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Update for knitr changes
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@wibeasley
wibeasley committed Nov 12, 2014
1 parent 201d506 commit 0d97706
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5 changes: 5 additions & 0 deletions Chapter03/Chapter03.Rmd
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---
output:
html_document:
keep_md: yes
---
Chapter 03 Graphs
=================================================
This report creates the chapter graphs.
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48 changes: 24 additions & 24 deletions Chapter03/Chapter03.html
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96 changes: 33 additions & 63 deletions Chapter03/Chapter03.md
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Expand Up @@ -5,14 +5,13 @@ This report creates the chapter graphs.
<!-- Set the working directory to the repository's base directory; this assumes the report is nested inside of only one directory.-->

```r
opts_knit$set(root.dir = "../") #Don't combine this call with any other chunk -especially one that uses file paths.
library(knitr)
opts_knit$set(root.dir='../') #Don't combine this call with any other chunk -especially one that uses file paths.
```


<!-- Set the report-wide options, and point to the external code file. -->

```r
require(knitr)
opts_chunk$set(
results='show',
message = TRUE,
Expand All @@ -23,146 +22,118 @@ opts_chunk$set(
out.width = "550px",
fig.path = 'figure_rmd/',
dev = "png",
# fig.path = 'figure_pdf/',
# dev = "pdf",
dpi = 400
# fig.path = 'figure_pdf/',
# dev = "pdf"
)
echoChunks <- FALSE
options(width=120) #So the output is 50% wider than the default.
read_chunk("./Chapter03/Chapter03.R")
```

<!-- Load the packages. Suppress the output when loading packages. -->



<!-- Load any Global functions and variables declared in the R file. Suppress the output. -->



<!-- Declare any global functions specific to a Rmd output. Suppress the output. -->



<!-- Load the datasets. -->



<!-- Tweak the datasets. -->



## Figure 3-1
<img src="figure_rmd/Figure03_01.png" title="plot of chunk Figure03_01" alt="plot of chunk Figure03_01" width="200px" />

<img src="figure_rmd/Figure03_01-1.png" title="" alt="" width="200px" />

## Figure 3-2
<img src="figure_rmd/Figure03_02.png" title="plot of chunk Figure03_02" alt="plot of chunk Figure03_02" width="550px" />

<img src="figure_rmd/Figure03_02-1.png" title="" alt="" width="550px" />

## Figure 3-3
<img src="figure_rmd/Figure03_03.png" title="plot of chunk Figure03_03" alt="plot of chunk Figure03_03" width="550px" />

<img src="figure_rmd/Figure03_03-1.png" title="" alt="" width="550px" />

## Figure 3-4
<img src="figure_rmd/Figure03_04.png" title="plot of chunk Figure03_04" alt="plot of chunk Figure03_04" height="150px" />

<img src="figure_rmd/Figure03_04-1.png" title="" alt="" height="150px" />

## Figure 3-5
<img src="figure_rmd/Figure03_05.png" title="plot of chunk Figure03_05" alt="plot of chunk Figure03_05" height="150px" />

<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;"/>

## Figure 3-7
<img src="figure_rmd/Figure03_07.png" title="plot of chunk Figure03_07" alt="plot of chunk Figure03_07" width="400px" />

<img src="figure_rmd/Figure03_07-1.png" title="" alt="" width="400px" />

## Figure 3-8
<img src="figure_rmd/Figure03_08.png" title="plot of chunk Figure03_08" alt="plot of chunk Figure03_08" width="600px" />

<img src="figure_rmd/Figure03_08-1.png" title="" alt="" width="600px" />

## Figure 3-9
<img src="figure_rmd/Figure03_09.png" title="plot of chunk Figure03_09" alt="plot of chunk Figure03_09" width="600px" />

<img src="figure_rmd/Figure03_09-1.png" title="" alt="" width="600px" />

## Figure 3-10
<img src="figure_rmd/Figure03_10.png" title="plot of chunk Figure03_10" alt="plot of chunk Figure03_10" width="550px" />

<img src="figure_rmd/Figure03_10-1.png" title="" alt="" width="550px" />

## Figure 3-11
<img src="figure_rmd/Figure03_11.png" title="plot of chunk Figure03_11" alt="plot of chunk Figure03_11" width="550px" />

<img src="figure_rmd/Figure03_11-1.png" title="" alt="" width="550px" />

## Figure 3-12
<img src="figure_rmd/Figure03_12.png" title="plot of chunk Figure03_12" alt="plot of chunk Figure03_12" width="550px" />

