Rename calculateDistance

[antagomir]

The calculateDistance is using the various dissimilarity indices that are available through vegan. Some of those are not distances, for instance Bray-Curtis is not a distance (it does not satisfy triangle inequality). This is an important difference.

I propose to rename this function as calculateDissimilarity.

In addition, it could be mentioned more clearly in the manpage that these same indices are often called beta diversity in (microbial and other) ecology.

[FelixErnst]

This function will be removed as well, since the functionality was just there to support runMDS2. There is need for it anymore.

[antagomir]

Add a .Deprecate note on this function, if this is going to be removed?

[TuomasBorman]

So function that will be removed is:

• calculateDistance

These functions utilize calculateDistance:

• estimateDivergence
• calculateUniFrac
• calculateJSD

I am not sure what was meant to do with these 3 functions

[antagomir]

Ok, so it was used for multiple functions. We can either

1) Keep this available but then I would change the name to maintain conceptual clarity

2) Hide the function (unexport), it could still be utilized by those other functions; but then Deprecation message would be necessary since some users may still have workflows with this.

[FelixErnst]

I think calculateDistance could be wrapped internally and the deprecation of the exported function done for current devel. It would gone by Bioc 3.15.

The usage in

• estimateDivergence
• calculateUniFrac
• calculateJSD can be switched to the internal wrapper now and the deletion after deprecation would be straightforward

[antagomir]

Ok to me.

[FelixErnst]

Can this be closed?

[TuomasBorman]

I think all is done for now, removing the function is the next step

So yes, this can be closed