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 s?n. 14. okt. 2018 kl. 18.07 skrev Irene Adamo <i.adamo90 at gmail.com>:
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
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