Fix to na.rm in decostand methods alr/clr

[antagomir]

This fixes #661

The na.rm option has been enabled in decostand methods "alr" and "clr".

Some notes:

1. "clr": With na.rm=TRUE, the NA entries in original data are replaced by 0 in the clr-transformed data; here zero is an arbitrary choice but no better solutions are available afaik, and the same approach is used in compositions::clr so at least we are in sync. With na.rm=FALSE, the entries that are NA in the original data will be also NAs in the clr-transformed data; the NAs are otherwise ignored in the calculations during the transformation. In the alternative implementation, compositions::alr NAs are always replaced with 0 (no na.rm option available). As far as I can see it is feasible to provide both options for na.rm for the "clr" method, we are providing that now.

2. "alr": similarly done for decostand "alr" transformation, user can choose whether to keep the NAs (na.rm=FALSE) or replace them by 0 (na.rm=TRUE). In comparison, I noticed that in the alternative implementation, compositions::alr NAs are always kept as NAs (no na.rm option available). As far as I can see it is feasible to provide both options for na.rm for the "alr" method, we are providing that now.

3. The "rclr" method will be handled separately in Matrix completion for robust CLR in decostand #619

@TuomasBorman can you test and confirm that these are as you expected?

[TuomasBorman]

I think now works as expected. See the comments.

[antagomir]

Great, fixed the remarks.