ENH: add evenness metrics

[colinbrislawn]

This should now to ready to merge.
Eventually, this will resolve #568.

[colinbrislawn]

TODO:

• Get feedback on naming metrics and incorporate that
• Add these metrics to vignettes
• Get plots to work
• Get Travis build to work

[colinbrislawn]

This build currently finishes, but is marked as failing due to three warning.

Status: 3 WARNINGs, 8 NOTEs
See
  ‘/home/travis/build/joey711/phyloseq/phyloseq.Rcheck/00check.log’
for details.

@joey711 Any ideas?

[colinbrislawn]

These are the three warning detected. I didn't change these files so I think these were standing problems before this PR. How should I resolve these?

checking whether package ‘phyloseq’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘ggplot2::Position’ when loading ‘phyloseq’
  Warning: replacing previous import by ‘scales::alpha’ when loading ‘phyloseq’

[Lots of notes, which I omit]
[...]

checking Rd cross-references ... WARNING
Missing link or links in documentation object 'import_uparse.Rd':
  ‘[data.table]{read.table}’

Missing link or links in documentation object 'psmelt.Rd':
  ‘ggplot2’

See section 'Cross-references' in the 'Writing R Extensions' manual.
 checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'microbio_me_qiime'
  ‘ext’ ‘parsef’ ‘...’

Undocumented arguments in documentation object 'rarefy_even_depth'
  ‘trimOTUs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.

[colinbrislawn]

How does this look @joey711? How should I add these to the vignettes?

[colinbrislawn]

@joey711 Does this look ready to merge?

[colinbrislawn]

I could update this make use of the current build process, and to show examples in the vignettes on the new website.

[colinbrislawn]

@joey711 Are you still accepting PRs for this project or you actively developing SecondGenomeR?