Home Range Bootstrap function for the Move package

Last week we introduced a further function to the move package. It is called the hrBootstrap() which stands for Home Range Bootstrap. It allows to calculate the area of a minimum convex polygon (abbr. MCP) for a set of locations. A polygon is called convex if it includes all line segments connecting any pair of points (see[1]). The minimum convex polygon is the one with the shortest edge length. Given a number of locations of an animal, e.g. due to GPS recordings, the MCP algorithm returns an area that may represent the home range of that animal.
Nowadays the MCP is scarcely if at all used to calculate home ranges. Kernel Density algorithms and Brownian Bridge Movement Models serve more sophisticated results. The results are much closer to the real observations. Nevertheless, the MCP calculation can still be used to compare own results with older studies.
The hrBootstrap() function in our ‘move’ package works for Move and MoveStack objects (individuals or groups of individuals). We implemented here the mcp() and mcp.area() function from the ‘adehabitatHR’ package [2]. We calculate for different number of random locations the mcp. For example for a set of 70 location fixes we calculate the mcp with 5, 6, 8, 10, 13, 16, 20, 25, 32, 40, 50, and 63 locations. Each step is repeated by default 100 times, each time with different locations. The returned data frame represents the calculated mcp area (you can specify the unit with the unout argument) for the according quantiles (0%, 25%, 50%, 75%, 100%) of the values.
By default the quantiles for the different number of locations are plotted as a line plot (see below).
The version will be available, as soon as the r-forge page is back online again.

References

[1] Minimum Conevx Polygon (MCP) http://www.stat.ufl.edu/STA6934/Minimum%20Convex%20Polygon%201%2017%2007.pdf

[2] Home Range Estimation in R: the adehabitatHR Package http://mirrors.fe.up.pt/CRAN/web/packages/adehabitatHR/vignettes/adehabitatHR.pdf

Reference list to the ‘Scientific Presentations’ workshop

In our ‘Scientific Presentations’ workshop I promised to send around the materials I used to prepare the workshop. Here are the links (little * indicate sources that I liked most):

Rethinking the design of presentation slides: Creating slides that are readily comprehended

How to create “Thriller” PowerPoints® in the classroom! Innovative

*How to Give A Talk

Good oral presentation of scientific work

Impress: Stylish Presentations

Slide:ology: Oder Die Kunst, Brillante Präsentationen Zu Entwickeln – Nancy Duarte 

A brief assessment of Michael Alley’s ideas regarding the design of PowerPoint slides

*How to Use PowerPoint for Best Educational Outcomes by Ellen Finkelstein

Visualizing Content for Lecture Capture 

How to give a good talk

Getting Beyond “Good Job”: How to Give Effective Feedback

Pimp your PowerPoint

*Keep Attendees Awake: Writing Effective Presentations for International Conferences

How to Give a Good Research Talk

Update fixes WebImport in move package

With the new version of the move package (0.5.4) that we uploaded on Friday many import issues were fixed. We tested the download function with all public available Movebank data sets. As long as the study has no double timestamps per individual ID the studies could be imported. Now, it makes much more fun to interact with the WebImport interface. Just import specific animals from a study to calculate their utilization distribution, UD, or other movement related parameters.

You find more about the move package on our lab page, or direct on r-forge.

Visit as well the Movebank site to see which studies are public available.

Make it visible

Soft tissue within small insect heads are hard to investigate. Muscles, glands and the brain are accessible by opening the head or cutting the head into thin slices.

I produced a chemical procedure that makes the surface of small insect heads durable for confocal laser-scanning microscopy (CLSM). Thus, I was able to scan whole insect heads and reconstruct soft tissue, like glands and individual neuropiles.

I also used fluorescent dyes for backfills, which appeared to work with this procedure.

Thermoregulation in Bumblebees

Variability is said to be beneficial for example in parasitic load, or nest-temperature regulation. Many studies were already done exploiting this topic mathematical and genetical. I wanted to do the first behavioral experiments to challenge this hypothesis.
Bumblebees are known to regulate nest-temperature. This gives them a certain degree of independence from environmental conditions.
If inter-individual variability is beneficial there must be a measurable difference between groups with high and low variability.

Move for Movebank

With a group of computational ecologists I’m working on a package for R. We implement functions that can import various animal track data into R. These data can then be visualized and analyzed. My colleague Bart Kranstauber created the dynamic Brownian Bridge Movement Model (dBBMM) that estimates the UD, utilization distribution, of an animal according to its track. The dBBMM is a part of the ‘move’ package.

The package is available at the r-forge page as a beta version.
More information are available on the ‘move’ package website.