Start a summary check list

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diff --git a/05_ReproducibleResearch/Checklist/index.Rmd b/05_ReproducibleResearch/Checklist/index.Rmd
@@ -13,3 +13,110 @@ url:
 widgets     : [mathjax]            # {mathjax, quiz, bootstrap}
 mode        : selfcontained # {standalone, draft}
 ---
+
+## DO: Start With Good Science
+
+* Garbage in, garbage out
+
+* Coherent, focused question simplifies many problems
+
+* Working with good collaborators reinforces good practices
+
+* Something that's interesting to you will (hopefully) motivate good
+  habits
+
+---
+
+## DON'T: Do Things By Hand
+
+
+
+* Editing spreadsheets of data to "clean it up"
+
+  - Removing outliers
+  - QA / QC
+  - Validating
+
+* Editing tables or figures (e.g. rounding, formatting)
+
+* Downloading data from a web site (clicking links in a web browser)
+
+* Moving data around your computer; splitting / reformatting data files
+
+* "We're just going to do this once...."
+
+
+Things done by hand need to be precisely documented (this is harder
+than it sounds)
+
+---
+
+## DON'T: Point And Click
+
+
+---
+
+## DO: Teach a Computer
+
+
+---
+
+## DO: Use Some Version Control
+
+* Slow things down
+
+* Add changes in small chunks (don't just do one massive commit)
+
+* Track / tag snapshots; revert to old versions
+
+* Software like GitHub / BitBucket / SourceForge make it easy to
+  publish results
+
+---
+## DO: Keep Track of Your Software Environment
+
+
+---
+
+## DO: Keep Track of Your Software Environment
+
+
+```{r}
+sessionInfo()
+```
+
+---
+
+## DON'T: Save Output
+
+
+---
+
+## DO: Think About the Pipeline
+
+* Data analysis is a lengthy process
+
+* How you got the end is just as important as the end itself
+
+* The farther back in the pipeline you can "preserve" the better
+
+---
+
+## Summary: Checklist
+
+* Are we doing good science?
+
+* Was any part of this analysis done by hand?
+  - If so, are those parts *precisely* document?
+
+* Have we taught a computer to do as much as possible (i.e. coded)?
+
+* Are we using a version control system?
+
+* Have we documented our software environment?
+
+* Have we saved any output that we cannot reconstruct from original
+  data + code?
+
+* How far back in the analysis pipeline can we go before our results
+  are no longer (automatically) reproducible?
diff --git a/05_ReproducibleResearch/Checklist/index.html b/05_ReproducibleResearch/Checklist/index.html
@@ -50,10 +50,169 @@ <h2>What to Do and What Not to Do</h2>
     <!-- SLIDES -->
       <slide class="" id="slide-1" style="background:;">
   <hgroup>
+    <h2>DO: Start With Good Science</h2>
+  </hgroup>
+  <article>
+    <ul>
+<li><p>Garbage in, garbage out</p></li>
+<li><p>Coherent, focused question simplifies many problems</p></li>
+<li><p>Working with good collaborators reinforces good practices</p></li>
+<li><p>Something that&#39;s interesting to you will (hopefully) motivate good
+habits</p></li>
+</ul>
+
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-2" style="background:;">
+  <hgroup>
+    <h2>DON&#39;T: Do Things By Hand</h2>
+  </hgroup>
+  <article>
+    <ul>
+<li><p>Editing spreadsheets of data to &quot;clean it up&quot;</p>
+
+<ul>
+<li>Removing outliers</li>
+<li>QA / QC</li>
+<li>Validating</li>
+</ul></li>
+<li><p>Editing tables or figures (e.g. rounding, formatting)</p></li>
+<li><p>Downloading data from a web site (clicking links in a web browser)</p></li>
+<li><p>Moving data around your computer; splitting / reformatting data files</p></li>
+<li><p>&quot;We&#39;re just going to do this once....&quot;</p></li>
+</ul>
+
+<p>Things done by hand need to be precisely documented (this is harder
+than it sounds)</p>
+
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-3" style="background:;">
+  <hgroup>
+    <h2>DON&#39;T: Point And Click</h2>
+  </hgroup>
+  <article>
 
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-4" style="background:;">
+  <hgroup>
+    <h2>DO: Teach a Computer</h2>
   </hgroup>
   <article>
 
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-5" style="background:;">
+  <hgroup>
+    <h2>DO: Use Some Version Control</h2>
+  </hgroup>
+  <article>
+    <ul>
+<li><p>Slow things down</p></li>
+<li><p>Add changes in small chunks (don&#39;t just do one massive commit)</p></li>
+<li><p>Track / tag snapshots; revert to old versions</p></li>
+<li><p>Software like GitHub / BitBucket / SourceForge make it easy to
+publish results</p></li>
+</ul>
+
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-6" style="background:;">
+  <hgroup>
+    <h2>DO: Keep Track of Your Software Environment</h2>
+  </hgroup>
+  <article>
+
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-7" style="background:;">
+  <hgroup>
+    <h2>DO: Keep Track of Your Software Environment</h2>
+  </hgroup>
+  <article>
+    <pre><code class="r">sessionInfo()
+</code></pre>
+
+<pre><code>## R version 3.0.2 Patched (2013-12-30 r64600)
+## Platform: x86_64-apple-darwin13.0.0 (64-bit)
+## 
+## locale:
+## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
+## 
+## attached base packages:
+## [1] stats     graphics  grDevices utils     datasets  base     
+## 
+## other attached packages:
+## [1] slidify_0.3.3
+## 
+## loaded via a namespace (and not attached):
+## [1] evaluate_0.5.1 formatR_0.10   knitr_1.5      markdown_0.6.3
+## [5] stringr_0.6.2  tools_3.0.2    whisker_0.3-2  yaml_2.1.8
+</code></pre>
+
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-8" style="background:;">
+  <hgroup>
+    <h2>DON&#39;T: Save Output</h2>
+  </hgroup>
+  <article>
+
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-9" style="background:;">
+  <hgroup>
+    <h2>DO: Think About the Pipeline</h2>
+  </hgroup>
+  <article>
+    <ul>
+<li><p>Data analysis is a lengthy process</p></li>
+<li><p>How you got the end is just as important as the end itself</p></li>
+<li><p>The farther back in the pipeline you can &quot;preserve&quot; the better</p></li>
+</ul>
+
+  </article>
+  <!-- Presenter Notes -->
+</slide>
+
+      <slide class="" id="slide-10" style="background:;">
+  <hgroup>
+    <h2>Summary: Checklist</h2>
+  </hgroup>
+  <article>
+    <ul>
+<li><p>Are we doing good science?</p></li>
+<li><p>Was any part of this analysis done by hand?</p>
+
+<ul>
+<li>If so, are those parts <em>precisely</em> document?</li>
+</ul></li>
+<li><p>Have we taught a computer to do as much as possible (i.e. coded)?</p></li>
+<li><p>Are we using a version control system?</p></li>
+<li><p>Have we documented our software environment?</p></li>
+<li><p>Have we saved any output that we cannot reconstruct from original
+data + code?</p></li>
+<li><p>How far back in the analysis pipeline can we go before our results
+are no longer (automatically) reproducible?</p></li>
+</ul>
+
   </article>
   <!-- Presenter Notes -->
 </slide>