similar to: The RV coinertia coefficient to interpret multivariate analysis plots

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 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 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

Dear all, Does anyone know how to run Principal Coordinates Analysis (PCoA) from a squared euclidean dissimilarity matrix with R ? Thanks, ************************* Arnaud DOWKIW Department of Primary Industries J. Bjelke-Petersen Research Station KINGAROY, QLD 4610 Australia T : + 61 7 41 600 700 T : + 61 7 41 600 728 (direct) F : + 61 7 41 600 760 **************************

Hello everyone, I mail you because of my lake of knowlegde regarding statistics. I'm using the CA and PCoA (but maybe should I use some other techniques) to determine the differences and similarities between a large sample of plants using different kind of traits through matrix of mixte variables. I understood that the daisy() function using the gower metric and defining the different type

Hi, I need to run a PCoA (PCO) for a data set wich has both positive and negative values for variables. I  could not find any distancecoefficient other than euclidean distace running for the data set. Are there any other coefficient works with negtive values.Also I cannot get summary out put (the eigen values) for PCO as for PCA.   Thanks. Dilshan [[alternative HTML version deleted]]

Dear all, I was looking for methods in R that allow assessing the number of significant principal coordinates. Unfortunatly I was not very successful. I expanded my search to the web and Current Contents, however, the information I found is very limited. Therefore, I tried to write code for doing a randomization. I would highly appriciate if somebody could comment on the following approach.

Dear R-Helpers, I am working on a dataset containing ca. 500 specimens of 17 different species. The data is three text columns, followed by ca 70 columns of binary data. I'm trying to write a function that will allow me to interactively exclude species using the inofrmation in the third text column. My function, matrix.slicer, appears to work as I intend. However, when I pass the

Hi, List The elastic net package (by Hastie and Zou at Stanford) is used to do regularization and variable selection, it can also do regression. I am wondering if it can perform binary classification (discrete outcome). Anybody having similar experience? Many thanks, -Jack [[alternative HTML version deleted]]

> If you just meant serverside generation, most people do use cgi to > do this, and I believe icecast has this built in, so a request for > http://icecast.server.net/stream.ogg.m3u will generate an > audio/mpegurl response that points to the .ogg url. > > Are either of those what you mean? exactly to link to an ogg vorbis stream on an icecast server you link it with

Version 4.06 of the caret package was sent to CRAN. caret can be used to tune the parameters of predictive models using resampling, estimate variable importance and visualize the results. There are also various modeling and "helper" functions that can be useful for training models. caret has wrappers to over 50 different models for classification and regression. See the package

Version 4.06 of the caret package was sent to CRAN. caret can be used to tune the parameters of predictive models using resampling, estimate variable importance and visualize the results. There are also various modeling and "helper" functions that can be useful for training models. caret has wrappers to over 50 different models for classification and regression. See the package

Dear all, I have a question about FD package. I?m trying to calculate functional diversity indices using insect data. My trait data includes dispersal ability (0, 0.5, 1), body size (continuous) and five feeding guilds coded as in percentages (for example; 0,0,0.5,0.5,0) since some of the species can have two different feeding guilds. However, the package only calculates when I run ?calc.Frich=

Hi everybody, i'm trying to draw rarefaction curves to estimate a population size from genotyped faeces. I used the Gimlet software which gave me a script and a "rarefaction.txt" file. I've copied both files in the work directory of R. I changed library(nls) by library(stats) in the script. But now, i'm still unable to run it. If i ask to show error messages, the software

Hi List, I’m using the vegan function specaccum to produce a rarefaction curve. In the function’s help it says: “Function ‘specaccum’ finds species accumulation curves or the number of species for a certain number of sampled sites or individuals”. Well, I would like to finds this curve for individuals, but when I compute it the function (using the ‘rarefaction’ method) gives me Sites, Richness

Dear R-helpers, I have two data frames, op and em4: > str(op) 'data.frame': 37 obs. of 5 variables: $ m : num 0.202 0.336 0.122 0.139 0.14 ... $ lln : num 0.798 0.643 0.863 0.835 0.823 ... $ rrn : num 0.789 0.702 0.894 0.895 0.923 ... $ asym2: num 0.177 0.304 0.108 0.187 0.274 ... $ asym3: num 0.0755 0.0975 0.0818 0.0651 0.13 ... > str(rownames(op)) chr

Hi all, I used R (vegan package) to make rarefaction curves and I calculated the Chao index for each curve. However, the plateau is far from reached. What I want to do now is the following: Based on the Chao index, I want to extrapolate the curve so I get an x-value which gives me an estimation of the total number of clones I'd have to pick up and sequence in order to have a full coverage of

Here's a question for ecologists on the r-help list-- I'm addressing this to ecologists in particular because they're most likely to be familiar with the equation in question but I'll be happy to discuss the problem with anyone who's willing to take a whack at it. I'm trying to write a function to calculate the large sample variance of species richness estimates by

> Date: Fri, 2 Jul 1999 18:40:16 +0200 (MET DST) > From: Agustin Lobo <alobo at ija.csic.es> > > Dear R makers and users: > > After reading the FAQ and the comments on the > comparison between R and S, I still have an important > (at least for me) question: How is R compared > to the new version of Splus 5.0 (for unix including Linux)? The current version of