rsetup.Rmd

% Setting Up R
% DPI R Bootcamp Dec. 3rd to 5th, 2012
% Jared Knowles

# Getting Ready for the DPI R Bootcamp
- How to get up and running with R in no time!

<p align="center"><img src="img/dpilogo.png" height="81" width="138"></p>

# Materials
- [Download R](http://cran.r-project.org/)
- [RStudio](http://www.rstudio.org/) 
- We'll also want to install a few basic packages. This can be done on the fly later, but a few include `ggplot2`;`knitr`;`plyr`

# Step 1: Install R
- Simply run the installer. If you have a 64-bit machine, choose 64 bit R, if you don't know, just choose the default
- The install should be less than 100mb
- There is a short video on the next slide for help installing on Windows machines


# Installing R on Windows
<p align='center'><iframe src="http://www.screenr.com/embed/kzT8" width="650" height="396" frameborder="0"></iframe></p>

# Installing R on a Mac
- Get the install file from [CRAN](http://cran.r-project.org/bin/macosx/)
- Get [RStudio](http://www.rstudio.org/) 
- Run the R installer, and then run the RStudio installer

# Installing R on Ubuntu or Debian Linux
- Read the [install notes online](http://cran.r-project.org/bin/linux/ubuntu/README)
- Get [RStudio](http://www.rstudio.org/) 
- Run the R installer, and then run the RStudio installer

# Step 2: RStudio
- Now run the RStudio installer
- RStudio will automatically find your R installation

# Step 3: Install packages
First, watch this tutorial<br>

<p align='center'><iframe src="http://www.screenr.com/embed/Fps8" width="650" height="396" frameborder="0"></iframe></p>

# Install Packages
- Are you running RStudio in administrator mode on Windows Vista or Windows 7?
- If not, you need to be to install packages (in most cases) 
- When you launch RStudio, right click on the icon for RStudio and then click "Run as Administrator" 
- If you are on a Mac or Windows XP you can disregard this

# Install Packages (2)
- Now, copy and paste the code below into the bottom left window in RStudio (the R terminal):

```{r, eval=FALSE,echo=TRUE,tidy=FALSE}
install_new<-function(mypkg){
  if (mypkg %in% installed.packages()) cat("Package already installed")
  else{cat("Package not found, so installing with dependencies...\n 
           Press CTRL C to abort.")
    Sys.sleep(5)
    install.packages(mypkg,repos="http://cran.wustl.edu/")
}
}

install_new('plyr')
install_new('lmtest')
install_new('ggplot2')
install_new('gridExtra')
install_new('eeptools')
install_new('stringr')
install_new('knitr')
install_new('quantreg')
install_new('xtable')
install_new('lme4')
install_new('caret')

```

# Alternate Install
- If you want or if you have troubles with the above, you can overwrite any existing versions of those packages and do the install in one line, shown below:

```{r eval=FALSE,echo=TRUE,tidy=FALSE}
install.packages(c('plyr','lmtest','ggplot2','gridExtra','stringr',
                   'knitr','quantreg','xtable','lme4','eeptools','caret'),
                 repos="http://cran.wustl.edu/")
```


# Run RStudio
- You should be able to run RStudio now and load any of the packages above.
- Run the code below in the RStudio terminal panel (bottom left) to test this:

```{r eval=FALSE,echo=TRUE}
library(lmtest)
example(gqtest)
```

# And you should see...
```{r eval=TRUE,echo=FALSE}
library(lmtest)
example(gqtest)
```

# And test the graphics...
Type in in the terminal (or copy and paste)
```{r echo=TRUE,eval=FALSE}
library(ggplot2)
y<-rt(200,df=5)
qplot(sample=y,stat="qq")
```

# Results
```{r,echo=TRUE,fig.width=9,fig.height=6}

library(ggplot2)
y<-rt(200,df=5)
qplot(sample=y,stat="qq")
```

# That's all
- Did you see the output like the slides above?
- Did you see the plot in the lower right? 

# Optional
- If you want to see the cutting edge of R development--interactive web-based data applications, you can install the following beta software

```{r,echo=TRUE,eval=FALSE}
options(repos=c(RStudio='http://rstudio.org/_packages', getOption('repos')))
install.packages('shiny')
```

# Optional Cont.
- To check if it worked (and it might not depending on your machine's configuration)

```{r echo=TRUE,eval=FALSE}
library(shiny)
runExample("06_tabsets")
```

- Does a new browser window or tab open up? 
- In RStudio hit the "stop" button in the terminal panel to exit the demo

# You are ready to go!
See you on December 3rd to the 5th to find out how to go from these basic steps to using R to learn from your data. 

Can't wait to see you in Madison!

# Attribution and License

This work (<span property="dct:title">R Tutorial for Education</span>, by <a href="www.jaredknowles.com" rel="dct:creator"><span property="dct:title">Jared E. Knowles</span></a>), in service of the <a href="http://www.dpi.wi.gov" rel="dct:publisher"><span property="dct:title">Wisconsin Department of Public Instruction</span></a>, is free of known copyright restrictions.
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