similar to: about cancor.R

Hi, from what I understand about the canonical correlation function 'cancor', it looks for correlations in two sets of variables, each represented in matrix form. Right? Sounds exactly like what I need. I have tried the following but I am not sure how to interpret the results. AudioPCs <- c(ArTHarF0PCA$x[,2], ArTHarF1PCA$x[,2], ArTHarF2PCA$x[,2], ArTHarF3PCA$x[,2],

Dear R's! I am strugling with cancor procedure in R. I cannot figure out the meaning of xcoef and of yxcoef. Are these: 1. standardized coefficients 2. structural coefficients 3. something else? I have tried to simulate canonical correlation analysis by checking the eigenstructure of the expression: Sigma_xx %*% Sigma_xy %*% Sigma_yy %*% t(Sigma_xy). The resulting eigenvalues were the same

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 ...

Hi everyone, Can I suggest an additional output component in cancor, from package mva? It would be useful to have the number of canonical correlation vectors, equivalently the rank of the covariance between x and y (label "rank"). This would usually be min(dx, dy), where dx and dy have already been computed for the svd function, but there might be situations where it was less than

When I use the function cancor of mva package, I found that it doesn't work when one of the matrix has only one column, or both have only one column. The function in Splus 5 with the same name works under those situations. The version of R I am using is 0.63.2 (released on Jan., 1999) on Solaris. Kenny Ye Assistant Professor Department of Applied Math and Statistics SUNY at Stony Brook

Performing CCA in R I know they say don't say please... or plead...but I'm sorry but I really need some help with this problem. I have tried to perform CCA in R and I can never do this successfully. Can someone please tell me what I'm doing wrong. I can't attach any file...so Please email me and I'll attach the necessary files. (there's only two) the files will be my CCA R

Colleagues, I'm developing a library of functions for community ecology analyses and have a couple of questions that I've not been able to answer via faqs or docs. 1) Are there existing functions for: a) Bray-Curtis (polar) ordination? b) non-metric multidimensional scaling (NMDS)? c) canonical correlation analyses (CCA and DCA)? d) TWINSPAN (doubtful...)? 2) If not,

I'm trying to write a formula method for canonical correlation analysis, that could be called similarly to lm() for a multivariate response: cancor(cbind(y1,y2,y3) ~ x1+x2+x3+x4, data=, ...) or perhaps more naturally, cancor(cbind(y1,y2,y3) ~ cbind(x1,x2,x3,x4), data=, ...) I've adapted the code from lm() to my case, but in this situation, it doesn't make sense to include an

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

Hello Tom, I tried the new UPnP support of shorewall, olny to stumble upon a LinuxIGD bug. Specificaly, the UPnP chain is read as UPn from the upnpd.conf . I double checked it, there some bug in the upnpd, it doesn''t process 4 lettered names correctly. Could you change this chains'' name to something a little longer? -- Costas Cavouracis <cca@freemail.gr> My PGP keys:

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 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)),

Dear List, I am trying to plot the result of cca using matplot but failed. Pls kindly help and thanks. Elaine The error message was error in xy.coords(x, y, xlabel, ylabel, log = log) : (list) object cannot be coerced to type 'double' code rm(list=ls()) library(vegan) library(MASS) # input richness birdrich

Dear r-Community, Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data. Step2: Then I want to plot environmental variables over it, using function envfit. The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. Therefore I

Dear List, I tried to do cca based on species data and environmental variables (formula instead of community data). However, there was an error saying row sums must be >0. I searched the previous related messages but found few solutions. Please kindly help and thank you in advance. code This is vegan 1.17-3 Warning message: package 'vegan' was built under R version 2.10.1

Dear List, I tried to conduct cca using csv data but failed. The message said that data.frame is required. Please kindly share how to convert a csv-imported file to a data.frame. 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,] envi

Hello Sir I am getting problem in plotting in CCA . Could you please help me? I wrote the below command but I don't know why it is taking only first 5 env data rather than all 9. > strain.data <- read.xlsx("Dee rhiz.xlsx", sheetName="strain", header = T, row.names = 1) > env.data <- read.xlsx("Dee rhiz.xlsx", sheetName="env", header = T,

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 everybody, I'm trying, without success, to avoid some variables labels to overlap on a capscale (vegan package) object graph. I was able to move the labels with the coding below, but it moves the entire vector... CAPobj<-CAPpotiFT for(i in c(2:8))CAPobj$CCA[[i]][,1]<-CAPpotiFTI$CCA[[i]][,1] CAPpotiFTI$CCA[[i]][,1][2]<-0.85 And here the graphic script

He everybody, Well I have a biplot CCA-like origined from plot.cca (vegan package). I need to rotate on y axis the lines and symbols of constrained and sites representation. If I do that on an image editor, I rotate everything, including titles, axes labels and positions. I just need to rotate the inner par and keep the variables names (constrained) and symbols in the new positions but with the