Adding script to render all reports at once

OuhscBbmc · Nov 19, 2014 · f9c8a1f · f9c8a1f
1 parent 2c93afa
commit f9c8a1f
Show file tree

Hide file tree

Showing 77 changed files with 277 additions and 297 deletions.
diff --git a/Chapter02/Chapter02.html b/Chapter02/Chapter02.html
@@ -91,7 +91,7 @@ <h2>Figure 2-3</h2>
 <div id="session-info" class="section level2">
 <h2>Session Info</h2>
 <p>For the sake of documentation and reproducibility, the current report was build on a system using the following software.</p>
-<pre><code>Report created by wibeasley at 2014-11-18, 21:38 -0600</code></pre>
+<pre><code>Report created by wibeasley at 2014-11-19, 00:43 -0600</code></pre>
 <pre><code>R version 3.1.2 (2014-10-31)
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/Chapter02/Chapter02.md b/Chapter02/Chapter02.md
@@ -39,7 +39,7 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by wibeasley at 2014-11-18, 21:38 -0600
+Report created by wibeasley at 2014-11-19, 00:43 -0600
 ```
 
 ```

diff --git a/Chapter03/Chapter03.Rmd b/Chapter03/Chapter03.Rmd
@@ -74,7 +74,7 @@ read_chunk("./Chapter03/Chapter03.R")
 ```
 
 ## Figure 3-6
-<img src="./../Chapter02/figure_rmd/Figure02_01.png" alt="Systolic" style="width: 600px;"/>
+<img src="./../Chapter02/figure_rmd/Figure02_01-1.png" alt="Systolic" style="width: 600px;"/>
 
 ## Figure 3-7
 ```{r Figure03_07, echo=echoChunks, fig.height=2.8, fig.width=3.5, out.width=NULL, out.width="400px"}

diff --git a/Chapter03/Chapter03.html b/Chapter03/Chapter03.html
diff --git a/Chapter03/Chapter03.md b/Chapter03/Chapter03.md
@@ -61,7 +61,7 @@ read_chunk("./Chapter03/Chapter03.R")
 <img src="figure_rmd/Figure03_05-1.png" title="" alt="" height="150px" />
 
 ## Figure 3-6
-<img src="./../Chapter02/figure_rmd/Figure02_01.png" alt="Systolic" style="width: 600px;"/>
+<img src="./../Chapter02/figure_rmd/Figure02_01-1.png" alt="Systolic" style="width: 600px;"/>
 
 ## Figure 3-7
 <img src="figure_rmd/Figure03_07-1.png" title="" alt="" width="400px" />
@@ -129,23 +129,24 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by Will at 2014-11-12, 12:50 -0600
+Report created by wibeasley at 2014-11-19, 00:43 -0600
 ```
 
 ```
-R version 3.1.2 Patched (2014-10-31 r66921)
-Platform: x86_64-w64-mingw32/x64 (64-bit)
+R version 3.1.2 (2014-10-31)
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 locale:
-[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
-[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+ [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 
 attached base packages:
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     epade_0.3.8        plotrix_3.5-10     reshape2_1.4       ggplot2_1.0.0     
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5
+ [7] dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0      knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    

