Hi, you may have a look to the following publication:
http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12362/abstract Barwell et al. 2015 nicely compare the characteristics of different pairwise beta-diversity measures. They give recommendations for choosing beta-diversity measures along the gradient of focusing on richness differences to turnover. HTH, Torsten On Wed, 3 Apr 2019 at 09:10, Botta-Dukát Zoltán < botta-dukat.zol...@okologia.mta.hu> wrote: > Dear Tim, > > You are right: Bray-Curtis distance will be non-zero if two communities > differ in size (sum of abundances), even if the relative abundances is > the same. If you have number of individuals data, rarefying is the best > solution. If you cannot apply it (e.g. because only cover data are > available), you can calculate distance from relative abundance, and yes, > this case BC is equivalent to Manhattan. Note that using relative > abundances don't remove fully the effect of different sampling effort, > because rare species could missing from the smaller sample. > > I don't recommend calculating BC-distance from Hellinger-transformed > data, because sum of transformed abundances are meaningless. > > Best regards, > > Zoltan > > 2019. 04. 02. 17:15 keltezéssel, Tim Richter-Heitmann írta: > > Dear list, > > > > i am not an ecologist by training, so please bear with me. > > > > It is my understanding that Bray Curtis distances seem to be sensitive > > to different community sizes. Thus, they seem to deliver inadequate > > results when the different community sizes are the result of technical > > artifacts rather than biology (see e.g. Weiss et al, 2017 on > > microbiome data). > > > > Therefore, i often see BC distances made on relative data (which seems > > to be equivalent to the Manhattan distance) or on data which has been > > subsampled to even sizes (e.g. rarefying). Sometimes i also see Bray > > Curtis distances calculated on Hellinger-transformed data, > > > > which is the square root of relative data. This again makes sample > > sizes unequal (but only to a small degree), so i wondered if this is a > > valid approach, especially considering that the "natural" distance > > choice for Hellinger transformed data is Euclidean (to obtain, well, > > the Hellinger distance). > > > > Another question is what different sizes (i.e. the sums) of Hellinger > > transformed communities represent? I tested some datasets, and > > couldnt find a correlation between original sample sizes and their > > hellinger transformed counterparts. > > > > Any advice is very much welcome. Thank you. > > > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
