Merge pull request PecanProject#2874 from infotroph/book-chunk-fix

make Rmarkdown code chunks use same number of ticks at start and end

book_source/03_topical_pages/01_advanced_vm.Rmd

@@ -90,9 +90,9 @@ Login to [Amazon Web Services (AWS)](http://console.aws.amazon.com/) and select
 +	Click “Add Rule”, leave the pull down on “Custom TCP Rule”, and then change the Port Range from 0 to 8787. Set “Source” to Anywhere. This rule allows you to access RStudio Server on PEcAn.
 +	Click “Review and Launch”  . You will then see this pop-up:
 
-  ```{r, echo=FALSE,fig.align='center'}
+```{r, echo = FALSE, fig.align = 'center'}
 knitr::include_graphics(rep("figures/pic2.jpg"))
-```    
+```
 
 Select the default drive volume type and click Next
 

documentation/tutorials/StateAssimilation/TreeRingSDA.Rmd

@@ -96,21 +96,21 @@ Perform a site-level SIPNET run using the following settings
   </state.data.assimilation>
 ```
 
-* Delete the ```<pfts>`` block from the settings
+* Delete the `<pfts>` block from the settings
 
-* In the PEcAn History, go to your PDA run and open ```pecan.pda[UNIQUEID].xml``` (the one PEcAn saved for you AFTER you finished the PDA)
+* In the PEcAn History, go to your PDA run and open `pecan.pda[UNIQUEID].xml` (the one PEcAn saved for you AFTER you finished the PDA)
 
-* Cut-and-paste the PDA ```<pfts>``` block into the SDA settings file
+* Cut-and-paste the PDA `<pfts>` block into the SDA settings file
 
-* Save the file as ```pecan.SDA.xml```
+* Save the file as `pecan.SDA.xml`
 
 #### Loading data
 
 * If you have not done so already, clone (new) or pull (update) the PalEON Camp2016 repository
  + Open a shell under Tools > Shell
- + ```cd`` to go to your home directory
- + To clone: ```git clone [email protected]:PalEON-Project/Camp2016.git```
- + To pull: ```cd Camp2016; git pull https://github.com/PalEON-Project/Camp2016.git master```
+ + `cd` to go to your home directory
+ + To clone: `git clone [email protected]:PalEON-Project/Camp2016.git`
+ + To pull: `cd Camp2016; git pull https://github.com/PalEON-Project/Camp2016.git master`
 
 * Open the tree-ring data assimilation workflow under Home > pecan > scripts > workflow.treering.R
 
@@ -158,7 +158,7 @@ $$\tau_{r} \sim Gamma(a_r,r_r)$$
 
 This model is encapsulated in the PEcAn function:
 
-``````{r echo= TRUE, eval=FALSE}
+```{r echo = TRUE, eval = FALSE}
 InventoryGrowthFusion(combined,n,iter)
 ```