<img src="figure_rmd/Figure03_12-1.png" title="" alt="" width="550px" />

## Figure 3-13
<img src="figure_rmd/Figure03_13.png" title="plot of chunk Figure03_13" alt="plot of chunk Figure03_13" width="550px" />

<img src="figure_rmd/Figure03_13-1.png" title="" alt="" width="550px" />

## Figure 3-14

```
Warning: Removed 17 rows containing missing values (geom_path).
```

<img src="figure_rmd/Figure03_14.png" title="plot of chunk Figure03_14" alt="plot of chunk Figure03_14" width="550px" />

<img src="figure_rmd/Figure03_14-1.png" title="" alt="" width="550px" />

## Figure 3-15
<img src="figure_rmd/Figure03_15.png" title="plot of chunk Figure03_15" alt="plot of chunk Figure03_15" width="200px" />

<img src="figure_rmd/Figure03_15-1.png" title="" alt="" width="200px" />

## Figure 3-16
<img src="figure_rmd/Figure03_16.png" title="plot of chunk Figure03_16" alt="plot of chunk Figure03_16" width="200px" />

<img src="figure_rmd/Figure03_16-1.png" title="" alt="" width="200px" />

## Figure 3-17
<img src="figure_rmd/Figure03_17.png" title="plot of chunk Figure03_17" alt="plot of chunk Figure03_17" width="200px" />

<img src="figure_rmd/Figure03_17-1.png" title="" alt="" width="200px" />

## Figure 3-18
<img src="figure_rmd/Figure03_18.png" title="plot of chunk Figure03_18" alt="plot of chunk Figure03_18" width="200px" />

<img src="figure_rmd/Figure03_18-1.png" title="" alt="" width="200px" />

## Figure 3-19
<img src="figure_rmd/Figure03_19.png" title="plot of chunk Figure03_19" alt="plot of chunk Figure03_19" height="200px" />

<img src="figure_rmd/Figure03_19-1.png" title="" alt="" height="200px" />

## Figure 3-20
<img src="figure_rmd/Figure03_20.png" title="plot of chunk Figure03_20" alt="plot of chunk Figure03_20" height="200px" />

<img src="figure_rmd/Figure03_20-1.png" title="" alt="" height="200px" />

## Figure 3-21
<img src="figure_rmd/Figure03_21.png" title="plot of chunk Figure03_21" alt="plot of chunk Figure03_21" height="200px" />

<img src="figure_rmd/Figure03_21-1.png" title="" alt="" height="200px" />

## Figure 3-22
<img src="figure_rmd/Figure03_22.png" title="plot of chunk Figure03_22" alt="plot of chunk Figure03_22" height="200px" />

<img src="figure_rmd/Figure03_22-1.png" title="" alt="" height="200px" />

## Figure 3-23

```
Warning: Removed 1 rows containing missing values (stat_summary).
```

<img src="figure_rmd/Figure03_23.png" title="plot of chunk Figure03_23" alt="plot of chunk Figure03_23" height="200px" />

<img src="figure_rmd/Figure03_23-1.png" title="" alt="" height="200px" />

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


```
Report created by Will at 2014-04-15, 21:39 -0500
Report created by Will at 2014-11-12, 12:50 -0600
```

```
R version 3.1.0 Patched (2014-04-10 r65396)
R version 3.1.2 Patched (2014-10-31 r66921)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
Expand All @@ -173,16 +144,15 @@ 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_3.5-5 reshape2_1.2.2 ggplot2_0.9.3.1
[7] scales_0.2.3 plyr_1.8.1 RColorBrewer_1.0-5 knitr_1.5
[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
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 digest_0.6.4 evaluate_0.5.3 extrafontdb_1.0 formatR_0.10 gtable_0.1.2
[7] labeling_0.2 MASS_7.3-31 munsell_0.4.2 proto_0.3-10 Rcpp_0.11.1 Rttf2pt1_1.3
[13] stringr_0.6.2 tools_3.1.0
[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_0.3.3 Rttf2pt1_1.3.2 stringr_0.6.2 tools_3.1.2 yaml_2.1.13
```


## License

<a rel="license" href="http://creativecommons.org/licenses/by/3.0/"><img alt="Creative Commons License" style="border-width:0" src="http://i.creativecommons.org/l/by/3.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported License</a>.
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