Merge pull request jtleek#79 from rdpeng/master

Thank goodness Roger hasn't become too despondent to merge his final changes before the move.
anupkumarsahu · Jan 21, 2014 · 192075b · 192075b
2 parents 76baad2 + 5273856
commit 192075b
Show file tree

Hide file tree

Showing 42 changed files with 597 additions and 569 deletions.
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();