[R] Discriminant Correspondence Analysis

Bastiaan Bergman Bastiaan.Bergman at wdc.com
Tue Dec 14 21:39:53 CET 2010

Read files, if you're on windows remember to include the path like this:
"C:\\Documents and Settings\\USER\\My Documents\\MyFile.csv"

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Wayne Sawtell
Sent: Tuesday, December 14, 2010 12:36 PM
To: r-help at r-project.org
Subject: [R] Discriminant Correspondence Analysis

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 files to .csv format, which I have done, no problem. That
is not an issue.
There are several parts to my problem.
1) When I try the read.table command, even if I include the directory name
in the filename, R still cannot read the file, even if it is in .csv format
2) I was able to copy my file and then read the clipboard contents into R
but then I do not know to assign a name to the data frame in order to
conduct any operations on it
3) I need the ADE4 program in order to perform Discriminant Correspondence
Analysis, so I used the "install.packages" command to install it. It
installed no problem but I do not know how to access the ADE4 program in R.
I am unable to open it directly, either.
4) I thought that using the ADE4 GUI (called "ade4TkGUI") would be easier
because I do not know many of the R commands; but, again, I downloaded it
but cannot open or access it.

The following is the suggested coding that I found through the R website,
but when I try to use this code, I don't know how to assign a name for the
df, or what to put for "fac", and what is worse, I get an error message
saying that the program cannot find the "discrimin.coa" command.


discrimin.coa(df, fac, scannf = TRUE, nf = 2)


df a data frame containing positive or null values

fac a factor defining the classes of discriminant analysis

scannf a logical value indicating whether the eigenvalues bar plot should be

nf if scannf FALSE, an integer indicating the number of kept axes



plot(discrimin.coa(perthi02$tab, perthi02$cla, scan = FALSE))
For clarification, my data consists of measurements of morphological
characters of an assemblage of biological specimens. I have already
performed Principal Co-ordinates Analysis, Principal Compionents Analysis
and Cluster Analysis in another program (PAST) in order to see if the data
fall into distinct groupings that might represent different morphological
species. I now want to test the groupings that I found on my test data set
using Discriminant Correspondence Analysis.There are both continuous and
categorical characters, which is the reason why I need to perform
Discriminant Correspondence Analysis, instead of Linear Discriminant
Analysis, which is only valid for continuous measurements. R seems to be the
only program in which I can perform Discriminant Correspondence Analysis.

Thanks for any help offered on any of these points.

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