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wibeasley authored Apr 2, 2017
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26 changes: 20 additions & 6 deletions chapter-02/chapter-02.Rmd
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Expand Up @@ -9,12 +9,13 @@ 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, echo=FALSE, message=F}
library(knitr)
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 set-options, echo=FALSE, results='hide'}
library(knitr)
report_render_start_time <- Sys.time()
opts_chunk$set(
results = 'show',
message = TRUE,
Expand All @@ -30,7 +31,7 @@ opts_chunk$set(
# dev = "pdf"
)
echoChunks <- FALSE
options(width=120) #So the output is 50% wider than the default.
options(width=80) # Default width
read_chunk("./chapter-02/chapter-02.R")
```
<!-- Load the packages. Suppress the output when loading packages. -->
Expand Down Expand Up @@ -65,14 +66,27 @@ read_chunk("./chapter-02/chapter-02.R")
```{r figure-02-03, echo=echoChunks}
```

## Session Info
For the sake of documentation and reproducibility, the current report was build on a system using the following software.
## Session Information
For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.

<details>
<summary>Environment <span class="glyphicon glyphicon-plus-sign"></span></summary>
```{r session-info, echo=FALSE}
cat("Report created by", Sys.info()["user"], "at", strftime(Sys.time(), "%Y-%m-%d, %H:%M %z"))
sessionInfo()
if( requireNamespace("devtools", quietly = TRUE) ) {
devtools::session_info()
} else {
sessionInfo()
}
```
</details>

```{r session-duration, echo=FALSE}
report_render_duration_in_seconds <- round(as.numeric(difftime(Sys.time(), report_render_start_time, units="secs")))
```

Report rendered by `r Sys.info()["user"]` at `r strftime(Sys.time(), "%Y-%m-%d, %H:%M %z")` in `r report_render_duration_in_seconds` seconds.


## 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>.
94 changes: 66 additions & 28 deletions chapter-02/chapter-02.html
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103 changes: 76 additions & 27 deletions chapter-02/chapter-02.md
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Expand Up @@ -31,41 +31,90 @@ This report creates the chapter graphs.
## Figure 2-3
<img src="figure-png/figure-02-03-1.png" width="550px" />

## Session Info
For the sake of documentation and reproducibility, the current report was build on a system using the following software.
## Session Information
For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.

<details>
<summary>Environment <span class="glyphicon glyphicon-plus-sign"></span></summary>

```
Report created by wibeasley at 2017-04-01, 21:30 -0500
Session info -------------------------------------------------------------------
```

```
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
locale:
[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] rgl_0.98.1 mnormt_1.5-5 MASS_7.3-45 ggthemes_3.4.0 gridExtra_2.2.1 wesanderson_0.3.2
[7] dichromat_2.0-0 extrafont_0.17 epade_0.3.8 plotrix_3.6-4 reshape2_1.4.2 ggplot2_2.2.1
[13] scales_0.4.1 plyr_1.8.4 RColorBrewer_1.1-2 knitr_1.15.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 highr_0.6 tools_3.3.3 digest_0.6.12 jsonlite_1.3
[6] evaluate_0.10 tibble_1.3.0 gtable_0.2.0 shiny_1.0.1 yaml_2.1.14
[11] Rttf2pt1_1.3.4 stringr_1.2.0 htmlwidgets_0.8 rprojroot_1.2 R6_2.2.0
[16] rmarkdown_1.4.0.9000 extrafontdb_1.0 magrittr_1.5 backports_1.0.5 htmltools_0.3.5
[21] rsconnect_0.7 assertthat_0.1 xtable_1.8-2 mime_0.5 colorspace_1.3-2
[26] httpuv_1.3.3 labeling_0.3 stringi_1.1.3 lazyeval_0.2.0 munsell_0.4.3
setting value
version R version 3.3.3 (2017-03-06)
system x86_64, linux-gnu
ui RStudio (1.0.136)
language en_US
collate en_US.UTF-8
tz America/Chicago
date 2017-04-02
```

```
Packages -----------------------------------------------------------------------
```

