added formats: pdf, docx, md

rmarkdown_example/test.Rmd

@@ -4,10 +4,18 @@ author: "Ben Best"
 date: "August 1, 2014"
 output:
   html_document:
-    toc: true
-    number_sections: true
-bibliography: test.bib
+    fig_caption: yes
+    keep_md: yes
+    number_sections: yes
+    toc: yes
+  pdf_document:
+    fig_caption: yes
+    number_sections: yes
+    toc: yes
+  word_document:
+    fig_caption: yes
 csl: apa.csl
+bibliography: test.bib
 ---
 
 ## Introduction {-}
@@ -42,11 +50,11 @@ summary(cars)
 
 You can also embed plots, for example:
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, fig.cap='Scatterplot of cars.'}
 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.
 
 ## References {-}
-\
+<!-- placeholder for References in toc --!>

rmarkdown_example/test.md

@@ -0,0 +1,53 @@
+# Trying Rmarkdown
+Ben Best  
+August 1, 2014  
+
+## Introduction {-}
+
+The Ocean Health Index [@halpern_index_2012; @selig_assessing_2013] derives most of its pressures from Halpern et al. [-@halpern_global_2008].
+
+## Food Provision: Fisheries
+
+Amount of sustainable wild-caught seafood compared to the max sustainable
+
+$$
+x_{FIS} =  (\prod_{g=1}^{6} SS_{i,g}^{C_{i,g}})^\frac{1}{\sum{C_{i,g}}}
+$$
+
+Variables:
+
+- $SS$: stock status score, based on B/Bmsy and an underharvest penalty adjustment
+- $C$: total catch
+- $i$: OHI reporting region
+- $g$: level of taxonomic grouping (ISSCAAP)</small>
+
+
+## Default Rmarkdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+
+```r
+summary(cars)
+```
+
+```
+##      speed           dist    
+##  Min.   : 4.0   Min.   :  2  
+##  1st Qu.:12.0   1st Qu.: 26  
+##  Median :15.0   Median : 36  
+##  Mean   :15.4   Mean   : 43  
+##  3rd Qu.:19.0   3rd Qu.: 56  
+##  Max.   :25.0   Max.   :120
+```
+
+You can also embed plots, for example:
+
+![Scatterplot of cars.](./test_files/figure-html/unnamed-chunk-2.png) 
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+
+## References {-}
+<!-- placeholder for References in toc --!>