similar to: example on front page doesn't work in R 2.0.1

Dear All, Thank you for helping me doing PCA. Please show me how to read Individuals factor map (PCA) and Variables factor map (PCA). http://www.nabble.com/file/p15975893/pca_var.jpg http://www.nabble.com/file/p15975893/pca_ind_q1.jpg Nguyen Tran Phuong Thao. Hue University, Viet Nam. -- View this message in context: http://www.nabble.com/How-to-Read--tp15975893p15975893.html Sent from the

Un saludo R-inómanos: Les escribo porque tengo una duda que no he podido resolver por mis medios y actuales conocimientos. He querido instalar el paquete "ade4" en R (OP linux-ubuntu) pero no he podido por un error que según entiendo está relacionado con una librería. Me permito mostrarles el texto que me aparece luego de tratar de instalarlo desde los repositorios: >

Hello, I'm a student in biology, writting from Strasbourg, France. I need to use the logiciel R to analyse biological results. I have ADE4 since 2001, but technology's now largely evoluted ! That's why I'm just trying to get the new version of : - ADE4_1.3-3.zip ; - R 2.0.1.ter ; - DCluster_0.1-3.zip. However, I don't know HOW TO INSTALL R on my computer ? I don't

Hello, I am trying to run some AMOVA analyses with the amova function in the package ade4. When running the example dataset provided in ade4, I noticed a difference between the published results from the same data (Excoffier et al. 1992) and what ade4 calculates. Below are the data for "within sample/population" from ade4 and from the haplotypic distance matrix in the paper:

Hi All, I am using canonical correspondence analysis to compare a community composition matrix to a matrix of sample spatial relationships and environmental variables. In order to parse out how much variance is explained purely by space (S/E) or the environment (E/S) I am using a conditional (partial) CCA. I want to test significance via Monte Carlo but I can not find a way to do this with a

Dear all, I didn't find any graphical solution in the package "mva" to plot the canonical scores from a CCA (canonical correlation analysis). Does anybody knows how to plot or has anybody already programmed : - the map of the canonical scores, - the graph of the canonical weights, - the correlation circle i.e. the canonical loadings ? Thank you for help ...

Dear R users, How can I extract the residuals from a pcaiv/rda in ade4? In Vegan there is the residuals() function, giving the approximation of the original data from the unconstrained ordination Is there something similar in ade4? Nikos

I want to invoke R on a Linux Web server from Java, in order to analyse data in ways that would take too long to code, and run too slowly, in Java. In particular, to do correspondence analyses. To this end, I've installed R version 2.15.0 on my Web host's x86_64 GNU/Linux machine, and tried using package "ca" to run the "author" example of correspondence analysis

I'm testing a FC5 machine for use in a student lab. R 2.3.1 is installed and seems to work fine. There is one peculiarity - the logins are authenticating to a server, and a "verbose" flag is set somewhere, leading to lots of spurious messages like this request done: ld 0xa227598 msgid 1 which may be confusing R. However, R CMD check seems to fail for packages with no

I would like to randomly shuffle a distance object, such as the one created by ade4{dist.binary} below. My first attempt, using sample(jc.dist) creates a shuffled vector, losing the lower triangular structure of the distance object. How can I Ishuffle the lower triangular part of a distance matrix without losing the structure? Thanks. --Dale x1 <- c(rep(0,4),1) x2 <- c(rep(0,2),rep(1,3))

Dear R-devel, googling for the single letter R yields R-home page as the firt hit, which is extremly nice. By clicking on the figure you get the code of the "Winner of the R Homepage graphics competition 2004." By copy/pasting in your R console it doesn't work because it is impossible to install the mva package. This is my point. As documented in ONEWS the reason is simple:

Hi! I try to install the R version of ade4 on a linux (suse7.3) box with R 1.6.2 (from rpm) and get /usr/local/bin/R INSTALL ade4_1.00.tar.gz tar: /usr/local/lib/libpthread.so.0: version `GLIBC_2.2' not found (required by /lib/librt.so.1) ERROR: cannot extract package from 'ade4_1.00.tar.gz' But I actually have glibc 2.2.4 (at least this is what my suse's Yast conf. tool

Dear Forum, I have a class variable 1 (populations A-E), and two other class variables, variable 2 and variable 3. What I want is to see if the combination of var 2 and var 3, will give me a pattern that allows to distinguish populations. I found several packages like ade4, with pcaiv function and factoMineR. but there are not working. Using the ade4 package, when I try to build the pca: pca1

Dear R-user, I am trying to use the function 'parLapply' from the 'snow' package which is supposed to work the same wys as 'lapply' but for a parallelized cluster of computers. The function I am trying to call in parallel is 'dudi.pca' (from the 'ade4' package) which performs principal component analyses. When I call this function on a list of

Dear List, I used spec and envi for cca in ade4. (both are data.frame) However, there is a message telling that error in if (nf > rank) nf <- rank R missing value in TRUE/FALSE Please kindly help how to modify the code below. Thank you. Elaine code rm(list=ls()) spec <-read.csv("c:/migration/M_R_20100718_winterM_spec_vegan.csv",header=T, row.names=1) dim(spec) spec[1,]

Hello everyone, I am totally new to the R program. I have had a look at some pdf documents that I downloaded and that explain how to do many things in R; however, I still cannot figure out how to do what I want to do, which is to perform Discriminant Correspondence Analysis on a rectangular matrix of data that I have in an Excel file. I know R users frown upon Excel and recommend converting Excel

Hi all, thank you for your answers; i've tried both cca from vegan library, and dudi.coa from ade4 library; one last question: my deal is mainly with contingency tables, like the one i'm posting here acciaieria<-c(.41,.02,.44,.04,.09) laminatoio<-c(.34,.28,.26,.01,.11) fonderia<-c(.48,.05,.34,.08,.05) leghe<-c(.45,.19,.25,.03,.08)

Is it possible to make disappear the id numbers from scatter.dudi (mc analysis) ? a <- as.factor(c(1, 2, 3, 2, 1)) b <- as.factor(c(3, 2, 3, 1, 1)) x <- as.factor(c(1, 2, 2, 1, 3)) y <- as.factor(c(2, 2, 3, 1, 1)) dat <- data.frame(a=a, b=b,x=x,y=y) summary(dat) dat require(ade4) dat.acm <- dudi.acm(dat, scann = FALSE, nf = 2) scatter.dudi(dat.acm) Thank you very much !

Hello, first, big thank you to the developers of R, the release of recent version is very nice.! Well, it seems that I've messed up my current installation by using two update mechanism at the same time on my Debian Sid box. That is : 1)Debian Way per apt-get freshing up my R installation 2) irregularily "update packages()" from within R. I guess this obviousely resulted in

I'm trying to perform a mantel test that ignores specific pairs in my distance matrices. The reasoning is that some geographic distances below a certain threshold suffer from spatial autocorrelation, or perhaps ecological relationships become less relevant that stochastic processes above a certain threshold. The problem is that I can't find a way to do it. If I replace values in either or