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May 18, 2013 16:46
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| diff -r _site_maruku/1900-01-01-example-page/index.html _site_rdiscount/1900-01-01-example-page/index.html | |
| 30c30 | |
| < <h1 id='an_example'>An Example</h1> | |
| --- | |
| > <h1>An Example</h1> | |
| 32,34c32,39 | |
| < <p>Our posturings, our imagined self-importance, the delusion that we have some privileged position in the Universe, are challenged by this point of pale light. Our planet is a lonely speck in the great enveloping cosmic dark. In our obscurity, in all this vastness, there is no hint that help will come from elsewhere to save us from ourselves.</p> | |
| < <div class='highlight'><pre><code class='python'><span class='k'>def</span> <span class='nf'>hello_world</span><span class='p'>():</span> | |
| < <span class='k'>print</span> <span class='s'>'Hello, world!'</span> | |
| --- | |
| > <p>Our posturings, our imagined self-importance, the delusion that we have some | |
| > privileged position in the Universe, are challenged by this point of pale light. | |
| > Our planet is a lonely speck in the great enveloping cosmic dark. In our | |
| > obscurity, in all this vastness, there is no hint that help will come from | |
| > elsewhere to save us from ourselves.</p> | |
| > | |
| > <div class="highlight"><pre><code class="python"><span class="k">def</span> <span class="nf">hello_world</span><span class="p">():</span> | |
| > <span class="k">print</span> <span class="s">'Hello, world!'</span> | |
| 35a41,44 | |
| > | |
| > | |
| > | |
| > | |
| diff -r _site_maruku/2013-05-16-nescent/content.html _site_rdiscount/2013-05-16-nescent/content.html | |
| 1c1,2 | |
| < <a id='location' /> | |
| --- | |
| > <h1><a id="location"></a> Location</h1> | |
| > | |
| 3,6c4,11 | |
| < <a id='logistics' /> | |
| < <p>Google doc for sharing notes and links: <a href='http://bit.ly/11HfaOP'>http://bit.ly/11HfaOP</a></p> | |
| < <a id='schedule' /> | |
| < <h3 id='day_1'>Day 1</h3> | |
| --- | |
| > | |
| > <h1><a id="logistics"></a> Logistics</h1> | |
| > | |
| > <p>Google doc for sharing notes and links: <a href="http://bit.ly/11HfaOP">http://bit.ly/11HfaOP</a></p> | |
| > | |
| > <h1><a id="schedule"></a> Schedule</h1> | |
| > | |
| > <h3>Day 1</h3> | |
| 10d14 | |
| < | |
| 12d15 | |
| < | |
| 14d16 | |
| < | |
| 16d17 | |
| < | |
| 18d18 | |
| < | |
| 20,21c20,21 | |
| < | |
| < <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for reproducibility and share ability</li> | |
| --- | |
| > <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for | |
| > reproducibility and share ability</li> | |
| 24d23 | |
| < <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): * lattice graphics</p> | |
| 26c25,28 | |
| < <h3 id='day_2'>Day 2</h3> | |
| --- | |
| > <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): | |
| > * lattice graphics</p> | |
| > | |
| > <h3>Day 2</h3> | |
| 30d31 | |
| < | |
| 32d32 | |
| < | |
| 34d33 | |
| < | |
| 36d34 | |
| < | |
| 38d35 | |
| < | |
| 40d36 | |
| < | |
| 43,44d38 | |
| < <a id='install' /> | |
| < <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files we will use, just in case we have any network problems. It is recommended to also install a few add-on packages.</p> | |
| 46d39 | |
| < <h3 id='r_and_rstudio'>R and RStudio</h3> | |
| 48,51c41 | |
| < <ul> | |
| < <li> | |
| < <p>Download and install <a href='http://www.r-project.org'>R, a free software environment for statistical computing and graphics</a> from <a href='http://cran.rstudio.com'>CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system – use the links up at the top of the CRAN page linked to above!</p> | |
| < </li> | |
| --- | |
| > <h1><a id="install"></a> Installation</h1> | |
| 53,56c43,45 | |
| < <li> | |
| < <p>Install RStudio, a powerful user interface for R: <a href='http://www.rstudio.com/ide/download/'>http://www.rstudio.com/ide/download/</a></p> | |
| < </li> | |
| < </ul> | |
| --- | |
| > <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files | |
| > we will use, just in case we have any network problems. It is recommended to also install a few | |
| > add-on packages.</p> | |
| 58c47 | |
| < <h3 id='testing_testing'>Testing testing</h3> | |
| --- | |
| > <h3>R and RStudio</h3> | |
| 61,63c50,52 | |
| < <li> | |
| < <p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href='http://www.rstudio.com/ide/'>here</a>, but yours will be more boring because you haven’t written any code or made any figures yet!</p> | |
| < </li> | |
| --- | |
| > <li><p>Download and install <a href="http://www.r-project.org">R, a free software environment for statistical computing and graphics</a> from <a href="http://cran.rstudio.com">CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system -- use the links up at the top of the CRAN page linked to above!</p></li> | |
| > <li><p>Install RStudio, a powerful user interface for R: <a href="http://www.rstudio.com/ide/download/">http://www.rstudio.com/ide/download/</a></p></li> | |
| > </ul> | |
| 65,67c54,59 | |
| < <li> | |
| < <p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p> | |
| < </li> | |
| --- | |
| > | |
| > <h3>Testing testing</h3> | |
| > | |
| > <ul> | |
| > <li><p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href="http://www.rstudio.com/ide/">here</a>, but yours will be more boring because you haven't written any code or made any figures yet!</p></li> | |
| > <li><p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p></li> | |
| 70c62,66 | |
| < <h3 id='gapminder_stuff'>Gapminder stuff</h3> | |
| --- | |
| > | |
| > <h3>Gapminder stuff</h3> | |
| > | |
| > <ul> | |
| > <li>We will work with some of the data from the <a href="http://www.gapminder.org">Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! | |
| 73c69,71 | |