```
package * version date source
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
backports 1.0.5 2017-01-18 CRAN (R 3.3.1)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.1)
devtools 1.12.0 2016-06-24 CRAN (R 3.3.1)
dichromat * 2.0-0 2013-01-24 CRAN (R 3.3.0)
digest 0.6.12 2017-01-27 CRAN (R 3.3.1)
epade * 0.3.8 2013-02-22 CRAN (R 3.3.3)
evaluate 0.10 2016-10-11 CRAN (R 3.3.1)
extrafont * 0.17 2014-12-08 CRAN (R 3.3.0)
extrafontdb 1.0 2012-06-11 CRAN (R 3.3.0)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.1)
ggthemes * 3.4.0 2017-02-19 CRAN (R 3.3.1)
gridExtra * 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
highr 0.6 2016-05-09 CRAN (R 3.3.0)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.1)
httpuv 1.3.3 2015-08-04 CRAN (R 3.3.0)
jsonlite 1.3 2017-02-28 CRAN (R 3.3.1)
knitr * 1.15.1 2016-11-22 CRAN (R 3.3.1)
labeling 0.3 2014-08-23 CRAN (R 3.3.0)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
MASS * 7.3-45 2016-04-21 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
mime 0.5 2016-07-07 CRAN (R 3.3.1)
mnormt * 1.5-5 2016-10-15 CRAN (R 3.3.1)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
plotrix * 3.6-4 2016-12-30 CRAN (R 3.3.3)
plyr * 1.8.4 2016-06-08 CRAN (R 3.3.0)
R6 2.2.0 2016-10-05 CRAN (R 3.3.1)
RColorBrewer * 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.10 2017-03-19 CRAN (R 3.3.1)
reshape2 * 1.4.2 2016-10-22 CRAN (R 3.3.1)
rgl * 0.98.1 2017-03-08 CRAN (R 3.3.1)
rmarkdown 1.4.0.9000 2017-04-01 Github (rstudio/rmarkdown@5f7cd3c)
rprojroot 1.2 2017-01-16 CRAN (R 3.3.1)
rsconnect 0.7 2016-12-21 CRAN (R 3.3.1)
rstudioapi 0.6 2016-06-27 CRAN (R 3.3.1)
Rttf2pt1 1.3.4 2016-05-19 CRAN (R 3.3.0)
scales * 0.4.1 2016-11-09 CRAN (R 3.3.1)
shiny 1.0.1 2017-04-01 CRAN (R 3.3.3)
stringi 1.1.3 2017-03-21 CRAN (R 3.3.1)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.1)
tibble 1.3.0 2017-04-01 CRAN (R 3.3.3)
wesanderson * 0.3.2 2015-01-22 CRAN (R 3.3.3)
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
yaml 2.1.14 2016-11-12 CRAN (R 3.3.1)
```
</details>



Report rendered by wibeasley at 2017-04-02, 00:17 -0500 in 2 seconds.


## 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>.
28 changes: 21 additions & 7 deletions chapter-03/chapter-03.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,14 @@ 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, echo=F, message=F}
library(knitr)
opts_knit$set(root.dir='../') #Don't combine this call with any other chunk -especially one that uses file paths.
knitr::opts_knit$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 set-options, echo=F}
report_render_start_time <- Sys.time()
opts_chunk$set(
results='show',
results = 'show',
message = TRUE,
comment = NA,
tidy = FALSE,
Expand All @@ -31,7 +32,7 @@ opts_chunk$set(
# dev.args=list(pdf = list(colormodel = 'cmyk'))
)
echoChunks <- FALSE
options(width=120) #So the output is 50% wider than the default.
options(width=80) # Default width
read_chunk("./chapter-03/chapter-03.R")
```
<!-- Load the packages. Suppress the output when loading packages. -->
Expand Down Expand Up @@ -145,13 +146,26 @@ read_chunk("./chapter-03/chapter-03.R")
```{r figure-03-23, echo=echoChunks, fig.height=2, out.width=NULL, out.height="200px"}
```

## Session Info
For the sake of documentation and reproducibility, the current report was build on a system using the following software.
## Session Information
For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.

<details>
<summary>Environment <span class="glyphicon glyphicon-plus-sign"></span></summary>
```{r session-info, echo=FALSE}
cat("Report created by", Sys.info()["user"], "at", strftime(Sys.time(), "%Y-%m-%d, %H:%M %z"))
sessionInfo()
if( requireNamespace("devtools", quietly = TRUE) ) {
devtools::session_info()
} else {
sessionInfo()
}
```
</details>

```{r session-duration, echo=FALSE}
report_render_duration_in_seconds <- round(as.numeric(difftime(Sys.time(), report_render_start_time, units="secs")))
```

Report rendered by `r Sys.info()["user"]` at `r strftime(Sys.time(), "%Y-%m-%d, %H:%M %z")` in `r report_render_duration_in_seconds` seconds.


## License

Expand Down
94 changes: 66 additions & 28 deletions chapter-03/chapter-03.html
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Large diffs are not rendered by default.

103 changes: 76 additions & 27 deletions chapter-03/chapter-03.md
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Original file line number Diff line number Diff line change
Expand Up @@ -91,41 +91,90 @@ This report creates the chapter graphs.
## Figure 3-23
<img src="figure-png/figure-03-23-1.png" height="200px" />

## Session Info
For the sake of documentation and reproducibility, the current report was build on a system using the following software.
## Session Information
For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.