diff --git a/Chapter03/figure_rmd/Figure03_01-1.png b/Chapter03/figure_rmd/Figure03_01-1.png
diff --git a/Chapter03/figure_rmd/Figure03_02-1.png b/Chapter03/figure_rmd/Figure03_02-1.png
diff --git a/Chapter03/figure_rmd/Figure03_03-1.png b/Chapter03/figure_rmd/Figure03_03-1.png
diff --git a/Chapter03/figure_rmd/Figure03_04-1.png b/Chapter03/figure_rmd/Figure03_04-1.png
diff --git a/Chapter03/figure_rmd/Figure03_05-1.png b/Chapter03/figure_rmd/Figure03_05-1.png
diff --git a/Chapter03/figure_rmd/Figure03_07-1.png b/Chapter03/figure_rmd/Figure03_07-1.png
diff --git a/Chapter03/figure_rmd/Figure03_08-1.png b/Chapter03/figure_rmd/Figure03_08-1.png
diff --git a/Chapter03/figure_rmd/Figure03_09-1.png b/Chapter03/figure_rmd/Figure03_09-1.png
diff --git a/Chapter03/figure_rmd/Figure03_10-1.png b/Chapter03/figure_rmd/Figure03_10-1.png
diff --git a/Chapter03/figure_rmd/Figure03_11-1.png b/Chapter03/figure_rmd/Figure03_11-1.png
diff --git a/Chapter03/figure_rmd/Figure03_12-1.png b/Chapter03/figure_rmd/Figure03_12-1.png
diff --git a/Chapter03/figure_rmd/Figure03_13-1.png b/Chapter03/figure_rmd/Figure03_13-1.png
diff --git a/Chapter03/figure_rmd/Figure03_14-1.png b/Chapter03/figure_rmd/Figure03_14-1.png
diff --git a/Chapter03/figure_rmd/Figure03_15-1.png b/Chapter03/figure_rmd/Figure03_15-1.png
diff --git a/Chapter03/figure_rmd/Figure03_16-1.png b/Chapter03/figure_rmd/Figure03_16-1.png
diff --git a/Chapter03/figure_rmd/Figure03_17-1.png b/Chapter03/figure_rmd/Figure03_17-1.png
diff --git a/Chapter03/figure_rmd/Figure03_18-1.png b/Chapter03/figure_rmd/Figure03_18-1.png
diff --git a/Chapter03/figure_rmd/Figure03_19-1.png b/Chapter03/figure_rmd/Figure03_19-1.png
diff --git a/Chapter03/figure_rmd/Figure03_20-1.png b/Chapter03/figure_rmd/Figure03_20-1.png
diff --git a/Chapter03/figure_rmd/Figure03_21-1.png b/Chapter03/figure_rmd/Figure03_21-1.png
diff --git a/Chapter03/figure_rmd/Figure03_22-1.png b/Chapter03/figure_rmd/Figure03_22-1.png
diff --git a/Chapter03/figure_rmd/Figure03_23-1.png b/Chapter03/figure_rmd/Figure03_23-1.png
diff --git a/Chapter04/Chapter04.html b/Chapter04/Chapter04.html
diff --git a/Chapter04/Chapter04.md b/Chapter04/Chapter04.md
@@ -12,13 +12,6 @@ knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other ch
 
 ```r
 require(knitr)
-```
-
-```
-## Loading required package: knitr
-```
-
-```r
 opts_chunk$set(
   results = 'show', 
   message = TRUE,
@@ -88,28 +81,30 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by wbeasley at 2014-11-17, 11:24 -0600
+Report created by wibeasley at 2014-11-19, 00:43 -0600
 ```
 
 ```
-R version 3.1.2 Patched (2014-10-31 r66921)
-Platform: x86_64-w64-mingw32/x64 (64-bit)
+R version 3.1.2 (2014-10-31)
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 locale:
-[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
-[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+ [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 
 attached base packages:
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     reshape2_1.4       ggthemes_1.7.0     ggplot2_1.0.0      gridExtra_0.9.1   
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    
  [7] htmltools_0.2.6  labeling_0.3     MASS_7.3-35      munsell_0.4.2    proto_0.3-10     Rcpp_0.11.3     
-[13] rmarkdown_0.3.10 Rttf2pt1_1.3.2   stringr_0.6.2    tools_3.1.2      yaml_2.1.13     
+[13] rmarkdown_0.3.3  Rttf2pt1_1.3.2   stringr_0.6.2    tools_3.1.2      yaml_2.1.13     
 ```
 
 ## License

diff --git a/Chapter04/figure_rmd/Figure04_01-1.png b/Chapter04/figure_rmd/Figure04_01-1.png
diff --git a/Chapter04/figure_rmd/Figure04_02-1.png b/Chapter04/figure_rmd/Figure04_02-1.png
diff --git a/Chapter04/figure_rmd/Figure04_03-1.png b/Chapter04/figure_rmd/Figure04_03-1.png
diff --git a/Chapter04/figure_rmd/Figure04_04-1.png b/Chapter04/figure_rmd/Figure04_04-1.png
diff --git a/Chapter04/figure_rmd/Figure04_05-1.png b/Chapter04/figure_rmd/Figure04_05-1.png
diff --git a/Chapter04/figure_rmd/Figure04_07-1.png b/Chapter04/figure_rmd/Figure04_07-1.png
diff --git a/Chapter04/figure_rmd/Figure04_08-1.png b/Chapter04/figure_rmd/Figure04_08-1.png
diff --git a/Chapter04/figure_rmd/Figure04_08-2.png b/Chapter04/figure_rmd/Figure04_08-2.png
diff --git a/Chapter04/figure_rmd/Figure04_09-1.png b/Chapter04/figure_rmd/Figure04_09-1.png
diff --git a/Chapter04/figure_rmd/UnusedVariantsFigure04_04-1.png b/Chapter04/figure_rmd/UnusedVariantsFigure04_04-1.png
diff --git a/Chapter04/figure_rmd/UnusedVariantsFigure04_04-2.png b/Chapter04/figure_rmd/UnusedVariantsFigure04_04-2.png
diff --git a/Chapter04/figure_rmd/UnusedVariantsFigure04_04-3.png b/Chapter04/figure_rmd/UnusedVariantsFigure04_04-3.png
diff --git a/Chapter04/figure_rmd/UnusedVariantsFigure04_08-1.png b/Chapter04/figure_rmd/UnusedVariantsFigure04_08-1.png
diff --git a/Chapter05/Chapter05.html b/Chapter05/Chapter05.html
diff --git a/Chapter05/Chapter05.md b/Chapter05/Chapter05.md
@@ -12,13 +12,6 @@ knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other ch
 
 ```r
 require(knitr)
-```
-
-```
-## Loading required package: knitr
-```
-
-```r
 opts_chunk$set(
   results = 'show', 
   message = TRUE,
@@ -94,7 +87,7 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by wibeasley at 2014-11-18, 21:51 -0600
+Report created by wibeasley at 2014-11-19, 00:44 -0600
 ```
 
 ```
@@ -110,8 +103,9 @@ attached base packages:
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     reshape2_1.4       ggthemes_1.7.0     ggplot2_1.0.0      gridExtra_0.9.1   
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    

diff --git a/Chapter07/Chapter07.html b/Chapter07/Chapter07.html
diff --git a/Chapter07/Chapter07.md b/Chapter07/Chapter07.md
@@ -12,13 +12,6 @@ knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other ch
 