| < <li>We will work with some of the data from the <a href='http://www.gapminder.org'>Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! - <a href='http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt'>http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| --- | |
| > <li><a href="http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt">http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| > </ul> | |
| > </li> | |
| 76c74,75 | |
| < <h3 id='addon_packages'>Add-on packages</h3> | |
| --- | |
| > | |
| > <h3>Add-on packages</h3> | |
| 79c78 | |
| < <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href='http://plyr.had.co.nz'><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| --- | |
| > <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href="http://plyr.had.co.nz"><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| 81a81 | |
| > | |
| 83,85c83,87 | |
| < install.packages("plyr", dependencies = TRUE) | |
| < </code> Another package you may wish to play around with soon is <a href='http://yihui.name/knitr/'><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. <code> | |
| < install.packages("knitr", dependencies = TRUE) | |
| --- | |
| > install.packages("plyr", dependencies = TRUE) | |
| > </code> | |
| > Another package you may wish to play around with soon is <a href="http://yihui.name/knitr/"><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. | |
| > <code> | |
| > install.packages("knitr", dependencies = TRUE) | |
| 88c90 | |
| < <h3 id='unix_bash_shell'>Unix Bash Shell</h3> | |
| --- | |
| > <h3>Unix Bash Shell</h3> | |
| 91c93,94 | |
| < <li>Please follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “The Unix Bash Shell” to get a Bash shell on your machine.</li> | |
| --- | |
| > <li>Please follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "The Unix Bash Shell" to get a Bash shell on your machine.</li> | |
| 94d96 | |
| < <h3 id='git'>Git</h3> | |
| 96,99c98 | |
| < <ul> | |
| < <li> | |
| < <p>Follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “Git” to install Git.</p> | |
| < </li> | |
| --- | |
| > <h3>Git</h3> | |
| 101,106c100,107 | |
| < <li> | |
| < <p>If you don’t have a GitHub account, please go to <a href='https://github.com/'>https://github.com/</a> and register for a free account.</p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>You’ll have the choice of working with Git through either the command line, a GUI, or both, whatever you’re comfortable with (we’ll demonstrate both.) If you want to use the command line, no additional setup is required. The GUI we’ll be using is SourceTree, which is free and supports Windows and OS X. The installer can be downloaded here: <a href='http://www.sourcetreeapp.com/'>http://www.sourcetreeapp.com/</a>.</p> | |
| --- | |
| > <ul> | |
| > <li><p>Follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "Git" to install Git.</p></li> | |
| > <li><p>If you don't have a GitHub account, please go to <a href="https://github.com/">https://github.com/</a> and register for a free account.</p></li> | |
| > <li><p>You'll have the choice of working with Git through either the command line, a GUI, or both, whatever | |
| > you're comfortable with (we'll demonstrate both.) If you want to use the command line, no additional | |
| > setup is required. The GUI we'll be using is SourceTree, which is free and supports Windows and OS X. The | |
| > installer can be downloaded here: <a href="http://www.sourcetreeapp.com/">http://www.sourcetreeapp.com/</a>.</p> | |
| 108,109c109,111 | |
| < <p>When you first run SourceTree, enter the username and e-mail address you used for your GitHub account and click Next. For the remaining settings in the setup wizard, the default options will work fine.</p> | |
| < </li> | |
| --- | |
| > <p> When you first run SourceTree, enter the username and e-mail address you used for your GitHub account | |
| > and | |
| > click Next. For the remaining settings in the setup wizard, the default options will work fine.</p></li> | |
| 112c114,115 | |
| < <h3 id='further_resources'>Further resources</h3> | |
| --- | |
| > | |
| > <h3>Further resources</h3> | |
| 117,118c120,124 | |
| < <li> | |
| < <p>How to Use RStudio: - <a href='http://www.rstudio.com/ide/docs/'>http://www.rstudio.com/ide/docs/</a></p> | |
| --- | |
| > <li>How to Use RStudio: | |
| > | |
| > <ul> | |
| > <li><a href="http://www.rstudio.com/ide/docs/">http://www.rstudio.com/ide/docs/</a></li> | |
| > </ul> | |
| 119a126 | |
| > <li>RStudio Public Discussion & Troubleshooting Guide: | |
| 121,122c128,130 | |
| < <li> | |
| < <p>RStudio Public Discussion & Troubleshooting Guide: - <a href='http://support.rstudio.org/help/'>http://support.rstudio.org/help/</a></p> | |
| --- | |
| > <ul> | |
| > <li><a href="http://support.rstudio.org/help/">http://support.rstudio.org/help/</a></li> | |
| > </ul> | |
| 123a132 | |
| > <li>How to Install R: | |
| 125,126c134,137 | |
| < <li> | |
| < <p>How to Install R: - <a href='http://cran.r-project.org/doc/manuals/R-admin.html'>http://cran.r-project.org/doc/manuals/R-admin.html</a> - <a href='http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f'>http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></p> | |
| --- | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/manuals/R-admin.html">http://cran.r-project.org/doc/manuals/R-admin.html</a></li> | |
| > <li><a href="http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f">http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></li> | |
| > </ul> | |
| 127a139 | |
| > <li>R FAQ: | |
| 129,130c141,143 | |
| < <li> | |
| < <p>R FAQ: - <a href='http://cran.r-project.org/doc/FAQ/R-FAQ.html'>http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></p> | |
| --- | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/FAQ/R-FAQ.html">http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></li> | |
