You may want to look at the documentation for the vegan package. Hank Stevens On Jun 22, 2004, at 2:19 PM, christophe grova wrote:
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 ... I already tried by using the function 'corresp' in the MASS package
- it seems to work ... but how is it possible to get all the information concerning the non-centered PCA used by corresp (eigen-values, inertia, scree plot, square cos, ....)
In a second step I would like to use hirarchical clustering from the results of the correspondence analysis ...
If "Table" is my contingency table (i.e., the number of individuals seen in each case) ... I tried to implment it as follow (for the 2 first components for instance, but I would be interesting at looking to the other components ...I did not manage to get the eigen values !) :
A <- corresp(Table, nf = 2) biplot(A) hc <- hclust(dist(A$cscore), "ward") plot(hc)
Is that ok ??? ... here it is exemplae using Ward method for clustering ...
I would also be interested in using method of mutual neighbors to identify the clusters ... is it possible using hclust ?
Any help would be really appreciated,
Best regards ...
Christophe
*************************** Christophe Grova, PhD PostDoc - EEG department Montreal Neurological Institute, McGill University 3801 University Street, Montreal, Quebec, Canada, H3A 2B4 email : [EMAIL PROTECTED] tel : (514) 398 2184 fax : (514) 398 8106 web: http://idm.univ-rennes1.fr/users/grova ***************************
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