Displaying 20 results from an estimated 1000 matches similar to: "stress value remains so high(metaMDS)"
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.
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.,
2013 Apr 26
1
NMDS in Vegan: problems in stressplot, best solution
Hello,
I can draw a basic stress plot for NMDS with the following code in package
Vegan.
> stressplot(parth.mds, parth.dis)
When I try to specify the line and point types, it gives me error message.
> stressplot(parth.mds, parth.dis, pch=1, p.col="gray", lwd=2, l.col="red")
Error in plot.xy(xy, type, ...) : invalid plot type
In the above code, if I removed line type,
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
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 Sep 23
1
Envfit, inconsistant result?
Hi R-experts,
I am using the envfit function over an ordination of floristic data.
The problem is that every time that I run it changes the results. Sometimes
dramatically, selecting variables that the first time were not significant.
I do not get what could be the problem or if is normal given the
permutations are different.
# the NMDS ordination
gap_flor_NMDS_chord <- metaMDS(gaps_flor,
2011 May 22
0
Manipulating rownames for nMDS
I am trying to plot an nMDS plot using ggplot2. My rownames are coded so
that they can be broken down by Site, Species, Treatment, or Replicate based
on unique separators. There are no column headers. I am having trouble
coding ggplot2 to plot by Site -or- Species -or- Treatment and NOT by all
unique row names. This is probably a simple question but I'm still very new
with command line
2011 Mar 10
1
3 dimensional MDS plots
Hi,
I am trying to create 3 mds plots: one with axis 1 vs axis 2, one with axis 2 vs axis 3, and one with axis 1 vs axis 3. When inputting my code, I only end up with one diagram and when inputting
mdsg.mds$dims, the program returns 2 for 2 dimensions. How can I create the other two plots?
Any help would be greatly appreciated,
Calla Carbone
The table I use is number of each taxa on each
2010 Dec 01
1
procrustes results affected by order of sites in input file
Dear All,
I am using a Procrustes analysis to compare two NMDS ordinations for the
same set of sites. One ordination is based on fish data, the other is based
on invertebrate data. Ordinations were derived using metaMDS() from the
{vegan} library as follows:
fish.mds<-metaMDS(fish.data, distance="bray", k=3, trymax=100,
wascores=TRUE, trace=TRUE, zero="add")
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
2013 Sep 06
1
Fwd: calculating dissimilarity index of islands (vegan and betapart)
Dear List,
This is Elaine, a postgraduate studying in bird distributions in East Asia.
I want to calculate Simpson dissimilarity index,
based on a presence/absence matrix of bird species in islands in East Asia.
(matrix row: 36 islands/matrix column: species ID)
(R package vegan to make NMDS and R package betapart)
In most papers using vegan for NMDS and betapart for dissimilarity
2010 May 25
2
Calculation time of isoMDS and the optimal number of dimensions
Dear all,
I'm running a set of nonparametric MDS analyses, using a wrapper for isoMDS,
on a 800x800 distance matrix. I noticed that setting the parameter k to
larger numbers seriously increases the calculation time. Actually, with k=10
it calculates already longer than for k=2 and k=5 together. It's now
calculating for 6 hours, and counting...
There is quite a difference between the
2008 Feb 20
1
Stress with MDS
Hi,
I am looking for the best multidimensional configuration for my data (47*47
distance matrix).
I ve tried classical metric (cmdscale) and non metric MDS (isoMDS, nmds)
but it is now difficult to choose the best solution because of the
uncertainties in the definitions of the "stress" function.
So, same problem, several questions :
1. Statistical consideration : With
2010 Jul 22
1
interpretation of stress in NMDS
Among those users of Primer, stress values greater than 0.3 are
interpreted as "questionable". Using both isoMDS and metaMDS (vegan
package), the stress values returned are much higher using my own data
and using examples provided in R Help. For example Rstress = 8.3, and
the stressplot r2 = 0.99 indicating (to me) that the ordination is OK.
I am guessing that the "stress"
2011 Sep 09
2
NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity
Hi!
Thanks for providing great help in R-related statistics. Now, however I'm
stuck. I'm not a statistics person but I was recommended to use R to perform
a nmds plot and PerMANOVA of my dataset.
Sample(treatment) in the columns and species (OTU) in the rows. I have 4
treatments (Ambient Temperature, Ambient temperature+Low pH, High
temperature, High temperature+low pH), and I have 16
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 Sep 09
2
NMDS and varimax rotation
hello,
subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is
it possible to
rotate the axis through a varimax-rotation?
Thanks in advance.
Bernd Panassiti
2013 Feb 27
1
best ordination method for binary variables
Dear all,
I'm analyzing a dataset (A) of 400 cases with 11 binary variables.
Unfortunately, several (actually a lot) of cases are identical. NA are also
present.
I want to to plot distances between cases.
For this, I obtained a distance matrix by dist(A, method="binary"). I then
analyzed the obtained distance via Principal coordinate analysis with
cmdscale(). Results are fine.
2008 Jul 05
2
p-value for Nonmetric Multidimentional Scaling?
Dear R-helpers,
I am running metaMDS in the vegan package, which uses isoMDS in MASS, to perform Nonmetric Multidimentional Scaling (NMDS).
I have seen some authors report a p-value for the NMDS ordination based on randomization of the dataset. As I understand it this is meant to compare the stress in your dataset to multiple runs of randomized data.
I do not see a way to perform such a test in
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") :