diff --git a/Chapter04/Chapter04.R b/Chapter04/Chapter04.R index f3938e1..968a846 100644 --- a/Chapter04/Chapter04.R +++ b/Chapter04/Chapter04.R @@ -47,7 +47,7 @@ dsFibromyalgiaT1Control <- dsFibromyalgiaT1Control[order(dsFibromyalgiaT1Control ## @knitr Figure04_01 breaksX <- seq(from=7, to=23, by=1) histogramX <- ggplot(dsFibromyalgiaT1Control, aes(x=X)) + - geom_histogram(breaks=breaksX, fill=PaletteControlPsqi[1], color="gray95", alpha=.6) + + geom_histogram(breaks=breaksX, fill=PaletteControlPsqiLight[1], color=PaletteControlPsqiDark[2], alpha=.6) + chapterTheme + theme(panel.grid.minor=element_blank()) + theme(panel.grid.major.x=element_blank()) + @@ -125,7 +125,7 @@ histogramXInset <- histogramX + scale_x_continuous(breaks=breaksXSparse) + labs( # histogramZInset <- ggplot(dsFibromyalgiaT1Control, aes(x=Z)) + -# geom_histogram(breaks=breaksZ, fill=PaletteControlPsqi[2], color="gray95", alpha=.6) + +# geom_histogram(breaks=breaksZ, fill=PaletteControlPsqiLight[2], color="gray95", alpha=.6) + # labs(x="Z", y=NULL) + # chapterTheme + # theme(panel.grid.minor=element_blank()) + @@ -135,7 +135,7 @@ histogramXInset <- histogramX + scale_x_continuous(breaks=breaksXSparse) + labs( # ggplot(dsFibromyalgiaT1Control, aes(x=X)) + # # geom_histogram(breaks=breaksX, fill="#037995", color="gray95", alpha=.6) + -# geom_histogram(breaks=breaksX-.01, fill=PaletteControlPsqi[2], color="gray95", alpha=.6) + +# geom_histogram(breaks=breaksX-.01, fill=PaletteControlPsqiLight[2], color="gray95", alpha=.6) + # # scale_x_continuous(breaks=breaksXSparse, labels=round(breaksZSparse, 2)) + # labs(x="Z", y=NULL) + # chapterTheme + @@ -146,7 +146,7 @@ histogramXInset <- histogramX + scale_x_continuous(breaks=breaksXSparse) + labs( histogramZInset <- ggplot(dsFibromyalgiaT1Control, aes(x=X)) + # geom_histogram(breaks=breaksX, fill="#037995", color="gray95", alpha=.6) + - geom_histogram(breaks=breaksX, fill=PaletteControlPsqi[2], color="gray95", alpha=.6) + + geom_histogram(breaks=breaksX, fill=PaletteControlPsqiLight[2], color=PaletteControlPsqiDark[2], alpha=.6) + scale_x_continuous(breaks=breaksXSparse, labels=round(breaksZSparse, 2)) + chapterTheme + theme(panel.grid.minor=element_blank()) + diff --git a/Chapter04/Chapter04.html b/Chapter04/Chapter04.html index fe513fa..709f236 100644 --- a/Chapter04/Chapter04.html +++ b/Chapter04/Chapter04.html @@ -78,11 +78,11 @@

Chapter 04 Graphs

fig.height = 4, fig.width = 5.5, out.width = "550px", #This affects only the markdown, not the underlying png file. The height will be scaled appropriately. -# fig.path = 'figure_rmd/', -# dev = "png", -# dpi = 400 - fig.path = 'figure_pdf/', - dev = "pdf"#, + fig.path = 'figure_rmd/', + dev = "png", + dpi = 400 + # fig.path = 'figure_pdf/', + # dev = "pdf"#, # dev.args=list(pdf = list(colormodel = 'cmyk')) ) echoChunks <- FALSE @@ -105,23 +105,23 @@

Chapter 04 Graphs

Figure 4-1

-

+

Figure 4-2

-

+

Figure 4-3

-

+

Figure 4-4

-

+

Figure 4-5

-

+

Figure 4-6

@@ -129,24 +129,24 @@

Figure 4-6

Figures 4-7

-

+

Figure 4-8

-

+

Figure 4-9

-

+

Unused Graphics

-

+

Session Info

For the sake of documentation and reproducibility, the current report was build on a system using the following software.

