use _includes to separate set up instructions

_includes/setup-data.md

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+## Data
+
+You can download all of the data used in this workshop by clicking
+[this download link](https://ndownloader.figshare.com/articles/1314459/versions/9). The file is 38.4 MB.
+
+Clicking the download link will automatically download all of the files to your default download directory as a single compressed
+(`.zip`) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder
+application). 
+
+For a full description of the data used in this workshop see the [data page](data).

_includes/setup-openrefine.md

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+### OpenRefine
+
+* OpenRefine is a Java program that runs on your local machine (not on the cloud). Although it displays in your browser, no web 
+connection is needed and your data remains local. You need to have a ‘Java Runtime Environment’ (JRE) installed on your computer to run 
+OpenRefine. If you don’t already have one installed then you can download and install from http://java.com by going to the site and 
+clicking “Free Java Download”.
+
+* To install OpenOffice, go to their [download page](http://openrefine.org/download.html). From the download page, select either "Windows 
+kit", "Mac kit", or "Linux kit" - depending on your operating system - and follow the instructions next to your download link. This 
+lesson has been tested with all versions of OpenRefine up to the latest tested version, 3.2. **If you are using an older version, it is 
+recommended you upgrade to the latest tested version.** After installing, you can delete the installer `.dmg` file. 
+
+* You may get an error message: "OpenRefine.app can't be opened because it is from an unidentified developer." If you get this message, 
+open your system preferences and click "Security & Privacy". You will see a message "OpenRefine.app was blocked from opening because it
+is from an unidentified developer." Click "Open Anyway" and "Yes". OpenRefine should open in your default web browser. 
+
+* OpenRefine does not support Internet Explorer or Edge. Please use Firefox, Chrome or Safari instead.

_includes/setup-overview.md

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+## Overview
+
+This workshop is designed to be run on your laptop. First, you will need to download the data we use in the workshop. Then, you need to 
+install some software. After following the instructions on this page, you should have everything you need to participate fully in the 
+workshop!

_includes/setup-python.md

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+### Python and Jupyter Notebooks
+
+* [Python](http://python.org) is a popular language for
+scientific computing, and great for general-purpose programming as
+well. For this workshop we use Python version 3.x. 
+Installing all of its scientific packages individually can be
+a bit difficult, so we recommend an all-in-one installer.
+We will use Anaconda or Miniconda.
+They both use [Conda](http://conda.pydata.org/docs/), the main difference is
+that Anaconda comes with a lot of packages pre-installed.
+With Miniconda you will need to install the required packages.
+We recommend using the Anaconda installation instructions. 
+
+> ## Anaconda installation
+> 
+> Download and install [Anaconda](https://www.anaconda.com/distribution/#download-section).
+> Remember to choose the installer for Python 3.x.
+> Anaconda does not include the plotting package plotnine.  To install this package, open your terminal application and
+> type:
+> 
+> ~~~
+> conda install -c conda-forge plotnine
+> ~~~
+> {: .language-bash}
+{: .solution}
+
+> ## Miniconda installation
+> 
+> Miniconda is a "light" version of Anaconda. If you install and use Miniconda
+> you will also need to install the workshop packages.
+> 
+> Download and install [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+> following the instructions. Remember to choose the installer for
+> Python 3.x.
+> 
+> From your terminal application, type: 
+> ~~~
+> conda list
+> ~~~
+> {: .language-bash}
+> 
+> To install the packages we'll be using in the workshop, type:
+> ~~~
+> conda install -y numpy pandas matplotlib jupyter
+> conda install -c conda-forge plotnine
+> ~~~
+> {: .language-bash}
+{: .solution}
+
+After installing either Anaconda or Miniconda and the workshop packages,
+launch a Jupyter notebook by typing this command from the terminal:
+
+~~~
+jupyter notebook
+~~~
+{: .language-bash}
+
+The notebook should open automatically in your browser. If it does not or you
+wish to use a different browser, open this link: <http://localhost:8888>.
+
+For a brief introduction to Jupyter Notebooks, please consult our
+[Introduction to Jupyter Notebooks](https://datacarpentry.org/python-ecology-lesson/jupyter_notebooks/) page.
+