| > </ul> | |
| 131a145 | |
| > <li>More about add-on packages in the R Installation and Administration Manual | |
| 133,134c147,149 | |
| < <li> | |
| < <p>More about add-on packages in the R Installation and Administration Manual - <a href='http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages'>http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></p> | |
| --- | |
| > <ul> | |
| > <li> <a href="http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages">http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></li> | |
| > </ul> | |
| 136a152,153 | |
| > | |
| > | |
| 139c156,162 | |
| < (quite rough at this point) --><!-- we don't need this if we remove Q4c, right? --> | |
| \ No newline at end of file | |
| --- | |
| > (quite rough at this point) --> | |
| > | |
| > | |
| > | |
| > | |
| > <!-- we don't need this if we remove Q4c, right? --> | |
| > | |
| diff -r _site_maruku/2013-05-20-duke/content.html _site_rdiscount/2013-05-20-duke/content.html | |
| 1c1,2 | |
| < <a id='location' /> | |
| --- | |
| > <h1><a id="location"></a> Location</h1> | |
| > | |
| 5,6c6,9 | |
| < <a id='schedule' /> | |
| < <h3 id='day_1'>Day 1</h3> | |
| --- | |
| > | |
| > <h1><a id="schedule"></a> Schedule</h1> | |
| > | |
| > <h3>Day 1</h3> | |
| 10d12 | |
| < | |
| 12d13 | |
| < | |
| 14d14 | |
| < | |
| 16d15 | |
| < | |
| 18d16 | |
| < | |
| 20,21c18,19 | |
| < | |
| < <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for reproducibility and share ability</li> | |
| --- | |
| > <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for | |
| > reproducibility and share ability</li> | |
| 24d21 | |
| < <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): * lattice graphics</p> | |
| 26c23,26 | |
| < <h3 id='day_2'>Day 2</h3> | |
| --- | |
| > <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): | |
| > * lattice graphics</p> | |
| > | |
| > <h3>Day 2</h3> | |
| 30d29 | |
| < | |
| 32d30 | |
| < | |
| 34d31 | |
| < | |
| 36d32 | |
| < | |
| 38d33 | |
| < | |
| 40d34 | |
| < | |
| 43,44d36 | |
| < <a id='install' /> | |
| < <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files we will use, just in case we have any network problems. It is recommended to also install a few add-on packages.</p> | |
| 46d37 | |
| < <h3 id='r_and_rstudio'>R and RStudio</h3> | |
| 48,51c39 | |
| < <ul> | |
| < <li> | |
| < <p>Download and install <a href='http://www.r-project.org'>R, a free software environment for statistical computing and graphics</a> from <a href='http://cran.rstudio.com'>CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system – use the links up at the top of the CRAN page linked to above!</p> | |
| < </li> | |
| --- | |
| > <h1><a id="install"></a> Installation</h1> | |
| 53,56c41,43 | |
| < <li> | |
| < <p>Install RStudio, a powerful user interface for R: <a href='http://www.rstudio.com/ide/download/'>http://www.rstudio.com/ide/download/</a></p> | |
| < </li> | |
| < </ul> | |
| --- | |
| > <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files | |
| > we will use, just in case we have any network problems. It is recommended to also install a few | |
| > add-on packages.</p> | |
| 58c45 | |
| < <h3 id='testing_testing'>Testing testing</h3> | |
| --- | |
| > <h3>R and RStudio</h3> | |
| 61,63c48,50 | |
| < <li> | |
| < <p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href='http://www.rstudio.com/ide/'>here</a>, but yours will be more boring because you haven’t written any code or made any figures yet!</p> | |
| < </li> | |
| --- | |
| > <li><p>Download and install <a href="http://www.r-project.org">R, a free software environment for statistical computing and graphics</a> from <a href="http://cran.rstudio.com">CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system -- use the links up at the top of the CRAN page linked to above!</p></li> | |
| > <li><p>Install RStudio, a powerful user interface for R: <a href="http://www.rstudio.com/ide/download/">http://www.rstudio.com/ide/download/</a></p></li> | |
| > </ul> | |
| 65,67c52,57 | |
| < <li> | |
| < <p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p> | |
| < </li> | |
| --- | |
| > | |
| > <h3>Testing testing</h3> | |
| > | |
| > <ul> | |
| > <li><p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href="http://www.rstudio.com/ide/">here</a>, but yours will be more boring because you haven't written any code or made any figures yet!</p></li> | |
| > <li><p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p></li> | |
| 70c60,64 | |
| < <h3 id='gapminder_stuff'>Gapminder stuff</h3> | |
| --- | |
| > | |
| > <h3>Gapminder stuff</h3> | |
| > | |
| > <ul> | |
| > <li>We will work with some of the data from the <a href="http://www.gapminder.org">Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! | |
| 73c67,69 | |
| < <li>We will work with some of the data from the <a href='http://www.gapminder.org'>Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! - <a href='http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt'>http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| --- | |
| > <li><a href="http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt">http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| > </ul> | |
| > </li> | |
| 76c72,73 | |
| < <h3 id='addon_packages'>Add-on packages</h3> | |
| --- | |
| > | |
| > <h3>Add-on packages</h3> | |
| 79c76 | |
| < <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href='http://plyr.had.co.nz'><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| --- | |
| > <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href="http://plyr.had.co.nz"><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| 81a79 | |
| > | |
| 83,85c81,85 | |
| < install.packages("plyr", dependencies = TRUE) | |
