Add getAlpha

[TuomasBorman]

Currently, we have only addAlpha function that adds values to colData. getAlpha function returns data.frame with the indices without adding them to colData

[TuomasBorman]

This PR also simplifies the alpha diversity functions. Previously we combined different diversity functions to be used through addAlpha. We did minimal changes to get the functions working, however, that led to overhead and suboptimal solutions (internal function was calling other internal function that was calling other...). Moreover, ace index calculation was not even working correctly because of these suboptimal choices that were made previously.

[antagomir]

Seems good, just one note that the original functions were splitted into informative categories (richness, evenness, diversity, dominance, rarity). It would be good to keep that information (what index belongs to what category) in the documentation at least.

[TuomasBorman]

Yes, the documentation has this information

[TuomasBorman]

TODO and things to answer:

• Remove code that is not used anymore.
• Investigate why the rarefaction fails (might be also that the old code was incorrect)

[TuomasBorman]

TODO and things to answer:

* Remove code that is not used anymore.

* Investigate why the rarefaction fails (might be also that the old code was incorrect)

• Unused code removed.
• The old code was incorrect. Now rarefaction works as expected.

[codecov]

Codecov Report

Attention: Patch coverage is 92.47312% with 7 lines in your changes missing coverage. Please review.

Project coverage is 69.28%. Comparing base (e4b7e97) to head (759191f).
Report is 6 commits behind head on devel.

Files with missing lines	Patch %	Lines
R/addAlpha.R	97.14%	2 Missing ⚠️
R/estimateEvenness.R	80.00%	2 Missing ⚠️
R/estimateDiversity.R	66.66%	1 Missing ⚠️
R/estimateDominance.R	66.66%	1 Missing ⚠️
R/estimateRichness.R	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #669      +/-   ##
==========================================
- Coverage   70.11%   69.28%   -0.83%     
==========================================
  Files          47       47              
  Lines        5778     5828      +50     
==========================================
- Hits         4051     4038      -13     
- Misses       1727     1790      +63     

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