github md now to yaml metadata

Author: bbest

rmarkdown_example/test.Rmd

@@ -3,6 +3,8 @@ title: "Trying Rmarkdown"
 author: "Ben Best"
 date: "August 1, 2014"
 output:
+  md_document:
+    variant: markdown_github
   pdf_document:
     fig_caption: yes
     number_sections: yes
@@ -55,19 +57,17 @@ plot(cars)
 
 Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
 
-## Render Markdown
+## Github Markdown
 
-To get github friendly Markdown document for cleanly tracking changes to document in Github, use this command in the console (not within the document).
+To get github friendly Markdown document for cleanly tracking changes to document in Github, put the following output first:
 
-```{r, eval=FALSE}
-library(rmarkdown)
-render(
-  'test.Rmd', 
-  md_document(
-    'markdown_github', 
-    preserve_yaml=F, 
-    toc=T))
 ```
+output:
+  md_document:
+    variant: "markdown_github"
+```
+
+NOTE: You need to run this **LAST** though, since knitting other formats wipes out the `test_files` directory. To return to the Knit button having other options (HTML, PDF, Word), move this output type below the first option.
 
 ## References {-}
 <!-- placeholder for References in toc --!>

rmarkdown_example/test.docx

@@ -63,7 +63,7 @@ <h4 class="date"><em>August 1, 2014</em></h4>
 <li><a href="#introduction">Introduction</a></li>
 <li><a href="#food-provision-fisheries"><span class="toc-section-number">0.1</span> Food Provision: Fisheries</a></li>
 <li><a href="#default-rmarkdown"><span class="toc-section-number">0.2</span> Default Rmarkdown</a></li>
-<li><a href="#render-markdown"><span class="toc-section-number">0.3</span> Render Markdown</a></li>
+<li><a href="#github-markdown"><span class="toc-section-number">0.3</span> Github Markdown</a></li>
 <li><a href="#references">References</a></li>
 </ul>
 </div>
@@ -104,16 +104,13 @@ <h2><span class="header-section-number">0.2</span> Default Rmarkdown</h2>
 </div>
 <p>Note that the <code>echo = FALSE</code> parameter was added to the code chunk to prevent printing of the R code that generated the plot.</p>
 </div>
-<div id="render-markdown" class="section level2">
-<h2><span class="header-section-number">0.3</span> Render Markdown</h2>
-<p>To get github friendly Markdown document for cleanly tracking changes to document in Github, use this command in the console (not within the document).</p>
-<pre class="r"><code>library(rmarkdown)
-render(
-  'test.Rmd', 
-  md_document(
-    'markdown_github', 
-    preserve_yaml=F, 
-    toc=T))</code></pre>
+<div id="github-markdown" class="section level2">
+<h2><span class="header-section-number">0.3</span> Github Markdown</h2>
+<p>To get github friendly Markdown document for cleanly tracking changes to document in Github, put the following output first:</p>
+<pre><code>output:
+  md_document:
+    variant: &quot;markdown_github&quot;</code></pre>
+<p>NOTE: You need to run this <strong>LAST</strong> though, since knitting other formats wipes out the <code>test_files</code> directory. To return to the Knit button having other options (HTML, PDF, Word), move this output type below the first option.</p>
 </div>
 <div id="references" class="section level2 unnumbered">
 <h2>References</h2>

rmarkdown_example/test.html

@@ -1,9 +1,3 @@
--   Introduction
--   Food Provision: Fisheries
--   Default Rmarkdown
--   Render Markdown
--   References
-
 Introduction
 ------------
 
@@ -50,20 +44,16 @@ You can also embed plots, for example:
 
 Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
 
-Render Markdown
+Github Markdown
 ---------------
 
-To get github friendly Markdown document for cleanly tracking changes to document in Github, use this command in the console (not within the document).
+To get github friendly Markdown document for cleanly tracking changes to document in Github, put the following output first:
 
-``` {.r}
-library(rmarkdown)
-render(
-  'test.Rmd', 
-  md_document(
-    'markdown_github', 
-    preserve_yaml=F, 
-    toc=T))
-```
+    output:
+      md_document:
+        variant: "markdown_github"
+
+NOTE: You need to run this **LAST** though, since knitting other formats wipes out the `test_files` directory. To return to the Knit button having other options (HTML, PDF, Word), move this output type below the first option.
 
 References
 ----------