Computer programs for data collection and analysis.

If you wish, you can download and Install any of the ecology and behavior data collection programs. Permission is granted to other instructors to use these programs in their classrooms. All I ask is that you e-mail me telling me how the programs are being used (btietjen@bellarmine.edu). Suggestions are welcome. The home page for this site is here. Ecology and Evolution simulations are here.

Windows

  1. Download Video Analysis for Windows (Version 1). Digitized video can be stepped through frame-by-frame and behaviors recorded from the keyboard. This also can collect X-Y data for position analysis. Download it here. See a tutorial here. Please note: If you copy data to the clipboard, you must exit and re-start the program. Failure to do so will result in the program crashing. Do not save your file as uncompressed full frames. The video routines don't like that.
  2. Version 2 of Video Analysis for Windows. Digitized video can be stepped through frame-by-frame and behaviors recorded from the built-in keyboard (16 numbered behaviors are allowed). This also can collect X-Y data for position analysis. Download it here. See a tutorial here on using Video Analysis 2 with Timeline. Please note: If you copy data to the clipboard, you must exit and re-start the program. Failure to do so will result in the program crashing. Do not save your file as uncompressed full frames. The video routines don't like that. NOTE: Version two may crash in some versions of Windows (I don't know why). If it does, use version 1.
  3.   Behavior Collect (2006 version). Download the ZIP file here (right click). NOTE: This program allows you to step through digitized video and record X-Y data for position analysis. It also can record behavior codes from your keyboard. Both behavior codes and X-Y data can be simultaneously recorded. This program also writes a file that is compatible with Timeline for Windows. See the tutorial here. See a tutorial here on using Video Analysis 2 and Timeline (NOTE: This tutorial uses a different data collection program, but that doesn't make no never mind).
  4. Keyboard Collect: Use your keyboard to collect sequence data for data analysis. Download here. See the tutorial here.
  5. Download Timeline for Windows. Accepts input from the above program and constructs transition matrices along with summary data. Download it here. See a tutorial here on using Video Analysis 2 and Timeline.
  6. Intervalometer is used to collect accurate time-lapse video using the Video for Windows runtime (Item 1 in this list). Download Intervalometer here Directions on using Intervalometer are here.
  7. Distance XY. This program calculates the X-Y position of mouse clicks on a digitized image. Also calculates distances. Get it here (with tutorial) or see directions here.
  8. Download ZeroMaze for initial analysis of elevated zero maze data collected with Video Analysis for WIndows. A quick how-to is here.
  9. Download WaterPath to digitize the X/Y positions of mice for a water maze test (or any path an animal might follow). Three data files are produced and can be analyzed in a spreadsheet, stat package, using fractal analysis (as here). A tutorial is here.
  10. Path Analysis- Analyzes Water Path and Behavior Analysis files. Provides Time and Distance Output File, A Quad Data File, A fractal input file for Vilis O. Nams' Fractal program (his site is here). Download Path Analysis.
  11. Simple Chi-square calculator download. A tutorial is here.
  12. Advanced Chi-square calculator download. A tutorial is here.

Palm OS NOTE: On some OS5 devices the scroll bar doesn't show up in the help files. This is a problem with some of the launchers, not my program. If you experience this, you can get to the scroll bar by running the program from the classic launcher. Please see this FAQ for questions related to Pen Record, Pen Review, EZ Record, Track, and Counter.

  1. Pen Record and Pen Review allow you to record the behavior of animals or humans under field conditions. Any alphanumeric can be assigned a behavior (say "e" for "eat"), and when you enter that behavior through the Graffiti input, the time of the behavior and it's code are entered into the palm database. Pen review provides some simple statistics, a time line, and transition matrix for your data. Get the set with a tutorial here. NOTE: Pen record can also be used with a keyboard instead of just Graffiti input! Decuma Latin input works, but you need to hit the return button for each behavior. Therefore, Decuma input is not recommended!
  2. EZ Record and Pen Review allow you to record the behavior of animals or humans under field conditions. Behaviors are recorded by pressing a button to which you've assigned a behavior. Pen review provides some simple statistics, a time line, and transition matrix for your data. Get the set with a tutorial here. PLEASE NOTE: This version is limited when used as a research tool. It is mainly intended as a teaching tool for an laboratory in animal behavior. The full-tilt research version is Pen Record.
  3. Track allows you to track the movements and behavior or an animal or person on a map. Intended for behavioral ecologists. The X/Y coordinates, time, and behavior can be extracted from the data file. Get it here. See a short tutorial here. Instructions for converting palm data base (pdb) files to PC format is here. Instructions on how to delete files when your Palm fills up are here.
  4. Counter. Use the palm buttons to count the number of bacteria in a culture, times a behavior was seen, etc. This keeps your counts and allows you to save them in a database. Get it here.
  5. Insect Order Key. Get it here.
  6. Tree height: A clinometer for the palm. Allows you to estimate the height of a tree or other object if you know the distance you are from the object. The program is here. Instructions are here.
  7. For the programs that output a database you'll also need PDB Converter available here. NOTE: For some reason this will not install on my system. If you have trouble, download pdb reader here or here (this is NOT my program). PDB reader converts palm files into CSV Excel files. Alternately, use POSE (Palm OS Emulator) on your MSDOS or MAC system. Information on POSE is here.
  8. ThinkDb / Smartlist To Go Databases for Ecology Field Work and Mouse Behavior. This is a zipped file of all the following databases. Obviously, many of these programs will work for behavioral and laboratory data collection even if you're not working with mice.
    1. Install all the PlugIn files just in case. You will also need to purchase Smartlist to Go or ThinkDb. A 30 day trial will provide time for you to test the programs. Both can be found here (just search for Smartlist)
    2. Mouse Day 1- Record the genotype, weight, length, etc for arriving mice. Works with all the other programs! Links sex, genotype, etc.
    3. Mouse Test Battery- Irwin Psychopharmacologia 13: 222-257
    4. Mouse Behavioral Tests Database
    5. Daily Record (weight/length, etc.)
    6. Handle- Short daily behavioral tests performed in our lab.
    7. Paylor Screen Test
    8. Water Maze Pretest 10 days
    9. Water Maze Visual Platform 10 days
    10. Water Maze Hidden Platform 10 Days
    11. Water Maze Probe Trial 10 Days
    12. Water Maze Reverse Training 10 days
    13. Counter Thing (get counts of stuff in the field or lab- bacterial colonies, number of certain species, etc.)
    14. Field Collection and Field Data (collects similar kinds of things in different formats)
    15. Timer Thing (lots of timers to keep timed records)
    16. Water Quality (General water quality tests)
    17. Mistletoe- Accepts GPS location, tree species, tree height, girth, mistletoe count (infestation), and has fields for photo ID and comments.