Merge branch 'gh-pages' into ajstewartlang-patch-1

Author: jsta

01-what-and-why.Rmd

@@ -14,11 +14,11 @@ library(knitr)
 ## Global options
 options(max.print = "75")
 opts_chunk$set(cache = TRUE,
-               prompt = FALSE,
-               tidy = TRUE,
-               comment = "> #",
-               message = FALSE,
-               warning = FALSE)
+  prompt = FALSE,
+  tidy = TRUE,
+  comment = "> #",
+  message = FALSE,
+  warning = FALSE)
 opts_knit$set(width = 75)
 ```
 
@@ -65,4 +65,4 @@ container. You can have many running containers of the same image.
 
 
 Next: Go to [Lesson 02 Launching Docker](02-Launching-Docker.html) or back to the 
-[main page](http://ropenscilabs.github.io/r-docker-tutorial/).
+[main page](http://jsta.github.io/r-docker-tutorial/).

01-what-and-why.html

@@ -14,11 +14,11 @@ library(knitr)
 ## Global options
 options(max.print = "75")
 opts_chunk$set(cache = TRUE,
-               prompt = FALSE,
-               tidy = TRUE,
-               comment = "> #",
-               message = FALSE,
-               warning = FALSE)
+  prompt = FALSE,
+  tidy = TRUE,
+  comment = "> #",
+  message = FALSE,
+  warning = FALSE)
 opts_knit$set(width = 75)
 ```
 
@@ -159,5 +159,5 @@ in RStudio in your browser.
 
 
 Next: Go to [Lesson 03 Install packages](03-install-packages.html) or back to the 
-[main page](http://ropenscilabs.github.io/r-docker-tutorial/).
+[main page](http://jsta.github.io/r-docker-tutorial/).
 

02-Launching-Docker.Rmd

@@ -104,4 +104,4 @@ docker image contains. Write a README file which documents the details of the
 
 
 Next: Go to [Lesson 04 Dockerhub](04-Dockerhub.html) or back to the 
-[main page](http://ropenscilabs.github.io/r-docker-tutorial/).
+[main page](http://jsta.github.io/r-docker-tutorial/).

02-Launching-Docker.html

@@ -14,11 +14,11 @@ library(knitr)
 ## Global options
 options(max.print = "75")
 opts_chunk$set(cache = TRUE,
-               prompt = FALSE,
-               tidy = TRUE,
-               comment = "> #",
-               message = FALSE,
-               warning = FALSE)
+  prompt = FALSE,
+  tidy = TRUE,
+  comment = "> #",
+  message = FALSE,
+  warning = FALSE)
 opts_knit$set(width = 75)
 ```
 
@@ -125,5 +125,5 @@ know with your neighbour.
 
 
 Next: Go to [Lesson 05 Dockerfiles](05-dockerfiles.html) or back to the 
-[main page](http://ropenscilabs.github.io/r-docker-tutorial/).
+[main page](http://jsta.github.io/r-docker-tutorial/).
 

03-install-packages.Rmd

@@ -103,4 +103,4 @@ Find the Dockerfile of the `rocker/verse` image through Docker Hub.
  - Find the build details of the `rocker/verse` image. What do they tell us?
 
 Go to [Lesson 06 Share all your analysis](06-Sharing-all-your-analysis.html) or back to the  
-[main page](http://ropenscilabs.github.io/r-docker-tutorial/).
+[main page](http://jsta.github.io/r-docker-tutorial/).

03-install-packages.html

@@ -7,8 +7,8 @@ output:
     highlight: pygments
 ---
 
-Now that we have leanrned how to work with a dockerfile, we can send all our analysis to a collaborator. 
-We will share an image that contains all the dependencies that we need to ran our analysis, the data and the analysis.
+Now that we have learned how to work with a dockerfile, we can send all our analysis to a collaborator. 
+We will share an image that contains all the dependencies that we need to run our analysis, the data and the analysis.
 
 We will build this image via a dockerfile. Let's start with the basic verse rocker image we used before. 
 This time we want to have a specific R version (3.3.2), which the developers make possible by tagging the images with the version.
@@ -36,9 +36,8 @@ On a new R script let's write the following analysis.
 library(ggplot2)
 library(gapminder)
 
-life_expentancy_plot <- ggplot(data = gapminder) + 
-	geom_point(aes(x = lifeExp, y = gdpPercap, colour = continent)) 
-
+life_expentancy_plot <- ggplot(data = gapminder) +
+  geom_point(aes(x = lifeExp, y = gdpPercap, colour = continent))
 ```
 
 We will save this r script as analysis.R and add it to our dockerfile.
@@ -112,4 +111,5 @@ docker pull yourhubusername/gapminder_my_analysis:firsttry
 
 They now have the image of your analysis.
 
