Re: [R-sig-eco] distance matrix with chao-jaccard method
vegan::vegdist() function **has** Chao-Jaccard index (method = “chao”). In addition, vegan has function chaodist that is similar to designdist(), but uses the Chao terms (U, V) allowing you to define any Chao distance (see ?chaodist for examples). Vegan has these choices, but I don’t endorse them: it’s all up to your responsibility. cheers, Jari Oksanen > On 14 Oct 2018, at 19:07 pm, Irene Adamo wrote: > > Dear all, > I would like to create a distance matrix based on the similarity > Chao-Jaccard index based on raw abundances in R but so far I have not been > able to find a package that does it. The Vegan package does not have this > option and the dis.chao function of CommEcol creates a dissimilarity > matrix. I hope that you can help find a solution. > > thanks in advance! > Irene Adamo > > [[alternative HTML version deleted]] > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] distance matrix with chao-jaccard method
Dear Irene, The fossil package has a function for this: https://www.rdocumentation.org/packages/fossil/versions/0.3.7/topics/chao.sorenson If you want all pairwise comparisons on a community matrix (comm, with samples as columns): mat.cj <- sapply(1:ncol(comm), function(i) sapply(1:ncol(comm), function(j) chao.jaccard(comm[,i],comm[,j]))) Cheers, Jakob Den søn. 14. okt. 2018 kl. 18.07 skrev Irene Adamo : > Dear all, > I would like to create a distance matrix based on the similarity > Chao-Jaccard index based on raw abundances in R but so far I have not been > able to find a package that does it. The Vegan package does not have this > option and the dis.chao function of CommEcol creates a dissimilarity > matrix. I hope that you can help find a solution. > > thanks in advance! > Irene Adamo > > [[alternative HTML version deleted]] > > ___ > 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
[R-sig-eco] distance matrix with chao-jaccard method
Dear all, I would like to create a distance matrix based on the similarity Chao-Jaccard index based on raw abundances in R but so far I have not been able to find a package that does it. The Vegan package does not have this option and the dis.chao function of CommEcol creates a dissimilarity matrix. I hope that you can help find a solution. thanks in advance! Irene Adamo [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