-
Report created by wibeasley at 2015-02-08, 00:16 -0600
+
Report created by wibeasley at 2015-02-08, 14:58 -0600
R version 3.1.2 (2014-10-31)
 Platform: x86_64-pc-linux-gnu (64-bit)
 
diff --git a/Chapter04/Chapter04.md b/Chapter04/Chapter04.md
index a78ebdc..45e041a 100644
--- a/Chapter04/Chapter04.md
+++ b/Chapter04/Chapter04.md
@@ -20,11 +20,11 @@ opts_chunk$set(
   fig.height = 4, 
   fig.width = 5.5, 
   out.width = "550px", #This affects only the markdown, not the underlying png file.  The height will be scaled appropriately.
-#   fig.path = 'figure_rmd/',     
-#   dev = "png",
-#   dpi = 400
-  fig.path = 'figure_pdf/',     
-  dev = "pdf"#,
+  fig.path = 'figure_rmd/',     
+  dev = "png",
+  dpi = 400
+  # fig.path = 'figure_pdf/',     
+  # dev = "pdf"#,
   # dev.args=list(pdf = list(colormodel = 'cmyk'))
 )
 echoChunks <- FALSE
@@ -47,42 +47,42 @@ read_chunk("./Chapter04/Chapter04.R")
 
 
 ## Figure 4-1
-
+
 
 ## Figure 4-2
-
+
 
 ## Figure 4-3
-
+
 
 ## Figure 4-4
-
+
 
 ## Figure 4-5
-
+
 
 ## Figure 4-6
 See Table A: Standard normal distribution.
 
 ## Figures 4-7
-
+
 
 ## Figure 4-8
-
+
 
 ## Figure 4-9
-
+
 
 ## Unused Graphics
-
-
+
+
 
 ## Session Info
 For the sake of documentation and reproducibility, the current report was build on a system using the following software.
 
 
 ```
-Report created by wibeasley at 2015-02-08, 00:16 -0600
+Report created by wibeasley at 2015-02-08, 14:58 -0600
 ```
 
 ```
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diff --git a/Chapter04/figure_rmd/Figure04_01-1.png b/Chapter04/figure_rmd/Figure04_01-1.png
index b38277b..78fddb3 100644
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diff --git a/Chapter04/figure_rmd/Figure04_03-1.png b/Chapter04/figure_rmd/Figure04_03-1.png
index 3ac4c80..4ca849e 100644
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diff --git a/CommonCode/BookTheme.R b/CommonCode/BookTheme.R
index 883661e..124e479 100644
--- a/CommonCode/BookTheme.R
+++ b/CommonCode/BookTheme.R
@@ -51,7 +51,9 @@ PaletteObesityState <- transformColor(adjustcolor(brewer.pal(5, "Dark2"))[c(2,3)
 PaletteWorldDeathsRestricted <- transformColor(c("#497862", "#A54891")) #Hand-picked
 PaletteWorldDeathsRestrictedFaint <- transformColor(adjustcolor(PaletteWorldDeathsRestricted, alpha.f=.2))
 
-PaletteControlPsqi <- transformColor(c("#1A7F7C", "#1595B2")) #From http://colrd.com/palette/22521/; http://colrd.com/palette/18981/
+PaletteControlPsqiLight <- transformColor(c("#1A7F7C", "#1595B2")) #From http://colrd.com/palette/22521/; http://colrd.com/palette/18981/
+PaletteControlPsqiDark <- transformColor(c("#215f5c", "#225a88")) #From http://colrd.com/palette/22521/; http://colrd.com/palette/18981/
+#
 
 #Use the same palette as the crit graphs in Chapters 10-12.
 #  * Purple is the distribution line