Clarify what plain text and markdown are

recommendations.Rmd

@@ -179,49 +179,52 @@ researcher's institution can't afford a license, the text of that document will
 be inaccessible.
 
 More commonly, if one finds a document written using an older version of the
-software (e.g. `.doc` vs `.docx`), there is no guarantee it can be opened in the
-new version of the software. Documents can only be opened by people who can
-afford to purchase the products sold by the vendor. Opening the same document in
-different versions of the same software or on different computers could render
-different results (such as when opening a Windows PowerPoint presentation on a
-Mac). Storing either data or manuscripts in such formats means that they can be
-lost forever or could be inaccessible to certain groups of people. In contrast,
-writing in an open, text-based source format means that the document can be
-opened by anyone with access to a computer or mobile device.
-
-There are several plain-text "[markup language]" formates, such as [LaTeX] or
-[HTML]. However, there are major drawbacks to these "languages", including the
-difficulty and effort required to learn them. Luckily, there is the
-[Markdown] format which is simple to learn and to use. Since Markdown is just
-plain text, changes can also be easily tracked using [Git] and collaboration can
-happen on [GitHub] or [GitLab]. There are also promising online text editors
-emerging which support Markdown with track changes to ease the transition for
-those not wanting to learn GitHub, e.g. Authorea. Plus, when using 
-[Pandoc Markdown], the document can be converted to a large range of output
-formats, including Word `.docx`, beautifully typeset [LaTeX] PDFs, or web friendly
-[HTML] files. Markdown also has features typically required of scientific
-writing such as citation and bibliography insertion (including plain text
-formats such as [BibTeX]). Taken together Markdown is a simple, powerful plain
-text format that ensures documents will stick around well into the future.
+software (e.g. `.doc` vs `.docx`), there is no guarantee it can be opened in
+the new version of the software. Opening the same document in different
+versions of the same software or on different computers could render different
+results (such as when opening a Windows PowerPoint presentation on a Mac).
+Documents can only be opened by people who can afford to purchase the products
+sold by the vendor. Storing either data or manuscripts in such formats means
+that they can be lost forever or could be inaccessible to certain groups of
+people. In contrast, writing in an open, text-based source format means that
+the document can be opened by anyone with access to a computer or mobile
+device.
+
+Open, text-based formats are commonly referred to as plain text documents.
+Although plain text itself cannot be formatted into headings, bold font, etc;
+the addition of text-based markup, such as `*` or `[bold]` surrounding a word,
+enables text editors to display plain text as formatted documents. There are
+several plain-text "[markup language]", such as [LaTeX] or [HTML], but many of
+these have verbose markup that make them inefficient to type and difficult to
+learn. [Markdown] is a markup language that was designed from markup
+conventions used over email so it is simple to learn and easy to type. A flavor
+of Markdown called [Pandoc Markdown]) is specialized on scholarly communication
+and support features required in scientific writing such as automatic figure
+referencing, in text citations, and bibliography insertion (including plain
+text formats such as [BibTeX]). [Pandoc Markdown] documents can also be
+converted to a large range of output formats, including Word `.docx`,
+beautifully typeset [LaTeX] PDFs, or web friendly [HTML] files. [R Markdown] is
+an extension of [Pandoc Markdown] that allows R and Python code to be executed
+within and inserted into a document, increasing document-level reproducibility.
+
+Since Markdown is just plain text, changes can be easily tracked using [Git]
+and collaboration can happen on [GitHub] or [GitLab]. There are also promising
+online text editors emerging which support Markdown with track changes to ease
+the transition for people used to conventional word processors, e.g. [Authorea]
+and [Stencila]. Taken together the Markdown format is an open plain text format
+that is accessible and usable on all operating systems, has an active community
+of users, is well maintained and documented (e.g. the [Pandoc Markdown] manual
+or the [R Markdown Book]), can be converted in a wide range of document types
+(see the [Pandoc Markdown] about page for examples), is designed for simplicity
+and readability, and has flavors dedicated to scholarly communication.
 
 [HTML]: https://en.wikipedia.org/wiki/HTML
 [LaTeX]: https://www.latex-project.org/
 [markup language]: https://en.wikipedia.org/wiki/Markup_language
 [Markdown]: https://en.wikipedia.org/wiki/Markdown
 [BibTeX]: https://en.wikipedia.org/wiki/BibTeX
-
-TODO: Determine if there is a "Python Markdown" available
-
-The Markdown format is open source, is simple plain text (accessible and usable
-on all operating systems and versions), has an active community of users, is
-well maintained and documented (e.g. the [Pandoc Markdown] or the [R Markdown
-Book]), can be converted in a wide range of document types (see the [Pandoc
-Markdown] about page for examples), is designed for simplicity and readability.
-For R based projects, use [R Markdown], an extension of Markdown that allows R
-code to be executed within and inserted into a document, increasing
-document-level reproducibility. [RStudio] offers a great environment to write R
-Markdown.
-
+[Authorea]: https://www.authorea.com/
+[Stencila]: https://stenci.la/
 [R Markdown Book]: https://bookdown.org/yihui/rmarkdown/
 
 #### Dissemination phase