Displaying 20 results from an estimated 1000 matches similar to: "Fwd: calculating dissimilarity index of islands (vegan and betapart)"
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
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")
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
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
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,
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
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,
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 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.
2010 Jan 12
1
Non-metric multidimensional scaling (NMDS) help
Hi,
I am currently working on some data and feel that NMDS would return an
excellent result. With my current data set however I have been experiencing
some problems and cannot carry out metaMDS. I have tried with a few smaller
data sets which I created for practice sake and this has worked fine.
I think it is the set up of my data set that is causing me trouble. I have
18 columns and 18 rows,
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
2007 Nov 14
1
label plotting on nmds diagram
Hi,
I'm using nmds command (library vegan) to analyze some fishing data.
I'd like to plot not only points, but also the names of species and stations in
a specified position.
I used the command
text(nmds$points[,1], nmds $points[,2],labels=row.names(nmds
$points),pos=3,cex=0.5)
But the labels are sometimes overlapped.
Is there any way to use identify, or a similar command, to plot the
2015 Dec 23
2
Cannot allocate vector of size
Antes de nada, me gustaría daros las gracias por toda vuestra ayuda.
He estado probando todo lo que me habéis dicho a la vez, y no hay manera, sigo teniendo el problema con el espacio.
En cuanto al tamaño de la base de datos, es más grande de lo que puse, me equivoqué y puse el tamaño de una base anterior con la que estuve trabajando, la actual tiene 36866 filas x 6500 columnas.
He seguido todas
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
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,
2010 Jan 20
1
Problem in NMDS
Hi,
I am stuck in one problem when doing nonmetric multidimensional scaling. I use the function 'metaMDS' in the package 'vegan' to work on the presence/absence community data. The problem is when two samples are identical (dissimilarity = 0), metaMDS cannot work with zero dissimilarity.
I don't want to delete the duplicates as they are true samples from different locations.
2015 Dec 22
2
Cannot allocate vector of size
Yo creo que el problema principal está en betapart.core(), que crea y
mantiene simultáneamente en memoria varios objetos de alrededor de 1 Gb
que luego combina en una lista... Probablemente es entre las líneas el
código de betaper.core donde hay que ir eliminando objetos.
Saludos,
Marcelino
El 22/12/2015 a las 18:26, Carlos J. Gil Bellosta escribió:
> Hola, ¿qué tal?
>
> Yo no
2015 Dec 22
2
Cannot allocate vector of size
Hola Rubén,
Totalmente de acuerdo con los consejos de Carlos. Ten en cuenta que
aunque R disponga de varios (bastantes) GB de memoria, algunos de los
objetos que va creando durante el proceso pueden consumirla por
completo. Es decir, que aunque tu ordenador tenga 64GB de RAM, es
posible que no queden 10 GB libres para almacenar un objeto (porque ya
hay demasiados objetos grandes en la