Thanks for your answer!

I am not sure if I found the right thing when I googled it. Did you mean this: https://gforge.inria.fr/projects/somlib/

R itself has many guides and specially designed packages a simple search on google or the R website should throw up some useful items

Thanks Craig! The reason I was asking this question was more about, if there is something like a textbook which can be used to get an overview about such analysis and determine what is possible and impossible (or hard) to do. Lukas

Hi all,

To check for specific areas of interest within R you can look at the "Task views". The one concerning spatial analisys is here (maintained by R. Bivand):

http://cran.r-project.org/web/views/Spatial.html

Hope This Helps

Tito

Hi Lukas,

You can also do analysis in ArcGIS (using their extensions Geostatistical and Spatial Analyst, or external compatible extensions, such as those here: http://www.ian-ko.com/, http://www.spatialecology.com/, http://www.spatialecology.com/htools/tooldesc.php) and/or combine these ArcGIS analyses with data analysis in R, e.g. R libraries raster, maps and maptools which might be more flexible and free compared to ArcGIS.

Cheers,

Petr

Hi all,

Notwithstanding Argis being widely used and powerful, if you want to use opensource software then you can also try Qgis (http://www.qgis.org/) which also has R plugins allowing some interactions between both programs. Namely in Home-range analyses (http://hub.qgis.org/projects/quantum-gis/wiki/HomeRange_plugin) or exchange tools like manageR (http://www.ftools.ca/manageR/). Some knowledge of the Python computing language will help however (http://rpy.sourceforge.net/) and it is not so simple as stated.

Hope this helps,

Regards

Tito

If by chance you are interested in Levy walks or Levy flights (superdiffusive and scale-free random walks) -which have often been used to model animal movements e.g., (humans, monkeys, albatrosses) I can recommend some papers (Science, Nature, Ecology) I have found on the topic. For a book on this:

Levy Flights and Related Topics in Physics (Springer, Berlin, 1995)

Thanks Eric! This is actually a topic I´m interested in. Is there a specific paper you would recommend, perhaps with a detailed methodological section?

Here are a couple nice reads that may lead you in a fruitful direction:

Benhamou, S. (2007). How many animals really do the Levy walk?. Ecology, 88(8), 1962-1969.

Brown, C. T., Liebovitch, L. S., & Glendon, R. (2007). Lévy flights in Dobe Ju/’hoansi foraging patterns. Human Ecology, 35(1), 129-138.

Rhee, I., Shin, M., Hong, S., Lee, K., Kim, S. J., & Chong, S. (2011). On the levy-walk nature of human mobility. IEEE/ACM Transactions on Networking (TON), 19(3), 630-643.

Travis, J. (2007). Do wandering albatrosses care about math? Science 318:742-743

Viswanathan, G. M., Buldyrev, S. V., Havlin, S., Da Luz, M. G. E., Raposo, E. P., & Stanley, H. E. (1999). Optimizing the success of random searches. Nature, 401(6756), 911-914.

Hi all,

May I suggest a bit of caution regarding the use of Levy walk (or Levy flight), at least regarding fish and fisheries ?

In a recent (2011) paper, Edwards concluded that "Thus, Lévy flight movement patterns are not the common phenomena that was once thought, and are not suitable for use as ecosystem indicators for fisheries management, as has been proposed."

Read More: http://www.esajournals.org/doi/abs/10.1890/10-1182.1?journalCode=ecol

The paper is also available here:

http://www.chebucto.ns.ca/~english/edwards11ecology.pdf

Regards,

Tito

To jump on the back of Frederic and Tito's answers, you may also want to read "The Physics of Foraging" by Viswanathan, da Luz, Raposo and Stanley (University Press, Cambridge). It covers most of the papers published on the "Levy Flight Foraging Hypothesis". This book is a bit pro-levy, but it may help you to see both sides of this rather topical issue. Our team at Swansea recently published a paper detailing how the cost of turns could also add to the cost of transport for animals too, something which has thus far been overlooked in the majority of pro-levy literature. Feel free to have a read at; http://onlinelibrary.wiley.com/doi/10.1111/ele.12149/abstract

You might also be interested in state space models. I don't have experience with them but they are being increasingly used with animal movements, particularly animals tracked with telemetry (not sure if this is what you are looking for, however). State space models can also be implemented in R.

Jonsen, I.D., Flemming, J.M., Myers, R.A., 2005. ROBUST STATE-SPACE MODELING OF ANIMAL MOVEMENT DATA. Ecology 86, 2874–2880.

Patterson, T.A., Thomas, L., Wilcox, C., Ovaskainen, O., Matthiopoulos, J., 2008. State-space models of individual animal movement. Trends in Ecology & Evolution 23, 87–94.

In addition to SSM, there are a variety of other approaches used. The following use a fractal analyses (not in R but a free program):

Papastamatiou, Y.P., Cartamil, D.P., Lowe, C.G., Meyer, C.G., Wetherbee, B.M., Holland, K.N., 2011. Scales of orientation, directed walks and movement path structure in sharks. Journal of Animal Ecology 80, doi: 10.1111/j.1365-2656.2011.01815.x

Papastamatiou, Y.P., Lowe, C.A., Caselle, J.G., Friedlander, A.M., 2009. Scale-dependent effects of habitat on movements and path structure of reef sharks at a predator-dominated atoll. Ecology 90, 996–1008.

Lastly, simpler approaches look less at the movement processes themselves, but rather try to build associations between the locations of animals and the environmental conditions of those locations. Although one has be to be careful to account for potential spatial and temporal autocorrelation, forms of regression techniques, including generalized additive models (GAMs) and generalized estimation equations (GEE) can be used for such work. These can be implemented in R:

Pirotta, E., Matthiopoulos, J., MacKenzie, M., Scott-Hayward, L., Rendell, L., 2011. Modelling sperm whale habitat preference: a novel approach combining transect and follow data. MARINE ECOLOGY-PROGRESS SERIES 436, 257–272.

Aarts, G., MacKenzie, M., McConnell, B., Fedak, M., Matthiopoulos, J., 2008. Estimating space-use and habitat preference from wildlife telemetry data. Ecography 31, 140–160.