Update Methods section (greenelab#805)

content/08.methods.md

@@ -8,11 +8,11 @@ Accordingly, we collaboratively wrote this review in the open, enabling anyone w
 We wrote the manuscript in markdown and tracked changes using git.
 Contributions were handled through GitHub, with individuals submitting "pull requests" to suggest additions to the manuscript.
 
-To facilitate citation, we [defined](https://github.com/greenelab/deep-review/blob/master/CONTRIBUTING.md#markdown) a markdown citation syntax.
+To facilitate citation, we [defined](https://github.com/greenelab/deep-review/blob/master/USAGE.md#citations) a markdown citation syntax.
 We supported citations to the following identifier types (in order of preference): DOIs, PubMed Central IDs, PubMed IDs, arXiv IDs, and URLs.
 References were automatically generated from citation metadata by querying APIs to generate [Citation Style Language](http://citationstyles.org/) (CSL) JSON items for each reference.
 [Pandoc](http://pandoc.org/) and [pandoc-citeproc](https://github.com/jgm/pandoc-citeproc) converted the markdown to HTML and PDF, while rendering the formatted citations and references.
-In total, referenced works consisted of {{manuscript_stats.reference_counts.doi}} DOIs, {{manuscript_stats.reference_counts.pmcid}} PubMed Central records, {{manuscript_stats.reference_counts.pmid}} PubMed records, {{manuscript_stats.reference_counts.arxiv}} arXiv manuscripts, and {{manuscript_stats.reference_counts.url}} URLs (webpages as well as manuscripts lacking standardized identifiers).
+In total, referenced works consisted of {{manuscript_stats.reference_counts.doi}} DOIs, {{manuscript_stats.reference_counts.pmcid}} PubMed Central records, {{manuscript_stats.reference_counts.arxiv}} arXiv manuscripts, and {{manuscript_stats.reference_counts.url}} URLs (webpages as well as manuscripts lacking standardized identifiers).
 
 We implemented continuous analysis so the manuscript was automatically regenerated whenever the source changed [@doi:10.1038/nbt.3780].
 We configured Travis CI---a continuous integration service---to fetch new citation metadata and rebuild the manuscript for every commit.