Merge pull request #310 from butterflyskip/issue217

fixes issue #217
swcarpentry · Apr 6, 2018 · 0d5396a · 0d5396a
2 parents a9ebddd + 70b02ea
commit 0d5396a
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diff --git a/_episodes_rmd/05-cmdline.Rmd b/_episodes_rmd/05-cmdline.Rmd
@@ -18,6 +18,7 @@ keypoints:
 
 ```{r, include = FALSE}
 source("../bin/chunk-options.R")
+knitr_fig_path("05-cmdline-")
 ```
 
 The R Console and other interactive tools like RStudio are great for prototyping code and exploring data, but sooner or later we will want to use our program in a pipeline or run it in a shell script to process thousands of data files.

diff --git a/_episodes_rmd/06-best-practices-R.Rmd b/_episodes_rmd/06-best-practices-R.Rmd
@@ -27,6 +27,7 @@ keypoints:
 
 ```{r source, include = FALSE}
 source("../bin/chunk-options.R")
+knitr_fig_path("06-best-practices-R-")
 ```
 ### Keep track of who wrote your code and its intended purpose
 

diff --git a/_episodes_rmd/07-knitr-R.Rmd b/_episodes_rmd/07-knitr-R.Rmd
@@ -18,6 +18,7 @@ keypoints:
 
 ```{r, include = FALSE}
 source("../bin/chunk-options.R")
+knitr_fig_path("07-knitr-R-")
 ```
 
 `knitr` is an R package that allows you to organize your notes, code, and results in a single document. It's a great tool for "literate programming" -- the idea that your code should be readable by humans as well as computers! It also keeps your writing and results together, so if you collect some new data or change how you clean the data, you just have to re-compile the document and you're up to date!

diff --git a/_episodes_rmd/08-making-packages-R.Rmd b/_episodes_rmd/08-making-packages-R.Rmd
@@ -18,8 +18,10 @@ keypoints:
 
 ```{r, include = FALSE}
 source("../bin/chunk-options.R")
+knitr_fit_path("08-making-packages-R-")
 ```
 
+
 Why should you make your own R packages?
 
 **Reproducible research!**

diff --git a/_episodes_rmd/09-supp-intro-rstudio.Rmd b/_episodes_rmd/09-supp-intro-rstudio.Rmd
@@ -14,6 +14,8 @@ keypoints:
 
 ```{r, include= FALSE}
 source("../bin/chunk-options.R")
+knitr_fig_path("09-supp-intro-rstudio-")
+```
 ```
 
 Let's start by learning about our tool.

diff --git a/_episodes_rmd/10-supp-addressing-data.Rmd b/_episodes_rmd/10-supp-addressing-data.Rmd
@@ -14,6 +14,7 @@ keypoints:
 
 ```{r, include = FALSE}
 source('../bin/chunk-options.R')
+knitr_fig_path("10-supp-addressing-data-")
 ```
 
 R is a powerful language for data manipulation.

diff --git a/_episodes_rmd/11-supp-read-write-csv.Rmd b/_episodes_rmd/11-supp-read-write-csv.Rmd
@@ -17,6 +17,7 @@ keypoints:
 
 ```{r, include = FALSE}
 source('../bin/chunk-options.R')
+knitr_fig_path("11-supp-read-write-csv-")
 ```
 
 The most common way that scientists store data is in Excel spreadsheets.

diff --git a/_episodes_rmd/13-supp-data-structures.Rmd b/_episodes_rmd/13-supp-data-structures.Rmd
@@ -20,6 +20,7 @@ exercises: 0
 
 ```{r, include = FALSE}
 source("../bin/chunk-options.R")
+knitr_fig_path("13-supp-data-structures-")
 ```
 
 ### Understanding Basic Data Types in R

diff --git a/_episodes_rmd/14-supp-call-stack.Rmd b/_episodes_rmd/14-supp-call-stack.Rmd
@@ -16,6 +16,7 @@ keypoints:
 
 ```{r, include = FALSE}
 source("../bin/chunk-options.R")
+knitr_fig_path("14-supp-call-stack-")
 ```
 
 ### The Call Stack

diff --git a/_episodes_rmd/15-supp-loops-in-depth.Rmd b/_episodes_rmd/15-supp-loops-in-depth.Rmd
@@ -16,6 +16,7 @@ keypoints:
 
 ```{r, include = FALSE}
 source("../bin/chunk-options.R")
+knitr_fig_path("15-supp-loops-in-depth-")
 ```
 
 In R you have multiple options when repeating calculations: vectorized operations, `for` loops, and `apply` functions.