 ```r
 require(knitr)
-```
-
-```
-## Loading required package: knitr
-```
-
-```r
 opts_chunk$set(
   results='show', 
   message = TRUE,
@@ -85,23 +78,25 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by Will at 2014-11-18, 19:41 -0600
+Report created by wibeasley at 2014-11-19, 00:44 -0600
 ```
 
 ```
-R version 3.1.2 Patched (2014-11-14 r66984)
-Platform: x86_64-w64-mingw32/x64 (64-bit)
+R version 3.1.2 (2014-10-31)
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 locale:
-[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
-[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+ [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 
 attached base packages:
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     reshape2_1.4       ggthemes_1.7.0     ggplot2_1.0.0      gridExtra_0.9.1   
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    

diff --git a/Chapter07/figure_rmd/Figure07_01-1.png b/Chapter07/figure_rmd/Figure07_01-1.png
diff --git a/Chapter07/figure_rmd/Figure07_02-1.png b/Chapter07/figure_rmd/Figure07_02-1.png
diff --git a/Chapter07/figure_rmd/Figure07_03-1.png b/Chapter07/figure_rmd/Figure07_03-1.png
diff --git a/Chapter07/figure_rmd/Figure07_04-1.png b/Chapter07/figure_rmd/Figure07_04-1.png
diff --git a/Chapter07/figure_rmd/Figure07_05-1.png b/Chapter07/figure_rmd/Figure07_05-1.png
diff --git a/Chapter07/figure_rmd/Figure07_06-1.png b/Chapter07/figure_rmd/Figure07_06-1.png
diff --git a/Chapter08/Chapter08.html b/Chapter08/Chapter08.html
@@ -60,9 +60,8 @@ <h1>Chapter 08 Graphs</h1>
 <pre class="r"><code>knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other chunk -especially one that uses file paths.</code></pre>
 <!-- Set the report-wide options, and point to the external code file. -->
 
-<pre class="r"><code>require(knitr)</code></pre>
-<pre><code>## Loading required package: knitr</code></pre>
-<pre class="r"><code>opts_chunk$set(
+<pre class="r"><code>require(knitr)
+opts_chunk$set(
   results = 'show', 
   message = TRUE,
   comment = NA, 
@@ -153,7 +152,7 @@ <h2>Figure 8-14</h2>
 <div id="session-info" class="section level2">
 <h2>Session Info</h2>
 <p>For the sake of documentation and reproducibility, the current report was build on a system using the following software.</p>
-<pre><code>Report created by wibeasley at 2014-11-18, 21:59 -0600</code></pre>
+<pre><code>Report created by wibeasley at 2014-11-19, 00:44 -0600</code></pre>
 <pre><code>R version 3.1.2 (2014-10-31)
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -166,8 +165,9 @@ <h2>Session Info</h2>
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     reshape2_1.4       ggthemes_1.7.0     ggplot2_1.0.0      gridExtra_0.9.1   
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    

