Last updates from old repo

noamoss · Jan 21, 2014 · 2da9c6d · 2da9c6d
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diff --git a/01_DataScientistToolbox/02_06_01_createNewRepo/index.Rmd b/01_DataScientistToolbox/02_06_01_createNewRepo/index.Rmd
@@ -74,7 +74,7 @@ __...OR...__
 ```
 $ mkdir ~/test-repo
 ```
-* Note: The tilda (`~`) symbol refers to your "home" directory, so this will create a directory called `test-repo` in your home directory
+* Note: The tilde (`~`) symbol refers to your "home" directory, so this will create a directory called `test-repo` in your home directory
 * Navigate to this new directory using the following command (`cd` stands for "change directory"):
 
 ```

diff --git a/04_ExploratoryAnalysis/Colors/Colors.pdf b/04_ExploratoryAnalysis/Colors/Colors.pdf
diff --git a/04_ExploratoryAnalysis/Colors/Plotting and Color in R.pdf b/04_ExploratoryAnalysis/Colors/Plotting and Color in R.pdf
diff --git a/04_ExploratoryAnalysis/Colors/index.Rmd b/04_ExploratoryAnalysis/Colors/index.Rmd
@@ -1,7 +1,7 @@
 ---
 title : Plotting and Color in R
-subtitle : Computing for Data Analysis
-author : Roger Peng, Associate Professor
+subtitle : 
+author : Roger D. Peng, Associate Professor of Biostatistics
 job : Johns Hopkins Bloomberg School of Public Health
 logo : bloomberg_shield.png
 framework : io2012 # {io2012, html5slides, shower, dzslides, ...}
@@ -177,4 +177,4 @@ mode : selfcontained # {standalone, draft}
 - Careful use of colors in plots/maps/etc. can make it easier for the reader to get what you're trying to say (why make it harder?)
 - The `RColorBrewer` package is an R package that provides color palettes for sequential, categorical, and diverging data
 - The `colorRamp` and `colorRampPalette` functions can be used in conjunction with color palettes to connect data to colors
-- Transparency can sometimes be used to clarify plots with many points
+- Transparency can sometimes be used to clarify plots with many points
diff --git a/04_ExploratoryAnalysis/Colors/index.html b/04_ExploratoryAnalysis/Colors/index.html
@@ -4,7 +4,7 @@
  <title>Plotting and Color in R</title>
  <meta charset="utf-8">
  <meta name="description" content="Plotting and Color in R">
- <meta name="author" content="Roger Peng, Associate Professor">
+ <meta name="author" content="Roger D. Peng, Associate Professor of Biostatistics">
  <meta name="generator" content="slidify" />
  <meta name="apple-mobile-web-app-capable" content="yes">
  <meta http-equiv="X-UA-Compatible" content="chrome=1">
@@ -19,6 +19,11 @@
  </script>
 
  <link rel="stylesheet" href = "../../assets/css/custom.css">
+<link rel="stylesheet" href = "../../assets/css/custom.css.BACKUP.546.css">
+<link rel="stylesheet" href = "../../assets/css/custom.css.BASE.546.css">
+<link rel="stylesheet" href = "../../assets/css/custom.css.LOCAL.546.css">
+<link rel="stylesheet" href = "../../assets/css/custom.css.orig">
+<link rel="stylesheet" href = "../../assets/css/custom.css.REMOTE.546.css">
 <link rel="stylesheet" href = "../../assets/css/ribbons.css">
 
 </head>
@@ -37,8 +42,8 @@
  </aside>
  <hgroup class="auto-fadein">
  <h1>Plotting and Color in R</h1>
- <h2>Computing for Data Analysis</h2>
- <p>Roger Peng, Associate Professor<br/>Johns Hopkins Bloomberg School of Public Health</p>
+ <h2></h2>
+ <p>Roger D. Peng, Associate Professor of Biostatistics<br/>Johns Hopkins Bloomberg School of Public Health</p>
  </hgroup>
  </slide>
 

diff --git a/04_ExploratoryAnalysis/Colors/index.md b/04_ExploratoryAnalysis/Colors/index.md
@@ -1,7 +1,7 @@
 ---
 title : Plotting and Color in R
-subtitle : Computing for Data Analysis
-author : Roger Peng, Associate Professor
+subtitle : 
+author : Roger D. Peng, Associate Professor of Biostatistics
 job : Johns Hopkins Bloomberg School of Public Health
 logo : bloomberg_shield.png
 framework : io2012 # {io2012, html5slides, shower, dzslides, ...}

diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide01.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide01.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide02.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide02.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide03.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide03.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide04.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide04.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide05.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide05.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide06.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide06.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide07.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide07.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide08.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide08.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide09.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide09.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide10.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide10.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide11.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide11.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide12.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide12.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide13.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide13.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide14.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide14.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide15.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide15.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide16.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide16.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide17.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide17.png
diff --git a/04_ExploratoryAnalysis/Colors/slides/colors_slide18.png b/04_ExploratoryAnalysis/Colors/slides/colors_slide18.png
diff --git a/04_ExploratoryAnalysis/all_pdf_files.zip b/04_ExploratoryAnalysis/all_pdf_files.zip
diff --git a/04_ExploratoryAnalysis/announcements.html b/04_ExploratoryAnalysis/announcements.html
diff --git a/04_ExploratoryAnalysis/makefile b/04_ExploratoryAnalysis/makefile
@@ -0,0 +1,24 @@
+DELAY = 1000
+RMD_FILES = $(wildcard */index.Rmd)
+HTML_FILES = $(patsubst %.Rmd, %.html, $(RMD_FILES))
+PDF_FILES = $(patsubst %/index.html, lectures/%.pdf, $(HTML_FILES))
+
+listfiles:
+ @echo $(RMD_FILES)
+ @echo $(HTML_FILES)
+ @echo $(PDF_FILES)
+
+
+html: $(HTML_FILES)
+pdf: $(PDF_FILES)
+all: html pdf
+
+zip: $(PDF_FILES)
+ zip all_pdf_files.zip $^
+
+lectures/%.pdf: %/index.html
+ casperjs makepdf.js $< $@ $(DELAY)
+
+%/index.html: %/index.Rmd
+ cd $(dir $<) && Rscript -e "slidify::slidify('index.Rmd')" && cd ..
+
diff --git a/04_ExploratoryAnalysis/makepdf.js b/04_ExploratoryAnalysis/makepdf.js
@@ -0,0 +1,10 @@
+var casper = require('casper').create({viewportSize:{width:1500,height:1000}});
+var args = casper.cli.args;
+var imgfile = (args[1] || Math.random().toString(36).slice(2))
+casper.start(args[0], function() {
+ this.wait(args[2], function(){
+ this.captureSelector(imgfile, "slides");
+ });
+});
+
+casper.run();