_includes/setup-r.md

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+### R and RStudio
+
+* R and RStudio are separate downloads and installations. R is the
+underlying statistical computing environment, but using R alone is no
+fun. RStudio is a graphical integrated development environment (IDE) that makes
+using R much easier and more interactive. You need to install R before you
+install RStudio. After installing both programs, you will need to install 
+some specific R packages within RStudio. Follow the instructions below for
+your operating system, and then follow the instructions to install
+**`tidyverse`** and **`RSQLite`**.
+
+#### Windows
+
+> ## If you already have R and RStudio installed
+>
+> * Open RStudio, and click on "Help" > "Check for updates". If a new version is
+> available, quit RStudio, and download the latest version for RStudio.
+> * To check which version of R you are using, start RStudio and the first thing
+>  that appears in the console indicates the version of R you are
+>  running. Alternatively, you can type `sessionInfo()`, which will also display
+>  which version of R you are running. Go on
+>  the [CRAN website](https://cran.r-project.org/bin/windows/base/) and check
+> whether a more recent version is available. If so, please download and install
+> it. You can [check here](https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f) for
+> more information on how to remove old versions from your system if you wish to do so.
+{: .solution}
+
+> ## If you don't have R and RStudio installed
+>
+> * Download R from
+>  the [CRAN website](https://cran.r-project.org/bin/windows/base/release.htm).
+> * Run the `.exe` file that was just downloaded
+> * Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download)
+> * Under *Installers* select **RStudio x.yy.zzz - Windows Vista/7/8/10** (where x, y, and z represent version numbers)
+> * Double click the file to install it
+> * Once it's installed, open RStudio to make sure it works and you don't get any
+> error messages.
+{: .solution}
+
+
+#### macOS
+
+> ## If you already have R and RStudio installed
+>
+> * Open RStudio, and click on "Help" > "Check for updates". If a new version is
+>	available, quit RStudio, and download the latest version for RStudio.
+>	* To check the version of R you are using, start RStudio and the first thing
+>	  that appears on the terminal indicates the version of R you are running. Alternatively, you can type `sessionInfo()`, which will 
+>	also display which version of R you are running. Go on
+>	  the [CRAN website](https://cran.r-project.org/bin/macosx/) and check
+>	  whether a more recent version is available. If so, please download and install
+>	  it.
+{: .solution}
+
+> ## If you don't have R and RStudio installed
+>
+> * Download R from
+>   the [CRAN website](https://cran.r-project.org/bin/macosx/).
+> * Select the `.pkg` file for the latest R version
+> * Double click on the downloaded file to install R
+> * It is also a good idea to install [XQuartz](https://www.xquartz.org/) (needed
+>   by some packages)
+> * Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download)
+> * Under *Installers* select **RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit)**
+>   (where x, y, and z represent version numbers)
+> * Double click the file to install RStudio
+> * Once it's installed, open RStudio to make sure it works and you don't get any
+>   error messages.
+{: .solution}
+
+#### Linux
+
+* Follow the instructions for your distribution
+ from [CRAN](https://cloud.r-project.org/bin/linux), they provide information
+ to get the most recent version of R for common distributions. For most
+ distributions, you could use your package manager (e.g., for Debian/Ubuntu run
+ `sudo apt-get install r-base`, and for Fedora `sudo yum install R`), but we
+ don't recommend this approach as the versions provided by this are
+ usually out of date. In any case, make sure you have at least R 3.5.1.
+* Go to the [RStudio download
+  page](https://www.rstudio.com/products/rstudio/download/#download)
+* Under *Installers* select the version that matches your distribution, and
+   install it with your preferred method (e.g., with Debian/Ubuntu `sudo dpkg -i
+   rstudio-x.yy.zzz-amd64.deb` at the terminal).
+* Once it's installed, open RStudio to make sure it works and you don't get any
+   error messages.
+
+* After installing R and RStudio, you need to install the `tidyverse` and
+`RSQLite` packages. Start RStudio by double-clicking the icon and then type:
+  `install.packages(c("tidyverse", "RSQLite"))`. You can also do this by going to Tools -> Install Packages and 
+  typing the names of the packages you want to install, separated by a comma.