diff --git a/Chapter08/Chapter08.md b/Chapter08/Chapter08.md
@@ -12,13 +12,6 @@ knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other ch
 
 ```r
 require(knitr)
-```
-
-```
-## Loading required package: knitr
-```
-
-```r
 opts_chunk$set(
   results = 'show', 
   message = TRUE,
@@ -99,7 +92,7 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by wibeasley at 2014-11-18, 21:59 -0600
+Report created by wibeasley at 2014-11-19, 00:44 -0600
 ```
 
 ```
@@ -115,8 +108,9 @@ attached base packages:
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     reshape2_1.4       ggthemes_1.7.0     ggplot2_1.0.0      gridExtra_0.9.1   
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    

diff --git a/Chapter09/Chapter09.html b/Chapter09/Chapter09.html
@@ -60,9 +60,8 @@ <h1>Chapter 09 Graphs</h1>
 <pre class="r"><code>knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other chunk -especially one that uses file paths.</code></pre>
 <!-- Set the report-wide options, and point to the external code file. -->
 
-<pre class="r"><code>require(knitr)</code></pre>
-<pre><code>## Loading required package: knitr</code></pre>
-<pre class="r"><code>opts_chunk$set(
+<pre class="r"><code>require(knitr)
+opts_chunk$set(
   results = 'show',
   message = TRUE,
   comment = NA, 
@@ -141,7 +140,7 @@ <h2>Figure 9-11</h2>
 <div id="session-info" class="section level2">
 <h2>Session Info</h2>
 <p>For the sake of documentation and reproducibility, the current report was build on a system using the following software.</p>
-<pre><code>Report created by wibeasley at 2014-11-18, 22:07 -0600</code></pre>
+<pre><code>Report created by wibeasley at 2014-11-19, 00:44 -0600</code></pre>
 <pre><code>R version 3.1.2 (2014-10-31)
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -154,8 +153,9 @@ <h2>Session Info</h2>
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     reshape2_1.4       ggthemes_1.7.0     ggplot2_1.0.0      gridExtra_0.9.1   
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    

diff --git a/Chapter09/Chapter09.md b/Chapter09/Chapter09.md
@@ -12,13 +12,6 @@ knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other ch
 
 ```r
 require(knitr)
-```
-
-```
-## Loading required package: knitr
-```
-
-```r
 opts_chunk$set(
   results = 'show',
   message = TRUE,
@@ -90,7 +83,7 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by wibeasley at 2014-11-18, 22:07 -0600
+Report created by wibeasley at 2014-11-19, 00:44 -0600
 ```
 
 ```
@@ -106,8 +99,9 @@ attached base packages:
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] dichromat_2.0-0    extrafont_0.16     reshape2_1.4       ggthemes_1.7.0     ggplot2_1.0.0      gridExtra_0.9.1   
- [7] scales_0.2.4       plyr_1.8.1         RColorBrewer_1.0-5 knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    

diff --git a/Chapter10/Chapter10.html b/Chapter10/Chapter10.html
diff --git a/Chapter10/Chapter10.md b/Chapter10/Chapter10.md
@@ -12,13 +12,6 @@ knitr::opts_knit$set(root.dir='../')  #Don't combine this call with any other ch
 
 ```r
 require(knitr)
-```
-
-```
-## Loading required package: knitr
-```
-
-```r
 opts_chunk$set(
   results = 'show', 
   message=TRUE,
@@ -93,28 +86,30 @@ For the sake of documentation and reproducibility, the current report was build
 
 
 ```
-Report created by wbeasley at 2014-11-17, 11:26 -0600
+Report created by wibeasley at 2014-11-19, 00:44 -0600
 ```
 
 ```
-R version 3.1.2 Patched (2014-10-31 r66921)
-Platform: x86_64-w64-mingw32/x64 (64-bit)
+R version 3.1.2 (2014-10-31)
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 locale:
-[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
-[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+ [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 
 attached base packages:
 [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     ggplot2_1.0.0      scales_0.2.4       plyr_1.8.1        
-[7] knitr_1.8         
+ [1] ggthemes_1.7.0     gridExtra_0.9.1    epade_0.3.8        plotrix_3.5-10     reshape2_1.4       scales_0.2.4      
+ [7] plyr_1.8.1         RColorBrewer_1.0-5 dichromat_2.0-0    extrafont_0.16     wesanderson_0.3    ggplot2_1.0.0     
+[13] knitr_1.8         
 
 loaded via a namespace (and not attached):
  [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   extrafontdb_1.0  formatR_1.0      gtable_0.1.2    
  [7] htmltools_0.2.6  labeling_0.3     MASS_7.3-35      munsell_0.4.2    proto_0.3-10     Rcpp_0.11.3     
-[13] reshape2_1.4     rmarkdown_0.3.10 Rttf2pt1_1.3.2   stringr_0.6.2    tools_3.1.2      yaml_2.1.13     
+[13] rmarkdown_0.3.3  Rttf2pt1_1.3.2   stringr_0.6.2    tools_3.1.2      yaml_2.1.13     
 ```
 
 ## License

diff --git a/Chapter10/figure_rmd/Figure10_01-1.png b/Chapter10/figure_rmd/Figure10_01-1.png
diff --git a/Chapter10/figure_rmd/Figure10_03-1.png b/Chapter10/figure_rmd/Figure10_03-1.png
diff --git a/Chapter10/figure_rmd/Figure10_04-1.png b/Chapter10/figure_rmd/Figure10_04-1.png