Changes and Bug Fixes

A specific bug was introduced that prevented local machines and Travis CI servers from building
the package.
- This bug is attributed to a dplyr update (0.7.8 -> 0.8.0.1)
- See Joss branch #79
- See Joss debug branch #82
- See dplyr issue #4213
- See Travis CI forum post
Updated the paper for submission
Added the JOSS paper and draft vignette
Changed correlation plots
- Removed color from background
- Removed hard coded plot limits
- Added "1:1" line and Average lines
- Added a trans parameter to transform the x and y axis
Changed function names
- From create_metacoder to create_taxmap
- From agglomerate_metacoder to agglomerate_taxmap
- From melt_metacoder to melt_taxmap
Bugs
- Fixed output_dir bug where error should have been a warning
- Fixed correlation plot bug where treatments were on the wrong axis.
- Fixed output message for heat tree plots.
Fixed build-check Notes and Warnings

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