similar to: Correspondence analysis with R

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)

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: How can I calculate the cumulative variance (or variance for each component) in correspondence analysis? If were possible in ADE4 package Thank you -- Antonio Punzón Merino O__---- Instituto Español de Oceanografía c/ /'_ --- Centro Oceanográfico de Santander (*) \(*) -- Promontorio de San Martín S/N ~~~~~~~~~~ 39004-Santander; Spain PO BOX: 240 Tlf: +34 942 29 10 60 Fax: +34

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

Is there an R function that does canonical correspondence analysis. Can it be done using the VR function corresp()? If not, how hard it be to write R code to do it? I am a population biologist with long but patchy programming experience in C, Smalltalk, Java and other languages. Thanks, Patrick Foley patfoley at csus.edu

Dear R users, I m quite a novice in using R for factor analysis and I would need some help to choose the right function. I have a contingency table and I would like to perform a Correspondence analysis on this table, followed by a hirarchical clustering of my variables projected in on the first principal components. Here are my question : - what is the more appropriate function to do so ...

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 ...

I'm experienced in statistics, but I am a first-time R user. I would like to use R for correspondence analysis. I have installed R (Mac OSX). I have used the package installer to install the CA package. I have run the following line with no errors to read in the data for a table: NonLuxury <- read.table("/Users/myUserName/Desktop/nonLuxury.data.txt") The R online help

Hello, I am new to R and I have a question about the difference between correspondence analysis in R and SPSS. This is the input table I am working with (4 products and 18 attributes): > mytable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 1 15 11 20 4 14 7 1 2 1 4 12 12 17 19 11 20 9 10 2 19 18 14 14 16 4 14 11 11 15 22 19 22 16 21 19 15 16 3 16 13 10 9 15 4 10 7 11 13 18

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 am looking for a workaround of "species empty" plots in a correspondence analysis. I tried to do a community structure analysis with a ca via decorana(), ca() and CAIV(), but none of them allow 0 only-rows. I have species (abs./pres) in columns and sites in rows sp1 sp1 sp3 ... plot1 0 1 1 plot2 0 0 0 plot3 1 0 1 ..... but on some plots no

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,]

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)),

> Hi > I'm Ph.D student and I need an R code to compute the chi square diistance between n profile rows in a matrix. > > could you help me please? > Thanks > > Paola > ____________________________________________________________

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, How can I run a constrained correspondence analysis with the following data: 15 animals were measured repeatedly month-wise (over to 2 years) according to ther diet composition (8 food categories). our data.frame looks like this: food 1 2 ... 8 sex season year animal freq 12 8 ... 1 0 summer 2011 1 freq 0 7 ... 0 1 winter 2011 1 ... freq 0 7 ... 0 1 spring 2011 15 We

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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 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

Hi everybody, i'm dealing with some percentage tables, of which i should test rowwise if the entries are sgnificantly equal or not. Namely, on row 1, test H0: element 1= element2, H0: element 1= element3...H0: element 2= element3...H0: element n-1= element n. The same on the other rows. Anybody knows how this can be done in quick way? I don't have large matrices, but it seems quite