Slides and demos for the webinar R Markdown ecosystem

13-R-Markdown-Ecosystem/conditional-bad.Rmd

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+Darn it, the regression coefficient was not significant! Looks like I will have to go home by 2am tonight...
+
+```{r echo=FALSE}
+knitr::kable(b)
+```
+
+![](http://yihui.name/slides/images/sleepy.png)

13-R-Markdown-Ecosystem/conditional-good.Rmd

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+Oh yeah, the regression coefficient was significant! Time to go to Hawaii!!
+
+```{r echo=FALSE}
+knitr::kable(b)
+```
+
+![](http://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Lanikai_Strand_auf_Oahu.jpg/1920px-Lanikai_Strand_auf_Oahu.jpg)

13-R-Markdown-Ecosystem/conditional.Rmd

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+---
+title: "Include Content Conditionally"
+author: "Yihui Xie"
+date: "January 16, 2015"
+output:
+  html_document:
+    number_sections: yes
+    self_contained: no
+---
+
+# Introduction
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+# Data overview
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r}
+summary(cars)
+```
+
+You can also embed plots, for example:
+
+```{r}
+par(mar = c(4, 4, .2, .1))
+plot(cars, pch = 20)
+```
+
+# Model
+
+Now we build a linear regression model:
+
+```{r}
+fit = lm(dist ~ speed, data = cars)
+b = coef(summary(fit))
+# b
+```
+
+# Conclusion
+
+```{r child = if (b[2, 4] < 0.05) 'conditional-good.Rmd' else 'conditional-bad.Rmd'}
+```
+

13-R-Markdown-Ecosystem/document.Rmd

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+---
+title: "An R Markdown Document"
+author:
+- Li Lei
+- Han Meimei
+date: "2015/10/28"
+output:
+  html_document:
+    fig_caption: yes
+    number_sections: yes
+    theme: cerulean
+    toc: yes
+  pdf_document: default
+  word_document: default
+bibliography: references.bib
+---
+
+A bit _introduction_ here. We no longer need to start an article by writing this:
+
+```latex
+\documentclass{article}
+\begin{document}
+\end{document}
+```
+
+# Start with a cool section
+
+You can use traditional **Markdown** syntax, such as [links](http://yihui.name/knitr) and `code`. Here is a quote:
+
+> A girl phoned me the other day and said "Come on over, there's nobody home." I went over. Nobody was home. -- Rodney Dangerfield
+
+# Followed by another section
+
+Of course you can write lists:
+
+- apple
+- pear
+- banana
+
+Or ordered lists:
+
+1. items
+1. will
+1. be
+1. ordered
+    - nested
+    - items
+
+# Okay, some R code
+
+```{r linear-model}
+fit = lm(dist ~ speed + I(speed^2), data = cars)
+b = coef(fit)  # coefficients
+summary(fit)
+```
+
+The code will be highlighted in all output formats.
+
+# And some pictures
+
+```{r lm-vis, fig.cap='Regression diagnostics', fig.height=5}
+par(mfrow = c(2, 2), pch = 20, mar = c(4, 4, 2, .1), bg = 'white')
+plot(fit)
+```
+
+# A little bit math
+
+Our regression equation is $Y=`r b[1]`+`r b[2]`x$, and the model is:
+
+$$ Y = \beta_0 + \beta_1 x + \epsilon$$
+
+# Pandoc extension: definition lists
+
+Programmer
+:   A programmer is the one who turns coffee into code.
+LaTeX
+:   A simple tool that is nothing but a couple of backslashes.
+
+# Pandoc extension: examples
+
+We have some examples.
+
+(@) Think what is `0.3 + 0.4 - 0.7`. Zero. Easy.
+(@weird) Now think what is `0.3 - 0.7 + 0.4`. Still zero?
+
+People are often surprised by (@weird).
+
+# Pandoc extension: tables
+
+A table here.
+
+Table:  Demonstration of simple table syntax.
+
+  Right     Left     Center     Default
+-------     ------ ----------   -------
+     12     12        12            12
+    123     123       123          123
+      1     1          1             1
+
+# Pandoc extension: footnotes
+
+We can also write footnotes[^1].
+
+[^1]: hi, I'm a footnote
+
+Or write some inline footnotes^[as you can see here].
+
+# Pandoc extension: citations
+
+We compile the R Markdown file to Markdown through **knitr** [@xie2013] in R [@R-base]. For more about @xie2013, see <http://yihui.name/knitr>.
+
+# References