| < </code> Another package you may wish to play around with soon is <a href='http://yihui.name/knitr/'><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. <code> | |
| < install.packages("knitr", dependencies = TRUE) | |
| --- | |
| > install.packages("plyr", dependencies = TRUE) | |
| > </code> | |
| > Another package you may wish to play around with soon is <a href="http://yihui.name/knitr/"><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. | |
| > <code> | |
| > install.packages("knitr", dependencies = TRUE) | |
| 88c88 | |
| < <h3 id='unix_bash_shell'>Unix Bash Shell</h3> | |
| --- | |
| > <h3>Unix Bash Shell</h3> | |
| 91c91,92 | |
| < <li>Please follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “The Unix Bash Shell” to get a Bash shell on your machine.</li> | |
| --- | |
| > <li>Please follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "The Unix Bash Shell" to get a Bash shell on your machine.</li> | |
| 94d94 | |
| < <h3 id='git'>Git</h3> | |
| 96,103c96 | |
| < <ul> | |
| < <li> | |
| < <p>Follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “Git” to install Git.</p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>If you don’t have a GitHub account, please go to https://github.com/ and register for a free account.</p> | |
| < </li> | |
| --- | |
| > <h3>Git</h3> | |
| 105,106c98,105 | |
| < <li> | |
| < <p>You’ll have the choice of working with Git through either the command line, a GUI, or both, whatever you’re comfortable with (we’ll demonstrate both.) If you want to use the command line, no additional setup is required. The GUI we’ll be using is SourceTree, which is free and supports Windows and OS X. The installer can be downloaded here: http://www.sourcetreeapp.com/.</p> | |
| --- | |
| > <ul> | |
| > <li><p>Follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "Git" to install Git.</p></li> | |
| > <li><p>If you don't have a GitHub account, please go to https://github.com/ and register for a free account.</p></li> | |
| > <li><p>You'll have the choice of working with Git through either the command line, a GUI, or both, whatever | |
| > you're comfortable with (we'll demonstrate both.) If you want to use the command line, no additional | |
| > setup is required. The GUI we'll be using is SourceTree, which is free and supports Windows and OS X. The | |
| > installer can be downloaded here: http://www.sourcetreeapp.com/.</p> | |
| 108,109c107,109 | |
| < <p>When you first run SourceTree, enter the username and e-mail address you used for your GitHub account and click Next. For the remaining settings in the setup wizard, the default options will work fine.</p> | |
| < </li> | |
| --- | |
| > <p> When you first run SourceTree, enter the username and e-mail address you used for your GitHub account | |
| > and | |
| > click Next. For the remaining settings in the setup wizard, the default options will work fine.</p></li> | |
| 112c112,113 | |
| < <h3 id='further_resources'>Further resources</h3> | |
| --- | |
| > | |
| > <h3>Further resources</h3> | |
| 117,118c118,122 | |
| < <li> | |
| < <p>How to Use RStudio: - <a href='http://www.rstudio.com/ide/docs/'>http://www.rstudio.com/ide/docs/</a></p> | |
| --- | |
| > <li>How to Use RStudio: | |
| > | |
| > <ul> | |
| > <li><a href="http://www.rstudio.com/ide/docs/">http://www.rstudio.com/ide/docs/</a></li> | |
| > </ul> | |
| 119a124 | |
| > <li>RStudio Public Discussion & Troubleshooting Guide: | |
| 121,122c126,128 | |
| < <li> | |
| < <p>RStudio Public Discussion & Troubleshooting Guide: - <a href='http://support.rstudio.org/help/'>http://support.rstudio.org/help/</a></p> | |
| --- | |
| > <ul> | |
| > <li><a href="http://support.rstudio.org/help/">http://support.rstudio.org/help/</a></li> | |
| > </ul> | |
| 123a130 | |
| > <li>How to Install R: | |
| 125,126c132,135 | |
| < <li> | |
| < <p>How to Install R: - <a href='http://cran.r-project.org/doc/manuals/R-admin.html'>http://cran.r-project.org/doc/manuals/R-admin.html</a> - <a href='http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f'>http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></p> | |
| --- | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/manuals/R-admin.html">http://cran.r-project.org/doc/manuals/R-admin.html</a></li> | |
| > <li><a href="http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f">http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></li> | |
| > </ul> | |
| 127a137 | |
| > <li>R FAQ: | |
| 129,130c139,141 | |
| < <li> | |
| < <p>R FAQ: - <a href='http://cran.r-project.org/doc/FAQ/R-FAQ.html'>http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></p> | |
| --- | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/FAQ/R-FAQ.html">http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></li> | |
| > </ul> | |
| 131a143 | |
| > <li>More about add-on packages in the R Installation and Administration Manual | |
| 133,134c145,147 | |
| < <li> | |
| < <p>More about add-on packages in the R Installation and Administration Manual - <a href='http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages'>http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></p> | |
| --- | |
| > <ul> | |
| > <li> <a href="http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages">http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></li> | |
| > </ul> | |
| 136a150,151 | |
| > | |
| > | |
| 139c154,160 | |
| < (quite rough at this point) --><!-- we don't need this if we remove Q4c, right? --> | |
| \ No newline at end of file | |
| --- | |
| > (quite rough at this point) --> | |
| > | |
| > | |
| > | |
| > | |
| > <!-- we don't need this if we remove Q4c, right? --> | |
| > |
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| diff -r _site_maruku/1900-01-01-example-page/index.html _site_redcarpet/1900-01-01-example-page/index.html | |
| 30c30 | |
| < <h1 id='an_example'>An Example</h1> | |
| --- | |
| > <h1>An Example</h1> | |
