added a few comments for @cboettig to abstract
added a few comments to intro for @cboettig, inserted a single period
removed misplaced single quote after boettiger paper reference
inserted () parens in references to function calls in paragraphs in the manusript, #58
added parens after link to render properly
added comment about phylobase reference
added link to treebase where first mentioned
added comment about behavior when there are more than 1 taxa found when using taxize_nexml
Merge pull request #91 from ropensci/devel_sc

scotts comments/changes to ms