<details>
<summary>Environment <span class="glyphicon glyphicon-plus-sign"></span></summary>

```
Report created by wibeasley at 2017-04-01, 21:30 -0500
Session info -------------------------------------------------------------------
```

```
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
locale:
[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] rgl_0.98.1 mnormt_1.5-5 MASS_7.3-45 ggthemes_3.4.0 gridExtra_2.2.1 wesanderson_0.3.2
[7] dichromat_2.0-0 extrafont_0.17 epade_0.3.8 plotrix_3.6-4 reshape2_1.4.2 ggplot2_2.2.1
[13] scales_0.4.1 plyr_1.8.4 RColorBrewer_1.1-2 knitr_1.15.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 highr_0.6 tools_3.3.3 digest_0.6.12 jsonlite_1.3
[6] evaluate_0.10 tibble_1.3.0 gtable_0.2.0 shiny_1.0.1 yaml_2.1.14
[11] Rttf2pt1_1.3.4 stringr_1.2.0 htmlwidgets_0.8 rprojroot_1.2 R6_2.2.0
[16] rmarkdown_1.4.0.9000 extrafontdb_1.0 magrittr_1.5 backports_1.0.5 htmltools_0.3.5
[21] rsconnect_0.7 assertthat_0.1 xtable_1.8-2 mime_0.5 colorspace_1.3-2
[26] httpuv_1.3.3 labeling_0.3 stringi_1.1.3 lazyeval_0.2.0 munsell_0.4.3
setting value
version R version 3.3.3 (2017-03-06)
system x86_64, linux-gnu
ui RStudio (1.0.136)
language en_US
collate en_US.UTF-8
tz America/Chicago
date 2017-04-02
```

```
Packages -----------------------------------------------------------------------
```

```
package * version date source
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
backports 1.0.5 2017-01-18 CRAN (R 3.3.1)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.1)
devtools 1.12.0 2016-06-24 CRAN (R 3.3.1)
dichromat * 2.0-0 2013-01-24 CRAN (R 3.3.0)
digest 0.6.12 2017-01-27 CRAN (R 3.3.1)
epade * 0.3.8 2013-02-22 CRAN (R 3.3.3)
evaluate 0.10 2016-10-11 CRAN (R 3.3.1)
extrafont * 0.17 2014-12-08 CRAN (R 3.3.0)
extrafontdb 1.0 2012-06-11 CRAN (R 3.3.0)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.1)
ggthemes * 3.4.0 2017-02-19 CRAN (R 3.3.1)
gridExtra * 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
highr 0.6 2016-05-09 CRAN (R 3.3.0)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.1)
httpuv 1.3.3 2015-08-04 CRAN (R 3.3.0)
jsonlite 1.3 2017-02-28 CRAN (R 3.3.1)
knitr * 1.15.1 2016-11-22 CRAN (R 3.3.1)
labeling 0.3 2014-08-23 CRAN (R 3.3.0)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
MASS * 7.3-45 2016-04-21 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
mime 0.5 2016-07-07 CRAN (R 3.3.1)
mnormt * 1.5-5 2016-10-15 CRAN (R 3.3.1)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
plotrix * 3.6-4 2016-12-30 CRAN (R 3.3.3)
plyr * 1.8.4 2016-06-08 CRAN (R 3.3.0)
R6 2.2.0 2016-10-05 CRAN (R 3.3.1)
RColorBrewer * 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.10 2017-03-19 CRAN (R 3.3.1)
reshape2 * 1.4.2 2016-10-22 CRAN (R 3.3.1)
rgl * 0.98.1 2017-03-08 CRAN (R 3.3.1)
rmarkdown 1.4.0.9000 2017-04-01 Github (rstudio/rmarkdown@5f7cd3c)
rprojroot 1.2 2017-01-16 CRAN (R 3.3.1)
rsconnect 0.7 2016-12-21 CRAN (R 3.3.1)
rstudioapi 0.6 2016-06-27 CRAN (R 3.3.1)
Rttf2pt1 1.3.4 2016-05-19 CRAN (R 3.3.0)
scales * 0.4.1 2016-11-09 CRAN (R 3.3.1)
shiny 1.0.1 2017-04-01 CRAN (R 3.3.3)
stringi 1.1.3 2017-03-21 CRAN (R 3.3.1)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.1)
tibble 1.3.0 2017-04-01 CRAN (R 3.3.3)
wesanderson * 0.3.2 2015-01-22 CRAN (R 3.3.3)
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
yaml 2.1.14 2016-11-12 CRAN (R 3.3.1)
```
</details>



Report rendered by wibeasley at 2017-04-02, 00:17 -0500 in 16 seconds.


## 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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