[R] Correspondence and detrended correspondence analysis

Monica Pisica pisicandru at hotmail.com
Fri Apr 18 20:45:25 CEST 2008


I hope someone knows the answer to this or has a real good reference about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package. As far as i understand what i've done .... the relationships between vegetation categories and locations should be similar in all 3 analysis, although the 'arch' in locations / sites seen in the CA plot should be flatten out by the DCA - which it is!.

My problem is that the locations / sites are flipped in the DCA plot versus PCA or CA plots (locations with positive coordinates now have negative coordinates in DCA versus CA or PCA), although the vegetation categories keep same relationships between them in all three plots - which is expected. If some code is required i can provide it but i didn't want to clutter the message too much. But i am providing the resulting plots in case they will make my problem clearer.

PCA plot: ftp://stpfiles.er.usgs.gov/Monica/R_Data/pca_veg_lidarclass_phase2.pdf
CA plot: ftp://stpfiles.er.usgs.gov/Monica/R_Data/corresp_anal_phase2.pdf
DCA plot: ftp://stpfiles.er.usgs.gov/Monica/R_Data/detrend_corresp_anal_phase2.pdf
DCA how i would expect it: ftp://stpfiles.er.usgs.gov/Monica/R_Data/detrend_corresp_anal_phase2_a.pdf

Any thoughts on this will be very much appreciated,




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