Links to Software used in Course
We'll use Program MARK extensively in the course. Program MARK is freeware that was developed, and is maintained by Gary White, a recently retired professor from Colorado State University. Program MARK is the most flexible, widely used application currently available for parameter estimation using data from marked individuals. Software downloads and software documentation can be obtained from a site maintained by Gary White or by a site maintained by Evan Cooch. I have installed Program MARK on the computers in 407 Lewis Hall, and you are welcome to use those machined during labs and other hours that the room is not in use by other classes. Also, you can download and install Program MARK on your own computer if you wish.
Evan Cooch maintains a set of very useful Analysis Forums for mark-recapture data. You can post questions concerning analysis/theory using program MARK, PRESENCE, and other mark-recapture software. It also archives past questions and replies (very useful) and provides software announcements.
We'll occasionally use R, which is a free software environment for statistical computing and graphics. R is an integrated suite of software facilities for data manipulation, calculation and graphical display. Previous knowledge of R is NOT a pre-requisite for the course. I have installed R on the computers in 407 Lewis Hall, and you are welcome to use those machined during labs and other hours that the room is not in use by other classes. Also, you can download and install R on your own computer if you wish. Finally, you can use the software on various computers across campus. For lots of information on R, visit the CRAN repository. On the left side of the main CRAN page, look under "Documentation" to find links to lots of good resources for learning R. Please let me know if you find resources that are especially helpful.
- Download R (the first few links in the main frame)
- Learn about R -- lots here. Under Documentation, the six "manuals" are usually downloaded when you install R, so you can read them locally under the help menu after starting R. The FAQs contain lots of good info about R setup and operation."Other" has links to manuals and introductions written by others. If you find any of these to be particularly good, please let me know so I can bookmark them for others.
- Reference card: Here's a good 4-page handout for that provides an organized list of many commonly used commands/functions.
During the semester, you will have free access to DataCamp courses, which are excellent. You'll find great material there for learning about how to use R, Rstudio, useful R packages, probability theory, and more. You should have received an invite from DataCamp.
I prefer to run R through RStudio, which is an integrated development environment for R that makes many tasks easier and adds a variety of excellent tools to what's available in R.
If you want to be able to produce pdf's from RMarkdown, you'll need to install LaTex.
You can download the software for various computer platforms (e.g., Windows, Linux,
Mac OS) for free here.
RMark Library - The RMark library is a collection of R functions developed by Jeff Laake that can be used as an interface to MARK for analysis of capture-recapture data. The library contains various functions that import/export capture data, build capture-recapture models, run the FORTRAN program MARK.EXE, and extract and display output. I do not expect that we will use RMark in this course but some of you may be R users interested in this software once you have learned MARK.
Program PRESENCE - Estimates patch occupancy rates and related parameters.
Online teaching tool from the USGS Vermont Cooperative Fish & Wildlife Research Unit. A helpful set of spreadsheet exercises for learning occupancy modeling.
Related software - There are a variety of other useful software programs available for analysis of mark-recapture data. Evan Cooch maintains a set of links to many of the packages at his Program MARK web site.