Hi, On Mon, Jun 24, 2013 at 12:04 PM, Suparna Mitra <suparna.mitra...@gmail.com> wrote: > Dear Sarah, > Thanks for your reply. But I don't have any site where all the species are > 0.
Well, that's what this says: > 1: In distfun(comm, method = distance, ...) : > you have empty rows: their dissimilarities may be meaningless in method > “bray” > Is there anyway to calculate the dissimilarity between sites where it > computes only the non-zero species values. Excluding all the zero event will > result a big loss in species data. I don't want to delete the cases where > may be 5out of 8 sites have species info, only 3 don't have. There's no reason to delete those. Bray-Curtis and similar metrics consider only joint presences, not joint absences. If you have a lot of sites with no species in common, it can also cause problems. That's what vegan::stepacross is intended to deal with. > Should I replace zero with a very small number. What is the best thing to > do in such cases? The best thing to do in such cases is to provide a reproducible example to R-help. At the very least, str(X) str(data) # called in metaMDS() but not described; also, don't call your data data and double-check to make sure you don't have any all-zero rows or NA values in your data. Sarah > On 24 June 2013 21:24, Sarah Goslee <sarah.gos...@gmail.com> wrote: >> >> Hi, >> >> What do you expect the dissimilarity between a site with no species >> and a site with some species to be? >> >> If you want to use Bray-Curtis dissimilarity, you need to drop the >> sites with no species, as the error message suggests. >> >> But if you can answer my first question, you may be able to select a >> different dissimilarity metric that matches your expectations >> numerically. >> >> Sarah >> >> >> On Mon, Jun 24, 2013 at 7:33 AM, Suparna Mitra >> <suparna.mitra...@gmail.com> wrote: >> > H >> > ello R-experts, >> > I want to do ordination plots using vegan metaMDS. >> > I have a where many cells have zero values. >> > >> > Data structure: >> > X[1:10,1:14] >> > Height.1 Height.2 Height.3 Height.4 Height.5 Height.6 Height.7 >> > Height.8 Height.9 Height.10 Height.11 Height.12 Height.13 >> > D30I1A 46 0 0 0 0 0 0 >> > 0 0 0 39 0 98 >> > D30I1B 46 0 0 0 0 0 0 >> > 0 0 0 39 0 98 >> > D30I1C 70 0 0 0 0 0 0 >> > 0 0 0 0 85 0 >> > D30I2A 47 0 0 0 0 0 0 >> > 0 0 0 49 0 105 >> > D30I2B 68 0 0 0 0 0 0 >> > 0 0 0 83 0 214 >> > D30I2C 0 75 0 0 0 0 0 >> > 0 0 0 0 83 0 >> > D30I3A 48 0 0 0 0 0 0 >> > 0 0 0 42 0 107 >> > D30I3B 64 0 0 0 0 0 0 >> > 0 0 0 72 0 177 >> > D30I3C 72 0 0 0 0 0 0 >> > 0 0 0 0 96 0 >> > D30M1A 60 0 0 0 0 0 0 >> > 0 0 0 74 0 169 >> > >> > Another data structure >> >> Genus_data[1:10,1:14] >> > Sample Acanthamoeba Acidianus Aegilops Alphapapillomavirus >> > Asfivirus >> > Brassica Buchnera Coprinellus Diaphorobacter Hartmannella Ignicoccus >> > 1 HS1_S1 0 0 0 0 >> > 0 >> > 0 0 0 0 0 0 >> > 2 HS2_S2 0 1 1 0 >> > 0 >> > 0 0 0 0 1 0 >> > 3 HS3_S3 0 0 0 1 >> > 0 >> > 0 1 1 1 0 0 >> > 4 HS4_S4 0 0 0 0 >> > 1 >> > 0 0 0 0 0 0 >> > 5 HS13_S5 0 0 0 0 >> > 0 >> > 0 0 0 0 0 0 >> > 6 HS14_S6 0 0 0 0 >> > 0 >> > 1 0 0 0 0 0 >> > 7 HS15_S7 0 0 0 0 >> > 0 >> > 0 0 0 0 0 0 >> > 8 HS16_S8 0 0 0 0 >> > 0 >> > 0 0 0 0 0 1 >> > 9 HS25_S9 1 0 0 0 >> > 0 >> > 0 0 0 0 0 0 >> > >> > I am having two different kind of errors for these two data... >> > Error 1 >> >> ord1 <- metaMDS( >> > X >> > ="bray") >> > Square root transformation >> > Wisconsin double standardization >> > Error in if (any(dist < -sqrt(.Machine$double.eps))) warning("some >> > dissimilarities are negative -- is this intentional?") : >> > missing value where TRUE/FALSE needed >> > In addition: Warning messages: >> > 1: In distfun(comm, method = distance, ...) : >> > you have empty rows: their dissimilarities may be meaningless in >> > method >> > “bray” >> > 2: In distfun(comm, method = distance, ...) : missing values in results >> > >> > Error 2 >> > ord.data= metaMDS(data, distance="bray") >> > Error in if (any(autotransform, noshare > 0, wascores) && any(comm < 0)) >> > { >> > : >> > missing value where TRUE/FALSE needed >> > In addition: Warning message: >> > In Ops.factor(left, right) : < not meaningful for factors >> > >> > I searched all the details of metaMDS where it is suggested to avail the >> > argument 'zerodist' >> > So I tried both >> > >> > X.dist1 <- metaMDSdist(X, method="bray",zerodist = "ignore") >> > X.dist2 <- metaMDSdist(X, method="bray",zerodist = "add") >> > >> > Can Please help me with this. >> > Thanks, >> > Mitra >> > >> -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ 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.