similar to: plotting vector of symbols

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

Dr. Stevens, Hi, my name is Trey Scott, and I'm a grad student of Brian McCarthy's. He referred me to you because of your expertise in handling complex R problems. We were hoping you could help us solve a nagging problem that is prohibiting me from producing graphicl output. Here is a simple mock-up of the matrix I'm using a b c d e f 1i 1 4

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 -- Let's not spend our time and resources thinking

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, First I should note I am relatively new to R so I would appreciate answers that take this into account. I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such

Hi, I am working with a species-by-trait .csv file (columns=traits, rows=species) and get the following warning message when trying to plot results of both metaMDS and pcoa:  "Warning message: In ordiplot(x, choices = choices, type = type, display = display,  :   Species scores not available" I am using a Gower's transformation in both procedures within the metaMDS or pcoa

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,

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

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.

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

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.

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.,

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

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

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

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 there, I'm trying to plot vectors with p<0.1 in a NMDS ordination plot using p.max. Below the scripts I'm using. I guess I'm missing something! could you please give me a hand? species<-metaMDS(species_matrix)ef<-envfit(species,environmentaldata_file,permu=999,na.rm=TRUE)efplot(species, dis="sites")plot(ef,p.max=0.1) Error in plot.envfit(ef, p.max = 0.1) :

Hi, I could use a hand solving a fairly straightforward ordination plot problem: I am conducing NMDS on some community data for roughly 300 localities and 650 species. I have a community matrix, a species attribute matrix, and an environmental attributes matrix. After running metaMDS {vegan} on the community matrix, I can successfully use either of the other two matrices to draw hulls around

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"