_includes/setup-spreadsheet.md

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+### Spreadsheet program
+
+* To interact with spreadsheets, we can use LibreOffice, Microsoft Excel, Gnumeric, OpenOffice.org, or other programs. 
+Commands may differ a bit between programs, but the general ideas for thinking about spreadsheets are the same. For this workshop, 
+we recommend using either Microsoft Excel (paid software) or LibreOffice (free and open source). Other spreadsheet programs may
+not have all of the features we will be exploring in this workshop.
+
+* To install LibreOffice, go to their [download page](https://www.libreoffice.org/download/download/). The website should
+automatically select the correct option for your operating system. Click the "Download" button. You will go to a page that asks about a
+donation, but you don’t need to make one. Your download should begin automatically. Once the installer is downloaded, double click on it (you may need to open your Downloads folder) and LibreOffice should install.

_includes/setup-sql.md

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+## SQL
+
+* SQL is a specialized programming language used with databases.  We
+use a simple database manager called [SQLite](http://www.sqlite.org/)
+in our lessons. We will use the [DB Browser for SQLite](http://sqlitebrowser.org/) program,
+which is available for all major platforms.
+
+* To install the DB Browser, go to their [download page](http://sqlitebrowser.org/dl/) and choose the correct installer for 
+your operating system. Once the installer is downloaded, double click on it (you may need to open your Downloads folder), follow
+any other instructions that appear, and
+DB Browser should install. After installing, you can delete the installer `.dmg` file. 
+

setup-python-workshop.md

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+---
+layout: page
+title: Setup for Python workshop
+---
+
+{% include setup-overview.md %}
+
+{% include setup-data.md %}
+
+## Software
+
+| Software | Install | Manual | Available for | Description |
+| -------- | ------------ | ------ | ------------- | ----------- |
+| Spreadsheet program | [Link](https://www.libreoffice.org/download/download/) | [Link](https://documentation.libreoffice.org/en/english-documentation/) | Linux, MacOS, Windows | Spreadsheet program for organizing tabular data. |
+| OpenRefine |[Link](http://openrefine.org/download.html) | [Link](http://openrefine.org/documentation.html) | Linux, MacOS, Windows | 
+| Python | See install instructions below. |  | Linux, MacOS, Windows | |
+| SQLite Browser | [Link](http://sqlitebrowser.org/dl/) | | | 
+
+
+{% include setup-spreadsheet.md %}
+
+{% include setup-openrefine.md %}
+
+{% include setup-python.md %}
+
+{% include setup-sql.md %}
+
+Congratulations! You are now ready for the workshop!

setup-r-workshop.md

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+---
+layout: page
+title: Setup for R workshops
+---
+
+{% include setup-overview.md %}
+{% include setup-data.md %}
+
+
+## Software
+
+| Software | Install | Manual | Available for | Description |
+| -------- | ------------ | ------ | ------------- | ----------- |
+| Spreadsheet program | [Link](https://www.libreoffice.org/download/download/) | [Link](https://documentation.libreoffice.org/en/english-documentation/) | Linux, MacOS, Windows | Spreadsheet program for organizing tabular data. |
+| OpenRefine |[Link](http://openrefine.org/download.html) | [Link](http://openrefine.org/documentation.html) | Linux, MacOS, Windows | 
+| R | See install instructions below. | | Linux, MacOS, Windows | |
+| RStudio | [Link](https://www.rstudio.com/products/rstudio/download/#download) | [Cheatsheet](https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf) | Linux, MacOS, Windows| |
+| SQLite Browser | [Link](http://sqlitebrowser.org/dl/) | | | 
+
+{% include setup-spreadsheet.md %}
+
+{% include setup-openrefine.md %}
+
+{% include setup-r.md %}
+
+{% include setup-sql.md %}
+
+Congratulations! You are now ready for the workshop!