Hi, I misunderstand the definition of Canberra distance in R.
On Internet and in function description pages of dist() from stats and Dist() from amap, Canberra distance between vectors x and y, d(x,y), is : d(x,y) = sum(abs(x-y)/(x+y)) But in use, through simple examples, we find that the formula is : d(x,y) = (NZ + 1)/NZ * sum(abs(x-y)/(x+y)) with NZ = nb of pairs of coordinates that are different from (0,0) (Non Zeros) Functions vegdist() from vegan and gdist() from mvpart, like documentation of ADE4 software, use (for positive variables) : d(x,y) = 1/NZ * sum(abs(x-y)/(x+y)) Can someone help me to understand the differences in the choice of the formula and why there's a difference between calculus and explaination for dist() ? Thank you for your help. Best regards, Fred PS : Be careful with function dudi.pca() from ade4 ; in values, "norm" doesn't give you what is written in the help page : "norm" returns the vector of standard deviations of initial variables when you choose "normed" PCA and the vector of standard deviations of normed variables, ie 1, when you choose non "normed" PCA. We contacted authors of the package unsuccessly to rectify the information. -- Dr. Frédéric Chiroleu Biométricien CIRAD-Systèmes Biologiques (Cirad-Bios) UMR 53 PVBMT (Peuplements Végétaux et Bio-agresseurs en Milieu Tropical) Laboratoire d'Ecologie Terrestre et de Lutte Intégrée (LETLI) Pôle de Protection des Plantes (3P) 7, chemin de l'IRAT Ligne Paradis 97410 Saint-Pierre Île de la Réunion - France Tél. : +262 (0)262 499 230 Standard : +262 (0)262 499 200 Fax : +262 (0)262 499 293 Courriel : [EMAIL PROTECTED] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
