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Capture–Recapture for Spatial Data Course

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Capture–Recapture for Spatial Data Course

August 7-9, 2012

Yukon College, Whitehorse, Yukon, Canada


Instructor: Dr. Murray Efford, Otago University, New Zealand

Dr. Murray Efford is a population ecologist with long experience in live-trapping studies. He has recently focused on developing spatially explicit capture–recapture (SECR) methods, and acoustic methods for assessing bird populations. He is the author of the Windows software "Density" and the R package "secr", and has presented SECR workshops in New Zealand, Malaysia, UK, and Canada.


Course description

Animal populations are often studied by trapping individuals, marked or otherwise distinguishable, at discrete points in space or by searching an area for sign. The statistical analysis of such data to estimate population density or size is more robust and effective if it accounts for the spatial distribution of sampling. There has been rapid growth of relevant methods and software in the last few years, but these have yet to appear in standard texts. SECR analyses are used widely for bear populations sampled with hair snags and for large cats caught on automatic cameras. The methods extend to grid trapping of small mammals, mist-netting of birds, DNA from feces, and sounds

recorded on microphone arrays.



This 3-day short course introduces the core concepts of SECR, the free Windows software "Density" and the R package "secr". There will be some time set aside to discuss participants=92 data. Specific topics to be covered include:

  • spatial data types
  • detection functions
  • the use of habitat masks
  • modelling of trap response and spatial, temporal or individual covariates
  • interpreting output and troubleshooting
  • study design
  • density surfaces
  • open-population analysis.



Participants should have some knowledge of conventional capture–recapture methods and model selection using AIC. Familiarity with R is recommended.


Course preparation

  • Participants should bring their own laptop (Mac or Windows) preloaded with the software described below.
  • You may wish to bring an external monitor if your laptop has a small screen.
  • Participants are encouraged to bring their own formatted datasets (see "Input data" in the Density help file, or secr-datainput.pdf).
  • You will be provided with files for course exercises at the course.

Software to install before the course:

The Windows program Density will be discussed and used for demonstrations, but it is not essential. Download it from www.otago.ac.nz/density and use a program such as WinZip to unzip the single zip file in a folder of your choice.


If you do not already have a recent version of R (2.12 or later) then install it from, e.g., http://cran.stat.sfu.ca/. Click on Windows (or Linux or MacOS X) in the Download and Install R section. If installing for Windows select "base" in the R for Windows Section. Now download R-2.15 for Windows. Save the executable file (about 47Mb) to your hard drive. Next double-click the executable file to install R on your machine. Choose the default settings.


To install the R package "secr" in Windows, open R while you are connected to the internet and select Packages | Install package(s) from the menu. Select a suitable mirror site (e.g. Canada (BC)) and then find "secr" in the alphabetical package list. Selecting "secr" installs the package itself and any required packages. The process differs only slightly on Mac and other systems.


Some optional features of "secr" use suggested packages that you may also wish to install: "sp" and "maptools" for reading shapefiles; "spsurvey" for representative spatial sampling with GRTS; "gpclib", "rgdal" and "rgeos" for other GIS-related functions. You will need a PDF reader such as Adobe Reader.


Cost and registration

Course cost is $675CAD and is limited to 16 participants. For a registration form please contact Ramona Maraj at Ramona.Maraj@gov.yk.ca. Payment may be made by VISA or Mastercard. Receipts for payment will be provided at the course. Please do not email payment information. When the course fills, we will begin a wait list. Please note course fees cannot be refunded unless an individual is available to take your spot.


Where is the course?

The course will be held at Yukon College, Whitehorse, Yukon: http://www.yukoncollege.yk.ca/.


Registrants will be responsible for getting themselves to and from the college.


Information about Whitehorse can be found at:

http://www.visitwhitehorse.com/ and http://www.city.whitehorse.yk.ca/

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