Elaine: You would do better posting this on the R-sig-ecology list, I believe. THE r-help list is mostly for general R programming questions, while the ecology list readers will have expertise more closely related to your specific issues.
Cheers, Bert On Fri, Sep 6, 2013 at 3:25 PM, Elaine Kuo <elaine.kuo...@gmail.com> wrote: > Dear List, > > > > This is Elaine, a postgraduate studying in bird distributions in East Asia. > > > > I want to calculate Simpson dissimilarity index, > > based on a presence/absence matrix of bird species in islands in East Asia. > > (matrix row: 36 islands/matrix column: species ID) > > (R package vegan to make NMDS and R package betapart) > > > > In most papers using vegan for NMDS and betapart for dissimilarity index, > > the dissimilarity index is generated by grid data in continents. > > The calculation of this index is done by comparing species presence/absence > between a pair of grids adjacent to each other. > > > > However, in my case, the dissimilarity index needs to be generated per > island, > > and it is difficult for islands to find continuous landmass nearby. > > I would like ask if the calculation of dissimilarity index using metaMDS > and beta.pair in continents can work as well as in islands. > > If so, please kindly advice how the mechanisim behind the code generates > the dissimilarity index for island. > > (Does it compare species presence/absence between a pair of island? > > Should the two islands be specifically located or close to each other?) > > > > Thank you > > Elaine > > > > Code > > # NMDS > > library(MASS) > > library(vegan) > > island.NMDS <- metaMDS(island,k=2, distfun = betadiver, distance = > "sim",trymax=100,zerodist="add") > > plot(island.NMDS, type = "n") > > > > #Simpson Dissimilarity Index > > library(betapart) > > island.dist<-beta.pair(island, index.family="sor") > > class(island.dist) > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]] ______________________________________________ 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.