-Click to go back to the [main page](http://ropenscilabs.github.io/r-docker-tutorial/).
+
+Click to go back to the [main page](http://jsta.github.io/r-docker-tutorial/).

04-Dockerhub.Rmd

@@ -0,0 +1,12 @@
+
+RMD := $(wildcard *.Rmd)
+KNIT_HTML := $(patsubst %.Rmd, %.html, $(RMD))
+
+all: $(KNIT_HTML)
+
+test: 
+	echo $(RMD)
+	echo $(KNIT_HTML)
+
+%.html: %.Rmd
+	Rscript -e "rmarkdown::render('$<')"

04-Dockerhub.html

@@ -2,7 +2,7 @@
 A docker tutorial for reproducible research.
 
 This is an introduction to Docker designed for participants with knowledge
-about R and RStudio. The introduction is intended to be helping people who need Dockerfor a project. We first explain what Docker is and why it is useful. Then 
+about R and RStudio. The introduction is intended to be helping people who need Docker for a project. We first explain what Docker is and why it is useful. Then 
 we go into the the details on how to use it for a reproducible transportable project.
 
 
@@ -18,5 +18,5 @@ we go into the the details on how to use it for a reproducible transportable pro
 6. [Lesson 06 Sharing your analysis](06-Sharing-all-your-analysis.html)
 
 ## Links
-- [Website](http://ropenscilabs.github.io/r-docker-tutorial)
-- [For lesson developers](http://pad.software-carpentry.org/RopenSci-docker-tutorial)
+- [Website](http://jsta.github.io/r-docker-tutorial)
+- [For lesson developers](http://pad.software-carpentry.org/RopenSci-docker-tutorial)

05-dockerfiles.Rmd

@@ -17,13 +17,13 @@
       <header>
         <h1>R Docker tutorial</h1>
 
-        <p class="view"><a href="https://github.com/ropenscilabs/r-docker-tutorial">View the Project on GitHub <small>ropenscilabs/r-docker-tutorial</small></a></p>
+        <p class="view"><a href="https://github.com/jsta/r-docker-tutorial">View the Project on GitHub <small>jsta/r-docker-tutorial</small></a></p>
 
 
         <ul>
-          <li><a href="https://github.com/ropenscilabs/r-docker-tutorial/zipball/master">Download <strong>ZIP File</strong></a></li>
-          <li><a href="https://github.com/ropenscilabs/r-docker-tutorial/tarball/master">Download <strong>TAR Ball</strong></a></li>
-          <li><a href="https://github.com/ropenscilabs/r-docker-tutorial">View On <strong>GitHub</strong></a></li>
+          <li><a href="https://github.com/jsta/r-docker-tutorial/zipball/master">Download <strong>ZIP File</strong></a></li>
+          <li><a href="https://github.com/jsta/r-docker-tutorial/tarball/master">Download <strong>TAR Ball</strong></a></li>
+          <li><a href="https://github.com/jsta/r-docker-tutorial">View On <strong>GitHub</strong></a></li>
         </ul>
       </header>
       <section>
@@ -55,12 +55,12 @@ <h2>Before You Start</h2>
 
 <p>
   This tutorial is work in progress. If you have any suggestions how we could make it better please open
-  a new <a href="https://github.com/ropenscilabs/r-docker-tutorial/issues">issue</a>.
+  a new <a href="https://github.com/jsta/r-docker-tutorial/issues">issue</a>.
 </p>
       </section>
       <footer>
-        <p>This project is maintained by <a href="https://github.com/ropenscilabs">ropenscilabs</a>.</p>
-        <p>You can find the contributors <a href="https://github.com/ropenscilabs/r-docker-tutorial/graphs/contributors">here</a>.</p>
+        <p>This project is maintained by <a href="https://github.com/jsta">jsta</a>.</p>
+        <p>You can find the contributors <a href="https://github.com/jsta/r-docker-tutorial/graphs/contributors">here</a>.</p>
         <p><small>Hosted on GitHub Pages &mdash; Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
       </footer>
     </div>

05-dockerfiles.html

@@ -1,6 +1,6 @@
 ## Instructor's Guide
 
-This file contains the collected tips and tricks for teaching this lesson. After you teach it, please add your comments by sending us a pull request, or letting us know in an [issue](https://github.com/ropenscilabs/r-docker-tutorial/issues).
+This file contains the collected tips and tricks for teaching this lesson. After you teach it, please add your comments by sending us a pull request, or letting us know in an [issue](https://github.com/jsta/r-docker-tutorial/issues).
 
 ### General