| 32,34c32,39 | |
| < <p>Our posturings, our imagined self-importance, the delusion that we have some privileged position in the Universe, are challenged by this point of pale light. Our planet is a lonely speck in the great enveloping cosmic dark. In our obscurity, in all this vastness, there is no hint that help will come from elsewhere to save us from ourselves.</p> | |
| < <div class='highlight'><pre><code class='python'><span class='k'>def</span> <span class='nf'>hello_world</span><span class='p'>():</span> | |
| < <span class='k'>print</span> <span class='s'>'Hello, world!'</span> | |
| --- | |
| > <p>Our posturings, our imagined self-importance, the delusion that we have some | |
| > privileged position in the Universe, are challenged by this point of pale light. | |
| > Our planet is a lonely speck in the great enveloping cosmic dark. In our | |
| > obscurity, in all this vastness, there is no hint that help will come from | |
| > elsewhere to save us from ourselves.</p> | |
| > | |
| > <div class="highlight"><pre><code class="python"><span class="k">def</span> <span class="nf">hello_world</span><span class="p">():</span> | |
| > <span class="k">print</span> <span class="s">'Hello, world!'</span> | |
| 35a41 | |
| > | |
| diff -r _site_maruku/2013-05-16-nescent/content.html _site_redcarpet/2013-05-16-nescent/content.html | |
| 1c1,2 | |
| < <a id='location' /> | |
| --- | |
| > <h1><a id="location"></a> Location</h1> | |
| > | |
| 3,6c4,11 | |
| < <a id='logistics' /> | |
| < <p>Google doc for sharing notes and links: <a href='http://bit.ly/11HfaOP'>http://bit.ly/11HfaOP</a></p> | |
| < <a id='schedule' /> | |
| < <h3 id='day_1'>Day 1</h3> | |
| --- | |
| > | |
| > <h1><a id="logistics"></a> Logistics</h1> | |
| > | |
| > <p>Google doc for sharing notes and links: <a href="http://bit.ly/11HfaOP">http://bit.ly/11HfaOP</a></p> | |
| > | |
| > <h1><a id="schedule"></a> Schedule</h1> | |
| > | |
| > <h3>Day 1</h3> | |
| 10d14 | |
| < | |
| 12d15 | |
| < | |
| 14d16 | |
| < | |
| 16d17 | |
| < | |
| 18d18 | |
| < | |
| 20,21c20,21 | |
| < | |
| < <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for reproducibility and share ability</li> | |
| --- | |
| > <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for | |
| > reproducibility and share ability</li> | |
| 24c24,25 | |
| < <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): * lattice graphics</p> | |
| --- | |
| > <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): | |
| > * lattice graphics</p> | |
| 26c27 | |
| < <h3 id='day_2'>Day 2</h3> | |
| --- | |
| > <h3>Day 2</h3> | |
| 30d30 | |
| < | |
| 32d31 | |
| < | |
| 34d32 | |
| < | |
| 36d33 | |
| < | |
| 38d34 | |
| < | |
| 40d35 | |
| < | |
| 43,44d37 | |
| < <a id='install' /> | |
| < <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files we will use, just in case we have any network problems. It is recommended to also install a few add-on packages.</p> | |
| 46c39 | |
| < <h3 id='r_and_rstudio'>R and RStudio</h3> | |
| --- | |
| > <h1><a id="install"></a> Installation</h1> | |
| 48,51c41,45 | |
| < <ul> | |
| < <li> | |
| < <p>Download and install <a href='http://www.r-project.org'>R, a free software environment for statistical computing and graphics</a> from <a href='http://cran.rstudio.com'>CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system – use the links up at the top of the CRAN page linked to above!</p> | |
| < </li> | |
| --- | |
| > <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files | |
| > we will use, just in case we have any network problems. It is recommended to also install a few | |
| > add-on packages.</p> | |
| > | |
| > <h3>R and RStudio</h3> | |
| 53,55c47,49 | |
| < <li> | |
| < <p>Install RStudio, a powerful user interface for R: <a href='http://www.rstudio.com/ide/download/'>http://www.rstudio.com/ide/download/</a></p> | |
| < </li> | |
| --- | |
| > <ul> | |
| > <li><p>Download and install <a href="http://www.r-project.org">R, a free software environment for statistical computing and graphics</a> from <a href="http://cran.rstudio.com">CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system -- use the links up at the top of the CRAN page linked to above!</p></li> | |
| > <li><p>Install RStudio, a powerful user interface for R: <a href="http://www.rstudio.com/ide/download/">http://www.rstudio.com/ide/download/</a></p></li> | |
| 58c52 | |
| < <h3 id='testing_testing'>Testing testing</h3> | |
| --- | |
| > <h3>Testing testing</h3> | |
| 61,67c55,56 | |
| < <li> | |
| < <p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href='http://www.rstudio.com/ide/'>here</a>, but yours will be more boring because you haven’t written any code or made any figures yet!</p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p> | |
| < </li> | |
| --- | |
| > <li><p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href="http://www.rstudio.com/ide/">here</a>, but yours will be more boring because you haven't written any code or made any figures yet!</p></li> | |
| > <li><p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p></li> | |
| 70c59 | |
| < <h3 id='gapminder_stuff'>Gapminder stuff</h3> | |
| --- | |
| > <h3>Gapminder stuff</h3> | |
| 73c62,66 | |
| < <li>We will work with some of the data from the <a href='http://www.gapminder.org'>Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! - <a href='http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt'>http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| --- | |
| > <li>We will work with some of the data from the <a href="http://www.gapminder.org">Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! | |
| > | |
| > <ul> | |
| > <li><a href="http://www.stat.ubc.ca/%7Ejenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt">http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| > </ul></li> | |
| 76c69 | |
