Sampling, data management and visualization: University of Nebraska-Lincoln

General Information

This is an experimental, semester long course on Sampling, Data Management and Visualization at the University of Nebraska-Lincoln. Any Nebraska University graduate student may enroll using NRES 898 Special Topics. I will be relying on materials from Software Carpentry and Data Carpentry. The course is fully on-line, with synchronous help sessions every Tuesday afternoon at 2:00 pm. This hands-on course will introduce the tools and concepts of reproducible research.

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students from Nebraska University. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: My address is 3310 Holdrege Avenue, Lincoln, Nebraska. Get directions with OpenStreetMap or Google Maps. Online help sessions will use Adobe Connect.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). Participants should also have a USB headset with a microphone in order to participate in the online sessions effectively. The built-in microphone on a laptop is not sufficient. They are also required to abide by Software Carpentry's Code of Conduct and the UNL student code of conduct. Students are expected to adhere to guidelines concerning academic dishonesty outlined in Section 4.2 of University's Student Code of Conduct. Students are encouraged to contact the instructor for clarification of these guidelines if they have questions or concerns. The SNR policy on Academic Dishonesty is available here.
Students with disabilities: Students with disabilities are encouraged to contact the instructor for a confidential discussion of their individual needs for academic accommodation. It is the policy of the University of Nebraska-Lincoln to provide flexible and individualized accommodation to students with documented disabilities that may affect their ability to fully participate in course activities or to meet course requirements. To receive accommodation services, students must be registered with the Services for Students with Disabilities (SSD) office, 132 Canfield Administration, 472-3787 voice or TTY.

Contact: Please mail atyre2@unl.edu for more information.

Assessment

The primary goal of this course is skill building, but it is a university course and I do need to give you a grade. Each week I will have you turn in a text file containing your answers to a set of challenges. The challenges are listed at the end of each lesson page. Each assignment is due at 5pm on Friday of of the week it is assigned. Late assignments will receive a score of zero unless prior approval is granted. Each challenge will be worth 5 points, and I will give partial grades where possible. For example, in the first week there are 2 lesson pages with 5 challenges each. Therefore week 1 will be worth a total of 50 points. The total number of points over the entire semester will be approximately 13 * 50 = 650. There will be no challenges the first week, during spring break or during dead week. I may have to adjust this as we go forward, but in general assume that each week's work contributes equally to your overall grade. The final percentage score will be converted into letter grades as follows:
>90% A, >80% but </90% B, >70% but <80% C, >60% but <70% D, and <60% F.
Note that I am not grading attendance at the synchronous sessions. You are welcome to skip those or jump ahead as you wish.
NOTE: I may choose to "live code" some sessions, rather than provide video tutorials. These sessions will be recorded but the quality will not be as good. I am doing this because I want to learn the best way to present this material, and to do that I need to try some experiments.

Schedule

Weeks where a challenge assignment is due are marked with '*'. Sessions that I plan to do "live" are indicated with '!'.

Module 1

Week 1	Introductions, setup, project organization
Week 2	Introducing the Unix shell *
Week 3	Automating tasks with the Unix shell *!
Week 4	Version control with Git *

Module 2

Week 6	Reproducible Research in R
Week 7	moRe
Week 8	even moRe
Week 9	wRapping up

Module 3

Week 10	Still More R
Week 11	SPRING BREAK
Week 12	CLASS CANCELLED
Week 13	Data entry/organization in spreadsheets, QA/QC

Module 4

Week 14	Creating Metadata
Week 15	Introduction to SQL
Week 16	Random sampling in space

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Download the Git for Windows installer.
Run the installer and follow the steps bellow:
1. Click on "Next".
2. Click on "Next".
3. Click on "Next".
4. Click on "Next".
5. Click on "Next".
6. Select "Use Git from the Windows Command Prompt" and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
8. Select "Use Windows' default console window" and click on "Next".
9. Click on "Next".
10. Click on "Finish".

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Linux

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the RStudio IDE.

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

Windows

The Software Carpentry Windows installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.

Mac OS X

SQLite comes pre-installed on Mac OS X.

Linux

SQLite comes pre-installed on Linux.

If you installed Anaconda, it also has a copy of SQLite without support to readline. Instructors will provide a workaround for it if needed.