This page contains information for those participating in the density estimation tutorial at Mount Hood on August 21st, 2011 For a brief outline of the workshop contents, see this page.
During this workshop, there will some practical data analysis exercises for participants. We recommend that, if possible, participants download and install the relevant computer programs prior to the workshop, as this will save time on the day. We will be able to assist with any problems at the start of the workshop.
We look forward to seeing you on the 21st!
— Danielle Harris, Tiago Marques and Len Thomas
All participants will need the following (free) programs:
- ‘R’ – a statistical analysis program with the additional package ‘secr’ (http://www.r-project.org/).
- NB1: Packages can be easily installed from R once it is installed and run, provided you have internet access. To do this, open R, go to ‘Packages’ – ‘Install Packages’ then select an appropriate CRAN mirror, and packages can be chosen from a list. So, once you’ve installed R, go ahead and install the secr package.
- NB2: R’s learning curve can be steep. We will provide all the code needed for the practical sessions, and we’ll be there to help. However, if you are unfamiliar with R, you might want to run an example session before coming to the workshop, using the “Appendix A A sample session” in “An introduction to R” book. You can open this book as a pdf from R, by selecting Help|Manuals(in pdf)|An introduction to R.
- ‘Distance’ – distance sampling analysis software (http://distancesampling.org/Distance/index.html)
Note that while R runs on just about any operating system, Distance is Microsoft Windows only. If you’re bringing a computer running MacOS or Linux, you’ll have to work with someone else with a Windows machine for one case study.
During the workshop, several case studies will be introduced. The key references for these studies are listed below.
NB: An overview of all the case studies will be provided on the day, but the references contain more detail about data collection, processing and finer details of the analyses.
Case Study 1 – Right whales in the Bering Sea
- Marques, T.A., L. Thomas, L. Munger, S. Wiggins and J.A. Hildebrand. 2011. Estimating North Pacific right whale (Eubalaena japonica) density using passive acoustic cue counting. Endangered Species Research 13: 163-172. (pdf)
Case Study 2 – Beaked whales in the Bahamas
- Marques, T.A., L. Thomas, J. Ward, N. DiMarzio, P. L. Tyack. 2009. Estimating cetacean population density using fixed passive acoustics sensors: an example with beaked whales. Journal of the Acoustical Society of America 125(4): 1982-1994. (pdf)
Case Study 3 – Minke whales around Hawaii
- Marques, T. A., Thomas, L., Martin, S. W., Mellinger, D. K., Jarvis, S., Morrissey, R. P., Ciminello, C., DiMarzio, N. In press. Spatially explicit capture recapture methods to estimate minke whale abundance from data collected at bottom mounted hydrophones. Journal of Ornithology. (pdf). The final version can be downloaded from www.springerlink.com.
Case Study 4 – Blue whales in the northern Indian Ocean
NB: The following reference is for a different case study, but uses (nearly) the same method:
- Küsel, E.T., D.K. Mellinger, L. Thomas, T.A. Marques, D.J. Moretti, and J. Ward. 2011. Cetacean population density estimation from single fixed sensors using passive acoustics. Journal of the Acoustical Society of America. (pdf)
Other useful websites
- DENSITY website (http://www.otago.ac.nz/density/) – this gives an overview of spatially explicit capture-recapture methods and links to relevant publications.
- DECAF website – publications page (http://synergy.st-andrews.ac.uk/decaf/project-outputs/) – here is a complete list of all the papers that have been generated by the DECAF project, many will be referred to as well as the key references listed above.
- Distance website – publications page (http://distancesampling.org/dbib.html) – a large list of distance-sampling references.