| < <h3 id='addon_packages'>Add-on packages</h3> | |
| --- | |
| > <h3>Add-on packages</h3> | |
| 79c72 | |
| < <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href='http://plyr.had.co.nz'><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| --- | |
| > <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href="http://plyr.had.co.nz"><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| 81,84c74,77 | |
| < | |
| < <p><code> | |
| < install.packages("plyr", dependencies = TRUE) | |
| < </code> Another package you may wish to play around with soon is <a href='http://yihui.name/knitr/'><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. <code> | |
| --- | |
| > <div class="highlight"><pre><code class="text language-text" data-lang="text"> install.packages("plyr", dependencies = TRUE) | |
| > </code></pre></div> | |
| > <p>Another package you may wish to play around with soon is <a href="http://yihui.name/knitr/"><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. | |
| > <code> | |
| 88c81 | |
| < <h3 id='unix_bash_shell'>Unix Bash Shell</h3> | |
| --- | |
| > <h3>Unix Bash Shell</h3> | |
| 91c84,85 | |
| < <li>Please follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “The Unix Bash Shell” to get a Bash shell on your machine.</li> | |
| --- | |
| > <li>Please follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "The Unix Bash Shell" to get a Bash shell on your machine.</li> | |
| 94c88 | |
| < <h3 id='git'>Git</h3> | |
| --- | |
| > <h3>Git</h3> | |
| 97,99c91,97 | |
| < <li> | |
| < <p>Follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “Git” to install Git.</p> | |
| < </li> | |
| --- | |
| > <li><p>Follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "Git" to install Git.</p></li> | |
| > <li><p>If you don't have a GitHub account, please go to <a href="https://github.com/">https://github.com/</a> and register for a free account.</p></li> | |
| > <li><p>You'll have the choice of working with Git through either the command line, a GUI, or both, whatever | |
| > you're comfortable with (we'll demonstrate both.) If you want to use the command line, no additional | |
| > setup is required. The GUI we'll be using is SourceTree, which is free and supports Windows and OS X. The | |
| > installer can be downloaded here: <a href="http://www.sourcetreeapp.com/">http://www.sourcetreeapp.com/</a>.</p> | |
| 101,109c99,101 | |
| < <li> | |
| < <p>If you don’t have a GitHub account, please go to <a href='https://github.com/'>https://github.com/</a> and register for a free account.</p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>You’ll have the choice of working with Git through either the command line, a GUI, or both, whatever you’re comfortable with (we’ll demonstrate both.) If you want to use the command line, no additional setup is required. The GUI we’ll be using is SourceTree, which is free and supports Windows and OS X. The installer can be downloaded here: <a href='http://www.sourcetreeapp.com/'>http://www.sourcetreeapp.com/</a>.</p> | |
| < | |
| < <p>When you first run SourceTree, enter the username and e-mail address you used for your GitHub account and click Next. For the remaining settings in the setup wizard, the default options will work fine.</p> | |
| < </li> | |
| --- | |
| > <p>When you first run SourceTree, enter the username and e-mail address you used for your GitHub account | |
| > and | |
| > click Next. For the remaining settings in the setup wizard, the default options will work fine.</p></li> | |
| 112c104 | |
| < <h3 id='further_resources'>Further resources</h3> | |
| --- | |
| > <h3>Further resources</h3> | |
| 117,135c109,134 | |
| < <li> | |
| < <p>How to Use RStudio: - <a href='http://www.rstudio.com/ide/docs/'>http://www.rstudio.com/ide/docs/</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>RStudio Public Discussion & Troubleshooting Guide: - <a href='http://support.rstudio.org/help/'>http://support.rstudio.org/help/</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>How to Install R: - <a href='http://cran.r-project.org/doc/manuals/R-admin.html'>http://cran.r-project.org/doc/manuals/R-admin.html</a> - <a href='http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f'>http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>R FAQ: - <a href='http://cran.r-project.org/doc/FAQ/R-FAQ.html'>http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>More about add-on packages in the R Installation and Administration Manual - <a href='http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages'>http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></p> | |
| < </li> | |
| --- | |
| > <li>How to Use RStudio: | |
| > | |
| > <ul> | |
| > <li><a href="http://www.rstudio.com/ide/docs/">http://www.rstudio.com/ide/docs/</a></li> | |
| > </ul></li> | |
| > <li>RStudio Public Discussion & Troubleshooting Guide: | |
| > | |
| > <ul> | |
| > <li><a href="http://support.rstudio.org/help/">http://support.rstudio.org/help/</a></li> | |
| > </ul></li> | |
| > <li>How to Install R: | |
| > | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/manuals/R-admin.html">http://cran.r-project.org/doc/manuals/R-admin.html</a></li> | |
| > <li><a href="http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f">http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></li> | |
| > </ul></li> | |
| > <li>R FAQ: | |
| > | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/FAQ/R-FAQ.html">http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></li> | |
| > </ul></li> | |
| > <li>More about add-on packages in the R Installation and Administration Manual | |
| > | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages">http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></li> | |
| > </ul></li> | |
| 136a136 | |
| > | |
| 139c139,141 | |
| < (quite rough at this point) --><!-- we don't need this if we remove Q4c, right? --> | |
