Faith index

[antagomir]

We co-authored a fast Faith index calculation, potentially this could be called from R: https://genome.cshlp.org/content/31/11/2131

Ideally, we could utilize the same fast solution by calling it from mia. This might be doable, instead of using slower implementations in external R pkgs.

Leo

[cpauvert]

Hello, thanks for developing and maintaining this package. I just started to use it, so clearly a newbie here.

But I noted down that to use the fast Faith index (that is in python) it can be used in R apparently via Cpp : https://github.com/biocore/unifrac-binaries/tree/main/src/R_interface

More specifically the faith_pd function can be called directly:

Rcpp::List faith_pd(const char* table, const char* tree)

https://github.com/biocore/unifrac-binaries/blob/d4cbb7d98fbe356f4b50bddbb662b341ddb82e98/src/su_R.cpp#L30

Hope that helps,
best,

[TuomasBorman]

Hello, thanks for the comment! We will check this.

-Tuomas

[antagomir]

Now as ecodive is also providing Faith (see https://cmmr.github.io/ecodive/), we could make a quick check on the following:

• same results obtained
• what is the speed difference?

@jepasan could you have a look?