/3:
89-107.
2013 Jun 22
1
metaMDS Error, Nan similar or negative values
H
ello R-experts,
I want to do ordination plots using vegan metaMDS.
I have a where many cells have zero values.
Data structure:
X[1:10,1:14]
Height.1 Height.2 Height.3 Height.4 Height.5 Height.6 Height.7
Height.8 Height.9 Height.10 Height.11 Height.12 Height.13
D30I1A 46 0 0 0 0 0 0
0 0 0 39 0 98
D30I1B
2008 Apr 14
1
Vegan R^2 and tau values for metaMDS
I am using the function metaMDS with jaccard distances to ordinate a
set of constituent by site matrix. I can post this data if it would
be helpful, but it is large to include in an email. I can also
provide reproducable code if necessary. I would like to get an R^2
value for the axes of the ordination configuration that I get with
metaMDS in the vegan package is there a way to do this- is it
2013 May 27
1
metaMDS with large dataset produces 'insufficient data' warning
Greetings everyone,
I am running MDS on a very large dataset (12 x 25071 - 12 model runs with 25071 output values each), and also on a very much reduced version of the dataset (randomly select 1000 of the 25071 output values). I would like to look at similarities/dissimilarities between the 12 model runs. When I use metaMDS on the full dataset, I get a warning message:
Warning message:
In
2009 Sep 03
1
Confusion metaMDS and CA
Hello, I read a lot about ordination, but I am still confused... I have data
on species presence/absence for 8 different sites and I would like to
represent my species and the sites on an ordination plot to see if some
species are associated with specific sites. I used metaMDS function, which
displays both sites and species and it seems to work well. However why are
most people using CA instead of
2008 Dec 30
1
why stress value remains so high after invoking of metaMDS
Hello everyone!
metaMDS(cm, distance = "euclidean", k = 2, trymax = 50, autotransform
=TRUE, trace = 1, plot = T)
(cm is a similarity matrix, in which values are positive integers or 0)
I use this command to run NMDS on my matrix "cm". But the stress is very
high after analysis. About 14.
Actually, there is no improvment comparing with using isoMDS.
2009 Jan 21
1
vegan metaMDS
Hi,
I'm trying to use metaMDS with a dissimilarity matrix of angles, not
Bray-Curtis, and I wanted to know if there is an in-built function to
produce a plot of stress values against dimensions, that could be used to
determine the 'true' dimension of the solution. The number of objects is
only a lowly 8 so any solution higher than 2-dimensional is not likely to be
interpretable,
2009 Sep 09
2
"predict"-fuction for metaMDS (vegan)
Dear r-Community,
Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data.
Step2: Then I want to plot environmental variables over it, using function envfit.
The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. Therefore I
2008 Apr 23
1
problem with data for metaMDS analysis please help
am at my wit's end. I am not sure what is wrong with this data matrix. It
is sparse because it is a matrix of species, but I have looked at the row
totals and column totals and they are positive.
rmetaMDS(x.d)
Error in if (autotransform && xam > 50) { :
missing value where TRUE/FALSE needed
What is wrong? And in the future how in God's name do I easily diagnose
whatever
2008 Jan 24
4
using object.find() in a loop not returning an array
I''m running a loop (illustrated below) that retrieves records from a
table based on an id that might be different with each iteration. The
loop uses the array scrns (composed of IDs) to find the related records
in the Screens table. I''m attempting to store the returned results in
an instance variable so I can use that data in a view. However, this
code simply is overwriting