| \ No newline at end of file | |
| --- | |
| > (quite rough at this point) --> | |
| > | |
| > <!-- we don't need this if we remove Q4c, right? --> | |
| diff -r _site_maruku/2013-05-20-duke/content.html _site_redcarpet/2013-05-20-duke/content.html | |
| 1c1,2 | |
| < <a id='location' /> | |
| --- | |
| > <h1><a id="location"></a> Location</h1> | |
| > | |
| 5,6c6,9 | |
| < <a id='schedule' /> | |
| < <h3 id='day_1'>Day 1</h3> | |
| --- | |
| > | |
| > <h1><a id="schedule"></a> Schedule</h1> | |
| > | |
| > <h3>Day 1</h3> | |
| 10d12 | |
| < | |
| 12d13 | |
| < | |
| 14d14 | |
| < | |
| 16d15 | |
| < | |
| 18d16 | |
| < | |
| 20,21c18,19 | |
| < | |
| < <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for reproducibility and share ability</li> | |
| --- | |
| > <li>3:30-4:30 putting it all together: a bit of file-fu with R, organizing your workflow, strategies for | |
| > reproducibility and share ability</li> | |
| 24c22,23 | |
| < <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): * lattice graphics</p> | |
| --- | |
| > <p>optional content (will be covered by example as we go but might be tackled explicitly briefly): | |
| > * lattice graphics</p> | |
| 26c25 | |
| < <h3 id='day_2'>Day 2</h3> | |
| --- | |
| > <h3>Day 2</h3> | |
| 30d28 | |
| < | |
| 32d29 | |
| < | |
| 34d30 | |
| < | |
| 36d31 | |
| < | |
| 38d32 | |
| < | |
| 40d33 | |
| < | |
| 43,44d35 | |
| < <a id='install' /> | |
| < <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files we will use, just in case we have any network problems. It is recommended to also install a few add-on packages.</p> | |
| 46c37 | |
| < <h3 id='r_and_rstudio'>R and RStudio</h3> | |
| --- | |
| > <h1><a id="install"></a> Installation</h1> | |
| 48,51c39,41 | |
| < <ul> | |
| < <li> | |
| < <p>Download and install <a href='http://www.r-project.org'>R, a free software environment for statistical computing and graphics</a> from <a href='http://cran.rstudio.com'>CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system – use the links up at the top of the CRAN page linked to above!</p> | |
| < </li> | |
| --- | |
| > <p>You need to install and test R, RStudio, Git, and a Bash shell before the workshop. Download some files | |
| > we will use, just in case we have any network problems. It is recommended to also install a few | |
| > add-on packages.</p> | |
| 53,55c43,47 | |
| < <li> | |
| < <p>Install RStudio, a powerful user interface for R: <a href='http://www.rstudio.com/ide/download/'>http://www.rstudio.com/ide/download/</a></p> | |
| < </li> | |
| --- | |
| > <h3>R and RStudio</h3> | |
| > | |
| > <ul> | |
| > <li><p>Download and install <a href="http://www.r-project.org">R, a free software environment for statistical computing and graphics</a> from <a href="http://cran.rstudio.com">CRAN</a>, the Comprehensive R Archive Network. It is <em>highly recommended</em> to install a precompiled binary distribution for your operating system -- use the links up at the top of the CRAN page linked to above!</p></li> | |
| > <li><p>Install RStudio, a powerful user interface for R: <a href="http://www.rstudio.com/ide/download/">http://www.rstudio.com/ide/download/</a></p></li> | |
| 58c50 | |
| < <h3 id='testing_testing'>Testing testing</h3> | |
| --- | |
| > <h3>Testing testing</h3> | |
| 61,67c53,54 | |
| < <li> | |
| < <p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href='http://www.rstudio.com/ide/'>here</a>, but yours will be more boring because you haven’t written any code or made any figures yet!</p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p> | |
| < </li> | |
| --- | |
| > <li><p>Do whatever is appropriate for your OS to launch RStudio. You should get a window similar to the screenshot you see <a href="http://www.rstudio.com/ide/">here</a>, but yours will be more boring because you haven't written any code or made any figures yet!</p></li> | |
| > <li><p>Put your cursor in the pane labelled Console, which is where you interact with the live R process. Create a simple object with code like <code>x <- 2 * 4</code> (followed by enter or return). Then inspect the <code>x</code> object by typing <code>x</code> followed by enter or return. Obviously you should see the value 8 print to screen. If yes, you are good to go.</p></li> | |
| 70c57,60 | |
| < <h3 id='gapminder_stuff'>Gapminder stuff</h3> | |
| --- | |
| > <h3>Gapminder stuff</h3> | |
| > | |
| > <ul> | |
| > <li>We will work with some of the data from the <a href="http://www.gapminder.org">Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! | |
| 73c63,64 | |
| < <li>We will work with some of the data from the <a href='http://www.gapminder.org'>Gapminder project</a>. Here is an excerpt I have prepared for our use. Please save this file on your computer prior to the workshop and note the location! - <a href='http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt'>http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| --- | |
| > <li><a href="http://www.stat.ubc.ca/%7Ejenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt">http://www.stat.ubc.ca/~jenny/notOcto/STAT545A/examples/gapminder/data/gapminderDataFiveYear.txt</a></li> | |
| > </ul></li> | |
| 76c67 | |
| < <h3 id='addon_packages'>Add-on packages</h3> | |
| --- | |
| > <h3>Add-on packages</h3> | |
| 79c70 | |
| < <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href='http://plyr.had.co.nz'><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| --- | |
| > <li>Installing add-on packages. R is an extensible system and many people share useful code they have developed as a <em>package</em> via CRAN and github. To install a package, for example the <a href="http://plyr.had.co.nz"><code>plyr</code> package</a> for data aggregation, here is one way to do it in the R console (there are others).</li> | |
| 81,84c72,75 | |
