similar to: NMDS and varimax rotation

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"

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, 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 am trying to analyse with R a database that I have previously analysed with SPSS. Steps with SPSS: Factorial analysis Extraction options : I select = Principal component analysis Rotation: varimax Steps with R: I have tried it with varimax function with factanal or with princomp...and the results are different of what I have with SPSS. I think that varimax function is incorporated 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

Dear R users, in the example below the name of the genus will be displayed in the main titles using the variable predictor[i] and paste. I would like to have the genus name in italic. However all my attempts using expression and substitute failed. Does anybody know a solution? Thanks a lot in advance. bernd Acrobeles <-c(65.1,0.0,0.0,0.0,0.0,0.0) Acrobeloides

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

Hi everyone- I have used several methods to calculate principal components rotated using the varimax procedure. This is simple enough. But I would like to calculate the % of variance explained associated with each PC before and after rotation. factanal returns the % of variance explained associated with each PC but I cannot seem to get it to change after rotation. Many thanks for your

I am starting with a matrix in which rows are vegetation plots and columns are various characteristics including ID# and elevation. I removed elevation and ID columns to avoid having those characteristics influence the distances between points which I calculated using the "dist" command. The resulting distance file was then used in isoMDS. What I want to know is whether I can

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.

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

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, I am puzzeled with a differing result of princomp in R and FACTOR in SPSS. Regarding the amount of explained Variance, the two results are the same. However, the loadings differ substantially, in the unrotated as well as in the rotated form. In both cases correlation matrices are analyzed. The sums of the squared components is one in both programs. Maybe there is an obvious reason, but I

Hi I have just (finally) started to poke around in R and wanted to analyse a stream fish dataset with 28 sites and 18 species. When trying to follow the Vegan manual to run nmds from distance measures calculated by the vegdist function it turns out that I have two sites (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an

Dear R users the factanal pacakge is always MLE, which package can do varimax rotation with the results from princomp ? thank you yong

Hi: How i can make Varimax and Promax Rotation in R 0.63 thanks Jorge M. A. Magalhães -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at

Dear All, I was wondering whether anyone might be able to provide some advice with an nMDS / R problem. I?m trying to run nMDS on a dataset that contains many missing values and was wondering how I can account for the missing values when running nMDS? It seems as though the data are being grouped depending on where the zero values appear. Any suggestions greatly appreciated. Thank you very much

A bit of a newbee to R and factor rotation I am trying to understand factor rotations and their implementation in R, particularly the GPArotation library. I have tried to reproduce some of the examples that I have found, e.g., I have taken the values from Jacksons example in "Oblimin Rotation", Encyclopedia of Biostatistics

Hello all, I've run a principal component regression using the PLS package. I then applied varimax rotation (i.e., using http://stat.ethz.ch/R-manual/R-patched/library/stats/html/varimax.html). I cannot figure out how to extract the factor loadings post-varimax. Is there a command to do this? scores(x) does not do it. Thanks and happy holidays -- View this message in context:

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