[R-sig-eco] distance matrix with chao-jaccard method

[Jakob Russel]

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 <i.adamo90 using 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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

	[[alternative HTML version deleted]]