workshop

It was a great MESS – Movement Ecology Summer School 2015

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The second Movement Ecology Summer School, organized by the Ozgul’s group as part of the PhD Program in Ecology of the Life Science Zurich Graduate School, has been a great success. Twenty-five highly motivated students from UZH/ETHZ and from overseas gathered at the Ostello-Cappuccini in Faido (Ticino) for what has been an inspiring and productive week.

Under the guidance and supervision of leading scientists (Gabriela S, John F, Luca B, Garrett S, Frank P and Gabriele C) the participants learned to source and manipulate remote sensing imagery, to decompose movement trajectories, to compute home ranges and investigate habitat selection. All these skills combined were used to disentangle the movement behavior of Apollo, Botswana’s most famous spotted hyena!

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The movements of Apollo were thoroughly analysed during the entire week. All results pointed towards a univocal conclusion: Apollo is by far Botswana’s most famous spotted hyena.

 

Participants had the opportunity to alternate high-quality lectures with social activities, which had the scope to create a cohesive group and promote interactions and establish future collaborations.

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Great food, amazing people, stunning weather were the recipe for a successful week
work
And we also worked hard! Very hard!. Despite Prof Börger and Prof Street attempts nobody fell asleep…almost.

We received very positive feedbacks from all participants, which is very encouraging, and we are therefore keen to offer a similar, and even more exciting, course during the summer 2017! Stay tuned on this blog if you want to be part of the next MESS and learn everything about Apollo!

 

Movement Ecology Summer School 2015

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On the basis of the success obtained in 2013, our group, and in collaboration with the Life Science Zurich Graduate School,  is proud to announce the upcoming Movement Ecology Summer School 2015  that will be held in Faido, in the heart of the Swiss Alps (August 23–28 2015). We already secured the contribution of leading scientist: Prof. Luca Börger, Prof. John Fieberg, Dr. Gabriela Schaepman-Strub, Dr. Frank Pennekamp, Dr. Gabriele Cozzi.

PhD students from UZH and ETHZ will have priority, but few places shall be available for external participants too.

This one-week course covers several aspects of animal movement ecology and includes both theoretical/conceptual and practical sessions.

The course builds on analytical complexity and leads the participant through several steps. During day one, the participants will learn to source landscape information through available remote sensing imagery and to import, manipulate and represent geographical data into R. Day two will be dedicated to the decomposition of movement trajectories and characterisation of movement modes and phases. During day three the participants will be exposed to common methods used in the calculation of home ranges and discuss the pros and cons. During the next day we will use presence/absence data to analyze habitat selection and create species distribution models. Finally, during the last day, the participants will be exposed to some new tools and methodologies to include data from alternative sensors (e.g. accelerometers) in the study of animal movements. Fundamental aspects such as study design, spatial autocorrelation, sources of error and time varying covariates will be discussed.

Data sets will be provided but the participants are encouraged to bring their own data. Basic knowledge in R is required. Participants should bring their own laptop with the latest version of R installed. Active participation during the course is required to obtain the credit points.

Workshop Announcement: Fitting Flexible State-Space and Hierarchical Models Using the Laplace Approximation and Automatic Differentiation

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I, Mollie, am organizing a workshop here at the University of Zurich. I’ve recruited two experts to come help me teach: Hans Skaug (Dept of Mathematics, Univ of Bergen) and Kasper Kristensen (Dept of Applied Maths and Comp Sci, Technical Univ of Denmark). We’ll teach researchers from diverse fields how to fit state-space models via maximum likelihood estimation using the Laplace approximation to integrate out latent variables and automatic differentiation to calculate gradients. This is much faster than Bayesian methods.

These methods are implemented in AD Model Builder and a new R package called TMB. Currently, the course organizers are trying to decide if we should teach both, or only TMB. There are costs and benefits to being early adopters of new software. For example, several years ago, when the user base of ADMB was expanding beyond fisheries stock assessment, we found several bugs that weren’t exposed until people started trying different types of models and different computational platforms. We don’t want to expose students to these issues. On the other hand, learning one new program (rather than two) in a three day workshop might be preferable for some participants. Plus, most ecologists already use R, so learning the package TMB might be slightly easier for them than learning to use ADMB through the R2admb interface. TMB is more streamlined than ADMB because it had ADMB as an example and took advantage of existing free and open source C++ libraries. Whatever we decide to do, we’ll make sure the class exercises and examples are fully debugged before the workshop. Maybe I’ll use my lab mates’ computers as Guinea pigs.

The course will take place September 1-3, followed by 2 days of developing the TMB package and applications. We still have some openings for participants. Applications are due August 1.

More information can be found at the course website

https://sites.google.com/site/uzhstatespaceworkshop/

The workshop is funded by a GRC Grant from the University of Zurich.

Are the marmots fat or muscled?

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While some are tracking meerkats in South Africa, others are developing complex models in Zurich, I was doing laboratory work at the “Institut Pluridisciplinaire Hubert Curien” in collaboration with the Evolutionary EcoPhysiology Team (Strasbourg, France).

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No, no,no, I am not playing with liquid nitrogen for fun…
I am doing cryo-distillation to isolate water from biological fluids (here blood samples).
You probably wondering:  What? or Why ? I would answer because we want to demonstrate that:

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In other words, we want to validate the bioelectrical impedance analysis (BIA) by the deuterium dilution method to measure the body composition of marmots.
The bioelectrical impedance measurement is a non invasive method to estimate body composition and in particular body fat by determining absolute fluid volumes. It is doing exactly the same than the new scale you have at home! It is based on the fact that an electric current is conducted poorly by fat and bone but conducted well by tissues containing electrolytes and water.
BIA has been used in a number of species to evaluate total body water and thus body composition, including humans, cats, harbor seals, bear, dogs, pigs, horses but never used in marmots before.

So to ensure that this method is also appropriate in marmots, we evaluate the total body water by deuterium concentrations in condensed water from blood sample.

For more informations, you can read:
Kyle UG, Bosaeus I, De Lorenzo AD, Deurenberg P, Elia M, