please, if you have some questions about a particular package, do not send to R-Help. There is a list about ade4, see details at:
http://pbil.univ-lyon1.fr/ADE-4/adelist.html
cca is a correspondence analysis with constraint imposed by external information. Redundancy analysis (available in ade4 by the function pcaiv) is PCA with constraint.
Here is an example using pcaiv:
data(rhone) pca1 <- dudi.pca(rhone$tab, scan = FALSE, nf = 3) iv1 <- pcaiv(pca1, rhone$disch, scan = FALSE) iv1$param
iner inercum inerC inercumC ratio R2 lambda 6.27 6.27 5.52 5.52 0.879 0.671 3.7 4.14 10.4 4.74 10.3 0.984 0.747 3.54
iner represent eigenvalues of the unconstrained analysis: > pca1$eig[1:2] [1] 6.274265 4.140947
inercum is equivalent to cumsum(pca1$eig)
prediction of sites scores by environmental variables produce a new set score (often named LC scores), inerC represent variance of this scores:
diag(t(iv1$ls)%*%diag(iv1$lw)%*%as.matrix(iv1$ls)) Axis1 Axis2 5.515241 4.736362
inercumC is the cumsum.
ratio is simply inercum/inerCcum
Finally note that CCA or RDA find a site score that maximizes the variance explained by environmental variables. This is a product of variance by a R2:
0.671*5.52 # lambda = R2*inerC
[1] 3.70392
At 10:11 14/01/2005, Dominique Gr�ter wrote:
Does someone know the meaning of the following values relating to the "cca"-command?
iner, inercum, inerC, inercumC
Thanks! DOMI
______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
St�phane DRAY
--------------------------------------------------------------------------------------------------
D�partement des Sciences Biologiques Universit� de Montr�al, C.P. 6128, succursale centre-ville Montr�al, Qu�bec H3C 3J7, Canada
Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293
E-mail : [EMAIL PROTECTED]
--------------------------------------------------------------------------------------------------
Web http://www.steph280.freesurf.fr/
______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
