similar to: Ordination Plotting: Warning: Species scores not available

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

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.

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 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,

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,

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, 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

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.,

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

I think it is an easy question but i haven´t found a solution since I am r beginner. I did this plot3d(PCoA, type="p", col=rainbow(1000),size=5) text3d(PCoA, text=Nam) How can I save it including the labels to a jpg-file? Thanks in advance. Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351

Hello R user and helper! I would like to get a 3d plot with coloured points. I did that: colors<-c(rep("2",7), rep("3",12), rep("4", 24), rep("5", 13), rep ("6", 8), rep("7", 51), rep("8", 1), rep("9", 15), rep("10", 53), rep ("11",3), rep("12",3), rep("13", 8),

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

My question is with respect to mCLUST and the values of BIC and log likelihood. The relevant part of my R script is: ######################### BEGIN MDS ANALYSIS ######################### #load data data <- read.table("Ecoli33_Barry.dis", header = TRUE, row.names = 1) #perform MDS Scaling mds <- metaMDS(data, k = Dimensions, trymax = 20, autotransform =TRUE, noshare = 0.1,

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.

Hi all, I have site data with plant species cover and am looking for trends. I'm kind of new to this, but have done lots of reading and can't find an answer. I tried decorana (I know it's been replaced by ca.) and see a trend, but I'm not sure what it means. Is there a way to get the loadings/eigenvectors of the axes (like in PCA)? Is there a way to do this with rda() too? How

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 --

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") :

Dear All, It's Eszter from Hungary, a total beginner with R. My problem is the following: I have a dataset with binary values as a comma separated textfile. The samples are in the coloumns and the species are in the rows. I have to transpose it for the further PCoA analysis. There is no problem with reading the dataset. When I transpose the dataset, the original values become