Updates Reproducible research chapter.

TomGeens · Aug 18, 2016 · 4cf15b5 · 4cf15b5
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diff --git a/images/RMarkdownFlow.png b/images/RMarkdownFlow.png
diff --git a/images/how-1-file.png b/images/how-1-file.png
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diff --git a/images/interactive-1-htmlwidget.png b/images/interactive-1-htmlwidget.png
diff --git a/images/interactive-2-shiny.png b/images/interactive-2-shiny.png
diff --git a/images/outputs-2-pdf.png b/images/outputs-2-pdf.png
diff --git a/images/outputs-3-toc.png b/images/outputs-3-toc.png
diff --git a/images/params-1-hawaii.png b/images/params-1-hawaii.png
diff --git a/images/params-2-aleutians.png b/images/params-2-aleutians.png
diff --git a/images/params-3-florida.png b/images/params-3-florida.png
diff --git a/images/tables-2-kable.png b/images/tables-2-kable.png
diff --git a/images/website-2-website.png b/images/website-2-website.png
diff --git a/reproducible-research.Rmd b/reproducible-research.Rmd
diff --git a/rmarkdown-demos/1-example.Rmd b/rmarkdown-demos/1-example.Rmd
@@ -0,0  1,22 @@
 ---
 title: "Viridis Demo"
 output: html_document
 ---
 
 ```{r include = FALSE}
 library(viridis)
 ```
 
 The code below demonstrates two color palettes in the [viridis](https://github.com/sjmgarnier/viridis) package. Each plot displays a contour map of the Maunga Whau volcano in Auckland, New Zealand.
 
 ## Viridis colors
 
 ```{r}
 image(volcano, col = viridis(200))
 ```
 
 ## Magma colors
 
 ```{r}
 image(volcano, col = viridis(200, option = "A"))
 ```
diff --git a/rmarkdown-demos/11-dashboard.Rmd b/rmarkdown-demos/11-dashboard.Rmd
@@ -0,0  1,118 @@
 ---
 title: "Review Dashboard"
 output: 
   flexdashboard::flex_dashboard:
     orientation: columns
 ---
 
 ```{r include = FALSE}
 library(viridis)
 library(ggplot2)
 library(marmap)
 ```
 
 # Intro {.sidebar}
 
 This dashboard covers several topics:
 
 * The marmap package
 * The viridis package
 * Miscellaneous material
 
 # Marmap Package
 
 ## Column 1
 
 ### Florida
 
 ```{r echo = FALSE}
 data(florida)
 autoplot(florida)
 ```
 
 The [marmap](https://cran.r-project.org/web/packages/marmap/index.html) package provides tools and data for visualizing the ocean floor. Here is an example contour plot of marmap's `florida` dataset.
 
 ## Column 2
 
 ### Hawaii
 
 ```{r echo = FALSE}
 data(hawaii)
 autoplot(hawaii)
 ```
 
 ### Alaska
 
 ```{r echo = FALSE}
 data(aleutians)
 autoplot(aleutians)
 ```
 
 
 # Viridis Package
 
 ## Column 1
 
 ### Viridis colors
 
 ```{r fig.cap="Maunga Whao, Auckland, NZ"}
 image(volcano, col = viridis(200))
 ```
 
 ### Magma colors
 
 ```{r fig.cap="Maunga Whao, Auckland, NZ"}
 image(volcano, col = viridis(200, option = "A"))
 ```
 
 ## Column 2
 
 ### Inferno colors
 
 ```{r fig.cap="Maunga Whao, Auckland, NZ"}
 image(volcano, col = viridis(200, option = "B"))
 ```
 
 ### Plasma colors
 
 ```{r fig.cap="Maunga Whao, Auckland, NZ"}
 image(volcano, col = viridis(200, option = "C"))
 ```
 
 # Miscellaneous
 
 ## Column 1 {data-width=300}
 
 ### Bash support
 
 ```{bash}
 ls *.Rmd
 ```
 
 ***
 
 This chunk executes bash code.
 
 ### Python support
 
 ```{python}
 x = 'hello, python world!'
 print(x.split(' '))
 ```
 
 ***
 
 This chunk executes python code.
 
 ## Column 2 {data-width=700}
 
 ### Tables with Kable 
 
 ```{r echo = FALSE, results = 'asis'}
 library(knitr)
 kable(mtcars[1:5, ], caption = "A knitr kable.")
 ```
 
 ***
 
 It is very easy to make tables with knitr's `kable` function.
diff --git a/rmarkdown-demos/12-website.zip b/rmarkdown-demos/12-website.zip
diff --git a/rmarkdown-demos/12-website/1-example.Rmd b/rmarkdown-demos/12-website/1-example.Rmd
@@ -0,0  1,22 @@
 ---
 title: "Viridis Demo"
 output: html_document
 ---
 
 ```{r include = FALSE}
 library(viridis)
 ```
 
 The code below demonstrates two color palettes in the [viridis](https://github.com/sjmgarnier/viridis) package. Each plot displays a contour map of the Maunga Whau volcano in Auckland, New Zealand.
 
 ## Viridis colors
 
 ```{r}
 image(volcano, col = viridis(200))
 ```
 
 ## Magma colors
 
 ```{r}
 image(volcano, col = viridis(200, option = "A"))
 ```
diff --git a/rmarkdown-demos/12-website/3-inline.Rmd b/rmarkdown-demos/12-website/3-inline.Rmd
@@ -0,0  1,21 @@
 ---
 title: "More colors"
 output: html_document
 ---
 
 ```{r include = FALSE}
 
 # colorFunc <- "heat.colors"
 colorFunc <- "terrain.colors"
 # colorFunc <- "topo.colors"
 # colorFunc <- "cm.colors"
 # colorFunc <- "rainbow"
 ```
 
 Base R comes with many functions for generating colors. The code below demonstrates the `r colorFunc` function. 
 
 ## `r colorFunc`
 
 ```{r fig.cap = "The Maunga Whau volcano.", echo = FALSE}
 image(volcano, col = get(colorFunc)(200))
 ```
diff --git a/rmarkdown-demos/12-website/_site.yml b/rmarkdown-demos/12-website/_site.yml
@@ -0,0  1,10 @@
 name: "my-website"
 navbar:
   title: "My Website"
   left:
     - text: "Home"
       href: index.html
     - text: "Viridis Colors"
       href: 1-example.html
     - text: "Terrain Colors"
       href: 3-inline.html
diff --git a/rmarkdown-demos/12-website/_site/images/RMarkdownOutputFormats.png b/rmarkdown-demos/12-website/_site/images/RMarkdownOutputFormats.png