Ecological Statistics: University of Nebraska-Lincoln

General Information

This is a semester long course on Ecological Statistics at the University of Nebraska-Lincoln. Any Nebraska University graduate student may enroll using NRES 898 Special Topics. The course is fully on-line, with synchronous help sessions every Friday afternoon at 2:00 pm, as well as Monday and Wednesday mornings at 10am-11am. This hands-on course focuses on variations of the linear model and model selection. The goal is to equip students with the basic methods to analyse ecological data.

Who: The course is aimed at graduate students from Nebraska University. You should have a basic working knowledge of the statistical programming language R. You should be comfortable with estimating a linear model with normally distributed data, interpreting the results, and carrying out hypothesis tests on the overall model and individual coefficients.

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. Students are required to abide by 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.

Schedule

Module 1

Week	Topic	Assignment Due
Week 1 -- Aug 22	Introductions, setup, Review linear models I
Week 2 -- Aug 29	Review of linear models II
Week 3 -- Sep 5	Model Selection & Power	Linear Models
Week 4 -- Sep 12	Model Selection AIC, BIC and friends	Preproposal

Module 2

Week	Topic	Assignment Due
5 -- Sep 19	Generalized Linear Models	Nematodes
6 -- Sep 26	Generalized Additive Models	Mt Lofty Birds
7 -- Oct 3	What's the smoothest path?	Preproposal Discussion
8 -- Oct 10	Regression trees and forests

Module 3

Week	Topic	Assignment Due
9 -- Oct 17	FALL BREAK No Class
10 -- Oct 24	Mixing it up I	What's the Best Shape
11 -- Oct 31	Mixing it up II	Project Intro/methods
12 -- Nov 7	Choosing a mixed model

Module 4

Week	Topic	Assignment Due
13 -- Nov 14	Time to Event Data	Herbivore Shadows
14 -- Nov 21	THANKSGIVING BREAK
15 -- Nov 28	Multivariate I
16 -- Dec 5	Multivariate II

Setup

To succeed in this course 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.