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Draft -- please don't follow these instructions yet!

Make sure R is installed!

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In this workshop, a few different R packages will be used. To install R packages, you can either follow the steps described here or use the package installation tool in RStudio (Tools -> Install Packages... ). Please install the following packages:

• plyr
• ggplot2
• googleVisRcpp

Python

Although our focus will be on R, we will cover the interaction between R and Python. In order to install Python on your computer, you can follow one of Iain's installation guide: Modelling with Python Workshop - Installation Guide for OSX, Modelling with Python Workshop - Installation Guide for Linux, Modelling with Python Workshop - Installation Guide for Windows . You only need to follow the sections "Install Python" and "Install setuptools". For this workshop, we will keep the required Python knowledge to a minimum. However, since Python will be used extensively in other workshops, it's a good idea to go over some Resources for Learning Python.

Installing

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PypeR

OSX

1. Open a terminal
2. Type sudo python -m easy_install rpy2==2.2pyper
3. easy_install will download and install RPy2 PypeR to your computer

Linux

1. Open a terminal.
2. Type easy_install rpy2==2.2pyper
3. easy_install will download and install RPy2 to PypeR to your computer

Windows (because life can't always be simple)

1. Open a command prompt
2. Type R
   1. If this runs R, then exit with the command "q()" (no quotes) and skip step 3 below.
   2. If this doesn't run R (for most of you it won't), then do step 3 below.
3. Add R binary folder to your system path with the following procedure:
   1. Find the R binary folder on your computer; this is the folder "bin" in your R directory. For me it was at "C:\Program Files\R\R-2.12.2\bin", but yours will probably be different depending on your R version number.
   2. Navigate to Computer
   3. Right click and select "Properties"
   4. Select "Advanced system settings"
   5. Select "Environment variables..."
   6. In the bottom section called "System variables", click on the line for the variable "Path" and click "Edit..."
   7. Go to the end of the variable, add a semicolon, and then the path to the R folder. Click "Ok" a few times to update the system variables.
   8. Close the command prompt you were using and open a new one.
   9. Go to step 2 again and repeat (it should work now, and if it doesn't bug John at josilber@mit.edu).
4. Navigate and navigate to your Python folder's scripts folder, e.g. by running "cd C:/Python27/Scripts"
5. Type easy_install rpy2==2.2install pyper
6. easy_install will download and install RPy2 to PypeR to your computer

Testing your installation

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Don't forget to test your installation.