Speed up 2

[mooreryan]

This builds on #45 by adding one more commit. The reason I wanted to separate it out for y'all is that it changes up a lot about how things are stored in memory, both to speed it up a bit more and to get rid of a lot of reduce and apply calls that were causing a lot of memory churn.

[mooreryan]

Here is a profvis run using the original divnet function (i.e., the one from this commit: ad616a02f93800eb1e63e1088fdbc74f01bf78b0)

And here is the profvis output for the code in this pull request.

As you can see, much better overall! (Just over 3x faster and about 13x fewer memory allocations)

The data was a subset of 479 taxa from the Lee dataset.

[codecov-io]

Codecov Report

Merging #47 into master will increase coverage by 2.2%. The diff coverage is 83.33%.

@@           Coverage Diff            @@
##           master     #47     +/-   ##
========================================
+ Coverage      67%   69.2%   +2.2%     
========================================
  Files          12      11      -1     
  Lines         600     630     +30     
========================================
+ Hits          402     436     +34     
+ Misses        198     194      -4

Impacted Files	Coverage Δ
src/mcmh.cpp	100% <100%> (ø)
R/fit_aitchison.R	79.06% <50%> (-13.24%)	:arrow_down:
R/utility.R	61.11% <0%> (-5.56%)	:arrow_down:

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[mooreryan]

Some more updates....I tested compiling DivNet with a couple different compilers, a couple different optimizations, and with and without OpenMp for the Eigen matrix multiplications and it was basically the same runtime regardless.