Rmd for slidify

demo01.Rmd

```{r setup, echo = FALSE}
opts_knit$set(out.format = 'html')
opts_chunk$set(highlight = TRUE)
```

# Slidify

超簡単スライド作成

@kohske

---
### マークダウンからスライドを作成しましょう

このスライドの元になってるRmdはこちら

https://gist.github.com/2855525

---
### 手軽に資料を作りましょう

- markdown!!
- knitr!!
- slidify

やばいレベル。

---
### インストール

```{r f19, eval=FALSE}
library(devtools)
install_github('slidify', 'ramnathv')
```

以下も必要かも。

```{r f26, eval=FALSE}
install_github('knitr', 'yihui')
install_github('whisker', 'edwindj')
install_github('markdown', 'rstudio')
```

---
### コード評価ももちろんオーケー

```{r f31, prompt = TRUE, comment = NA}
ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2,10,20, labels=c("Ctl","Trt"))
weight <- c(ctl, trt)
lm.D9 <- lm(weight ~ group)

coef(lm.D9)
```

---
### プロットもオーケー

```{r f32, warning=FALSE, fig.height=5}
par(family = "sans")
curve(sin(x), -10, 10, main = "正弦波")
```

---
### ggplot2もオーケー

```{r f33, warning=FALSE, fig.height=5}
library(ggplot2)
ggplot(NULL, aes(c(-10, 10))) + stat_function(fun=sin)
```

---
## これはいいね。おしまい。

why-slidify.Rmd

```{r setup, echo = FALSE}
library(knitr)
library(grid)
opts_knit$set(out.format = 'html')
```
---

# Markdown, Knitr, and Slidify

state-of-the-art report/presentation generation in R

## @kohske

---
### Easy, fun, and beautiful

```{r ch1, echo=TRUE, fig.align='right', fig.height=5, fig.width = 5, dev ='png', dev.args = list(bg="transparent")}
txt <- rep(c("E", "a", "s", "y"), 10)
grid.text(txt, 0.5+sin(2*pi*seq_along(txt)/length(txt))/2.2, 0.5+cos(2*pi*seq_along(txt)/length(txt))/2.2, gp = gpar(fontsize = 30, col = rainbow(length(txt))))
```

---
### Reproducible

#### Freedom from
- Hand working
- Copy and paste
- Tweaking graphics by hand

#### All you need is
- Data
- Code
- Text
- Picture

---
### Tools

All tools are available for free.

- [R][link_R]: environment for data analysis
- [knitr][link_knitr]: report generation tool for R
- [slidify][link_slidify]: HTML5 slide generator
[link_R]: http://www.r-project.org/
[link_knitr]: http://yihui.name/knitr/
[link_slidify]: http://ramnathv.github.com/slidify/

- [Rstudio][link_rstudio]: excellent support for knitr.
[link_rstudio]: http://rstudio.org/

![R logo](figure/r-logo.png)

---
### Step-by-step tutorial

1. Prepare data
2. Write a code for data analysis
3. Write a code for summary output
4. Write a code for visualization
5. Knit them
6. Publish

---
### 1. Prepare data

Ok, use `iris`.

```{r ch3}
head(iris)
```

Of course, you may use data from your own experiment.

---
### 2. Write a code for data analysis

summary of `iris`
```{r ch4}
summary(iris)
```

---
### 2. Write a code for data analysis

Old-fashioned statistical test.

```{r ch5}
library(reshape2)
library(plyr)
iris2 <- melt(iris)
dlply(iris2, .(variable), function(x) pairwise.t.test(x$value, x$Species))
```

---
### 3. Write a code for summary output.

- For presentation, figures are better
- For report, [static html][link_static] version with detailed information may be better
[link_static]: http://kohske.github.com/sandbox/slidify/why-slidify/whyslidify_static.html

---
### 4. Visualization

```{r ch6, fig.width=9, fig.height=5.5}
library(ggplot2)
ggplot(iris2, aes(variable, value, colour = Species)) + 
  geom_boxplot() + theme_grey(base_size=24)
```

---
### 5. Markdown

You can knit text, codes, and pictures in a [markdown][mdofficial] file.
[mdofficial]: http://daringfireball.net/projects/markdown/


Here is the [markdown file][link_md] that [generates][link_generator] this slide.
[link_md]: http://kohske.github.com/sandbox/slidify/why-slidify/whyslidify.Rmd
[link_generator]: http://kohske.github.com/sandbox/slidify/why-slidify/generator.R

Then, all you need is:
- generate html

```{r ch7, eval = FALSE}
knit2html("whyslidify.Rmd")
```

- generate HTML5 slide

```{r ch8, eval = FALSE}
slidify("whyslidify.Rmd")
```

---
### 6. Publish

- Upload the html and relevant files.
- Let your boss or your client know the url.


---
### How to install

```{r ch9, eval = FALSE}
install.packages('devtools')
library(devtools)
install_github('slidify', 'ramnathv')
install_github('knitr', 'yihui')
install_github('whisker', 'edwindj')
install_github('markdown', 'rstudio')
```

- [Rstudio][link_rstudio] supports knitr.
- It also provides a space for publication of knitted report, [Rpubs][link_rpubs].
[link_rpubs]: http://www.rpubs.com/
[link_rstudio]: http://rstudio.org/

Great!!
Now I could upload the slide. Thanks.

http://rpubs.com/kohske/318