| < | |
| < <p><code> | |
| < install.packages("plyr", dependencies = TRUE) | |
| < </code> Another package you may wish to play around with soon is <a href='http://yihui.name/knitr/'><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. <code> | |
| --- | |
| > <div class="highlight"><pre><code class="text language-text" data-lang="text"> install.packages("plyr", dependencies = TRUE) | |
| > </code></pre></div> | |
| > <p>Another package you may wish to play around with soon is <a href="http://yihui.name/knitr/"><code>knitr</code></a>, which facilitates the creation of dynamic reports. You could install it in the same way. | |
| > <code> | |
| 88c79 | |
| < <h3 id='unix_bash_shell'>Unix Bash Shell</h3> | |
| --- | |
| > <h3>Unix Bash Shell</h3> | |
| 91c82,83 | |
| < <li>Please follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “The Unix Bash Shell” to get a Bash shell on your machine.</li> | |
| --- | |
| > <li>Please follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "The Unix Bash Shell" to get a Bash shell on your machine.</li> | |
| 94c86 | |
| < <h3 id='git'>Git</h3> | |
| --- | |
| > <h3>Git</h3> | |
| 97,103c89,95 | |
| < <li> | |
| < <p>Follow the <a href='http://software-carpentry.org/bootcamps/setup.html'>Software Carpentry instructions</a> in the section titled “Git” to install Git.</p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>If you don’t have a GitHub account, please go to https://github.com/ and register for a free account.</p> | |
| < </li> | |
| --- | |
| > <li><p>Follow the <a href="http://software-carpentry.org/bootcamps/setup.html">Software Carpentry instructions</a> | |
| > in the section titled "Git" to install Git.</p></li> | |
| > <li><p>If you don't have a GitHub account, please go to https://github.com/ and register for a free account.</p></li> | |
| > <li><p>You'll have the choice of working with Git through either the command line, a GUI, or both, whatever | |
| > you're comfortable with (we'll demonstrate both.) If you want to use the command line, no additional | |
| > setup is required. The GUI we'll be using is SourceTree, which is free and supports Windows and OS X. The | |
| > installer can be downloaded here: http://www.sourcetreeapp.com/. </p> | |
| 105,109c97,99 | |
| < <li> | |
| < <p>You’ll have the choice of working with Git through either the command line, a GUI, or both, whatever you’re comfortable with (we’ll demonstrate both.) If you want to use the command line, no additional setup is required. The GUI we’ll be using is SourceTree, which is free and supports Windows and OS X. The installer can be downloaded here: http://www.sourcetreeapp.com/.</p> | |
| < | |
| < <p>When you first run SourceTree, enter the username and e-mail address you used for your GitHub account and click Next. For the remaining settings in the setup wizard, the default options will work fine.</p> | |
| < </li> | |
| --- | |
| > <p>When you first run SourceTree, enter the username and e-mail address you used for your GitHub account | |
| > and | |
| > click Next. For the remaining settings in the setup wizard, the default options will work fine.</p></li> | |
| 112c102 | |
| < <h3 id='further_resources'>Further resources</h3> | |
| --- | |
| > <h3>Further resources</h3> | |
| 117,135c107,132 | |
| < <li> | |
| < <p>How to Use RStudio: - <a href='http://www.rstudio.com/ide/docs/'>http://www.rstudio.com/ide/docs/</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>RStudio Public Discussion & Troubleshooting Guide: - <a href='http://support.rstudio.org/help/'>http://support.rstudio.org/help/</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>How to Install R: - <a href='http://cran.r-project.org/doc/manuals/R-admin.html'>http://cran.r-project.org/doc/manuals/R-admin.html</a> - <a href='http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f'>http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>R FAQ: - <a href='http://cran.r-project.org/doc/FAQ/R-FAQ.html'>http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></p> | |
| < </li> | |
| < | |
| < <li> | |
| < <p>More about add-on packages in the R Installation and Administration Manual - <a href='http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages'>http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></p> | |
| < </li> | |
| --- | |
| > <li>How to Use RStudio: | |
| > | |
| > <ul> | |
| > <li><a href="http://www.rstudio.com/ide/docs/">http://www.rstudio.com/ide/docs/</a></li> | |
| > </ul></li> | |
| > <li>RStudio Public Discussion & Troubleshooting Guide: | |
| > | |
| > <ul> | |
| > <li><a href="http://support.rstudio.org/help/">http://support.rstudio.org/help/</a></li> | |
| > </ul></li> | |
| > <li>How to Install R: | |
| > | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/manuals/R-admin.html">http://cran.r-project.org/doc/manuals/R-admin.html</a></li> | |
| > <li><a href="http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f">http://cran.stat.sfu.ca/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f</a></li> | |
| > </ul></li> | |
| > <li>R FAQ: | |
| > | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/FAQ/R-FAQ.html">http://cran.r-project.org/doc/FAQ/R-FAQ.html</a></li> | |
| > </ul></li> | |
| > <li>More about add-on packages in the R Installation and Administration Manual | |
| > | |
| > <ul> | |
| > <li><a href="http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages">http://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages</a></li> | |
| > </ul></li> | |
| 136a134 | |
| > | |
| 139c137,139 | |
| < (quite rough at this point) --><!-- we don't need this if we remove Q4c, right? --> | |
| \ No newline at end of file | |
| --- | |
| > (quite rough at this point) --> | |
| > | |
| > <!-- we don't need this if we remove Q4c, right? --> |
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