similar to: Exporting NMDS distance matris to csv

Hello This is a simple question but I couldn't google an answer. In the procrustes function of the vegan package, one uses plot(procrustes_object, kind=2) to obtain a plot of the residual differences. For instance: data(varespec) vare.dist <- vegdist(wisconsin(varespec)) library(MASS) mds.null <- isoMDS(vare.dist, tol=1e-7) mds.alt <- isoMDS(vare.dist,

Dear List, I am writing a custom panel function and xyplot method to plot the results of a procrustes analysis from the vegan package. I am having trouble getting the call to panel.arrows to work as I wish when conditioning. The attached file contains the function definitions for the xyplot method and the custom panel and prepanel functions I am using. This example, using data and functions from

Dear all, I realised a correspondence analysis with function cca() of vegan library. Just like in Okansen (2010) in the example of R help: library(vegan) data(varespec) data(varechem) vare.cca<-cca(varespec~ Al + P + K, varechem) With plot.cca() function I represented the species matrix in the next way: plot(vare.cca,display="species") Being similar to: plot((c(-2,2)),(c(-2,2)),

I performed canonical correspondence analysis (cca) with the example data of vegan, but I'm not able to obtain a table like scores() for the constraining variables. I can see them in the summary() mode, but it would be great to have in a separate table. Any suggestion?, thanx Gianandrea require(vegan) data(varespec) data(varechem) vare.cca<-cca(varespec,varechem) scores(vare.cca)

Dear r-helpers, I just read in an article by Virtanen et al. (2006) where vegetation-environment relationships are studied by fitting smoothed surfaces on an NMDS ordination using GAMs (Wood 2000). The authors describe, that they used R? as goodness-of-fit statistic, which they compare to the R? of fitted vectors. Calculations were carried out using the package vegan (Oksanen). I know that I can

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

Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to

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

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! 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 have a couple questions about fitting environmental (land use factors, plant species presence-absence, and soil variables) constraints to my CCA biplot. 1. After successfully plotting species and site scores in my CCA, I have been trying to insert the biplot arrows of the environmental constraints in my data set using the text() function. When I do that, the plot changes completely. Is there

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

Estimados, Buenas Tardes, Estoy teniendo problema para testar la significancia de los ejes del RDA. NO se cual seria el error. Alguien me podría ayudar? Desde ya muchas gracias. Saludos, Luis # Tests of all canonical axes anova.cca(ssp.rda.hel, by="axis", step=1000)#Para saber la significancia de cada eje Error in anova.cca(ssp.rda.hel, by = "axis", step = 1000) :

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

I've been unable to find a R package that provides the means of performing Clarke & Ainsworth's BIO-ENV procedure or something comparable. Briefly, they describe a method for comparing two separate sample ordinations, one from species data and the second from environmental data. The analysis includes selection of the 'best' subset of environmental variables for explaining

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"

Let's say I have a program that returns variables whose names may be any string within the vector NAMES=c("varA","varB","varC","varD","varE","varF"..."varZ"), but I do not ever know which ones have actually been created. So in one example output, "varA", "varC", and "varD" could exist, but

Dear r-help users, I have just downloaded the package vegan and I have problems accessing the data to go through the examples in the tutorial. I can see the data when I type "data()" but I am told that the data doesn't exist when I type the name of one of the variables e.g.: > varespec Error: object 'varespec' not found I suspect this could be a way I have my

Hi all, ok, i know i can cut a dendrogram, which i did. all i get is three objects that a dendrograms itself. for example: myd$upper, myd$lower[[1]], myd$lower[[2]] and so on. of course i can plot them seperately now. but the lower parts still have hundreds of branches. i?ll need a 30 " widescreen to watch the whole picture. what i?d like to is group the lower branches , so that i get a

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