similar to: metaMDS with large dataset produces 'insufficient data' warning

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

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

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,

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

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

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

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,

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 -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3.5 - sicherer, schneller

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.,

Hi All, Another quick question - I noticed that COZIGAM has been removed from CRAN, and that you are referred to the archive for previous versions (last updated 23 July 2012). Is this package still ok to use? Or is there an alternative which might also fit zero-inflated GAMs? Thanks, Raeanne The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by

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.

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

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,

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") :

Hi there, My question is about the 'theta' parameter in specification of a NB GAMM. I have fit a GAM with an optimum structure of: SB.gam4<-gam(count~offset(vol_offset)+ s(Depth_m, by=StnF, bs="cs")+StageF*RegionF, family=negbin(1, link=log), data=Zoop_2011[Zoop_2011$SpeciesF=='SB',]) However, this GAM shows heterogeneity in the

Hi there, I'm using the lattice package to create an xy plot of abundance vs. depth for 5 stages of barnacle larvae from 5 species. Each panel of the plot represents a different stage, while different loess smoothers within each panel should represent different species. However, I would like depth to be on the y-axis and abundance to be on the x-axis, because this is more intuitive as an

Hello R-user community, I am applying the function metaMDS. However, I would like to know if there is any option to export the data I got from the axis as a data frame. I have tried as.data.frame.list but is not working. Any suggestion? Thank you in advance for your help, Lineth [[alternative HTML version deleted]]

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.

Hi, I'm new to R and have looked at the mail archives and not seen a solution to my problem. I have a set of data files with filenames in the following form haydn1stmvt.jtf.sim0.142292.et.dist, where the latter half changes, after the jtf. What I am trying to do is process the set of these files using R's batch mode. using the following : library(mva) mdsdata <- read.table(file) cm

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