similar to: NMDS Ordination Graphics Problem

I have a data matrix that contains site data for paired infested and control plots. For example: ab ac ad af ag ah 1 .024 x x x x x 2 .9 x x x x x 3 1.5 x x x x x 4 2.3 x x x x x 5 1.0 x x x x x 1c .75 x x x x x 2c 2.1 x x x x x 3c 1.7 x x x x x 4c 10.2 x x x x

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")

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

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,

Hi, I have used Vegan to construct an NMDS ordination plot. I plotted sites of three forest types with the site number in it. My reviewer has asked me to use different symbols for each of the forest types. Can anyone send me how I can do this in R in simple steps. I have used the options like ordiplot, sel and pl syntaxes that are not working for the question that I asked for. Best, Sinu --

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.

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

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,

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.

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

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

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.,

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,

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

Hello all, I have been using the function ordirgl to plot 3D dynamic ordinations. The ordirgl function works just fine. IN fact, I was even able to write a function that allows me to identify points in the 3D plot: identify.rgl<-function(env_var,ord,dim1,dim2,dim3) { tmp<-select3d(button="left") tmp.keep<-tmp(ord[,dim1],ord[,dim2],ord[,dim3])

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

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

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

Hi Im currently trying to plot my NMDS data together with fitted variables (envfit funct) on an ordination plot. The plot function shows two displays="sites" and "sp". I was wondering how to plot it so that the sites come up as different points for different sites but the species come up as actual names? It looks a little busy at the moment with everything in. Sya -- View

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,