13-R-Markdown-Ecosystem/htmlwidgets.Rmd

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+---
+title: "HTML Widgets"
+author: "Yihui Xie"
+date: "March 12, 2015"
+output: html_document
+---
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r}
+summary(cars)
+```
+
+You can also embed plots, for example:
+
+```{r, echo=FALSE}
+plot(cars)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+
+# DataTables
+
+```{r}
+library(DT)
+datatable(iris)
+```
+
+# Leaflet Maps
+
+```{r}
+library(leaflet)
+m = leaflet() %>% addTiles()
+m  # a map with the default OSM tile layer
+
+m = m %>% setView(-93.65, 42.0285, zoom = 17)
+# popup
+m %>% addPopups(-93.65, 42.0285, 'Here is the <b>Department of Statistics</b>, ISU')
+rand_lng = function(n = 10) rnorm(n, -93.65, .01)
+rand_lat = function(n = 10) rnorm(n, 42.0285, .01)
+
+# use automatic bounds derived from lng/lat data
+m = m %>% clearBounds()
+# marker
+m %>% addMarkers(rand_lng(), rand_lat())
+```
+
+# Dygraphs
+
+```{r}
+library(dygraphs)
+dygraph(sunspots) %>% dyRangeSelector()
+lungDeaths <- cbind(mdeaths, fdeaths)
+dygraph(lungDeaths)
+```
+
+# Network graphs
+
+```{r}
+library(networkD3)
+data(MisLinks, MisNodes)
+str(MisLinks)
+str(MisNodes)
+forceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source",
+             Target = "target", Value = "value", NodeID = "name",
+             Group = "group", opacity = 0.4)
+```
+
+# Three.js
+
+```{r}
+library(threejs)
+data(world.cities, package="maps")
+cities <- world.cities[order(world.cities$pop,decreasing=TRUE)[1:1000],]
+value  <- 100 * cities$pop / max(cities$pop)
+
+earth <- texture(system.file("images/world.jpg",package="threejs"))
+globejs(img=earth, lat=cities$lat, long=cities$long, value=value)
+```

13-R-Markdown-Ecosystem/presentation.Rmd

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+---
+title: "An R Markdown Document"
+author:
+- Li Lei
+- Han Meimei
+date: "2015/10/28"
+output:
+  ioslides_presentation: default
+  beamer_presentation:
+    theme: AnnArbor
+  slidy_presentation: default
+bibliography: references.bib
+---
+
+## Start with a cool section
+
+You can use traditional **Markdown** syntax, such as [links](http://yihui.name/knitr) and `code`. Here is a quote:
+
+> A girl phoned me the other day and said "Come on over, there's nobody home." I went over. Nobody was home. -- Rodney Dangerfield
+
+## Followed by another section
+
+Of course you can write lists:
+
+- apple
+- pear
+- banana
+
+Or ordered lists:
+
+1. items
+1. will
+1. be
+1. ordered
+    - nested
+    - items
+
+## Okay, some R code
+
+```{r linear-model}
+fit = lm(dist ~ speed, data = cars)
+b = coef(fit)  # coefficients
+summary(fit)
+```
+
+The code will be highlighted in all output formats.
+
+## And some pictures
+
+```{r lm-vis, fig.cap='Regression diagnostics'}
+par(mfrow = c(2, 2), pch = 20, mar = c(4, 4, 2, .1), bg = 'white')
+plot(fit)
+```
+
+## A little bit math
+
+Our regression equation is $Y=`r b[1]`+`r b[2]`x$, and the model is:
+
+$$ Y = \beta_0 + \beta_1 x + \epsilon$$
+
+## Pandoc extension: definition lists
+
+Programmer
+:   A programmer is the one who turns coffee into code.
+LaTeX
+:   A simple tool that is nothing but a couple of backslashes.
+
+## Pandoc extension: examples
+
+We have some examples.
+
+(@) Think what is `0.3 + 0.4 - 0.7`. Zero. Easy.
+(@weird) Now think what is `0.3 - 0.7 + 0.4`. Still zero?
+
+People are often surprised by (@weird).
+
+## Pandoc extension: tables
+
+A table here.
+
+Table:  Demonstration of simple table syntax.
+
+  Right     Left     Center     Default
+-------     ------ ----------   -------
+     12     12        12            12
+    123     123       123          123
+      1     1          1             1
+
+## Pandoc extension: footnotes
+
+We can also write footnotes[^1].
+
+[^1]: hi, I'm a footnote
+
+Or write some inline footnotes^[as you can see here].
+
+## Pandoc extension: citations
+
+We compile the R Markdown file to Markdown through **knitr** [@xie2013] in R [@R-base]. For more about @xie2013, see <http://yihui.name/knitr>.
+
+## References

13-R-Markdown-Ecosystem/references.bib

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+@book{xie2013,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {http://yihui.name/knitr/}
+}
+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2013},
+  url = {http://www.R-project.org/},
+}