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 th
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), fun
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
