similar to: species projected in a ordiplot

Hello, I've got a small dataset on box turtle shell measurements that I would like to perform a detrended correspondence analysis on. I thought that it would be interesting to examine the morphometrics for each species in the area of overlap and in areas where neither species occurs.  I've taken a look at the dune and dune.env datasets in vegan. Using the str() command gives me  >

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

I've tried a few things both with prcomp(), and rda() and its friends in vegan (including biplot.rda and ordiplot), but can't find a solution. I'd like to associate subsets of the points in a resulting biplot ("sites" in the rda object) with different plotting colors/text styles to emphasize certain sets of points. I can't figure out how to keep the arrows (for

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 hope someone knows the answer to this or has a real good reference about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package.

Hi I'd like to know if the R can do the DCCA? Because I can't find the package about the DCCA in R. If it can not, please introduce a free software to me, which you think can easily do the work , thanks! jeff

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

I'm using cocorresp package with predictive co-correspondence analysis model. i would need to visulize inside the graphic (plot function) the sample site numbers (is it possible to consider this a "label"?). is there any function to do this? thanks for your help. Elisa Dr. Elisa Santi Dipartimento di Scienze Ambientali "G. Sarfatti" Unità di Ricerca Biodiversità

Dear members, I am performing multivariate analysis on marine benthic populations using R. At first glance I found ca and VEGANO packages to be the suitable for the task, but neither has incorporated Detrended Canonical Correspondence Analysis (DCCA), which is just the method I want to apply on my data. I've looked for alternative packages containing the method, but my suspicion is that

Hello, I'm trying plot points in an NMDS according to a factor with two levels: fig<-ordiplot(canod.sol, type="none",cex.axis=0.9,cex.lab=0.1,pty="m",tck=-0.01) ordisymbol(fig, y = hab, factor = "habitat", rainbow = T,col = env, legend = F) This gets me part of the way - It produces a plot with blue triangles for the first factor level and red circles

Hi After trying a simple decorana analysis (from the vegan package) on a simple data frame which contains no NA's the following error was returned: > tt_decorana(covN) Error in decorana(covN) : NA/NaN/Inf in foreign function call (arg 1) Have any vegan users come across this error and know what can be done about it? Cheers, J

Dear all at the R-project help list. I have run into a problem when it comes to getting values for "total inertia" and "R-squared" for my DCA using "decorana" in the package "vegan". I have tried the "goodness" function, but the reply indicates that it does not work with "decorana" class objects. In Canoco one gets the Total inertia in

Hi! Is there a way to get biplot and identify to work togheter. Having the output of prcomp I would like to draw a biplot that. Instead of plotting the sample (row-names) names plots some "pch" symbols. (thats easy with xlabs) But now I would like to add using identify the names to only some of the points. I have noticed that both biplot.prcomp and biplot.default does a lot of

Hi, I've installed Dune 2000 and the 1.06 patch in Wine, and it runs very well, except that it doesn't accept keyboard input. It wasn't any better without the patch. The entry at the appdb doesn't mention anything about it. Does anybody know how to fix it? I've already tried changing all the settings on the "graphics" tab in "winecfg". Half-Life, for

hi i've been trying to get an old game (Dune 2) which i used to play through DOS to work on Linux systems, i've not used this before and am in need of an 'idiot's guide to Linux' i've gotten as far as having unpacked the file and installed it on terminal, it now to the point of running the Setup.exe however when i try to run the setup, i get the following command line

Hi Listers, This has a simple answer but it has been eluding me nonetheless. I have been building a PCA plot from scratch with the ability to plot predefined groups in different colors. This has worked fine but when I try to get a polygon drawn around each of the groups it is not recognising my colour file correctly and is only printing the first colour in the file....code is below

Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command don't accept a

Hi, I'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with: > CoastNear = subset(gel_data, Habitat != "I") The resulting data.frame has three levels for Habitat, but

Dear all, I have 4 sites and want to determine how different they are from each other. For this I have decided to use R though it seems a bit daunting to learn. I have read data in from a CSV the structure is : Species1 Species2 Species3 Site1 4 4 7 Site2 3 1 0 Site3 0 99 6 Site4 75 3 33 There are many more species than shown above this is just an example. Here are the

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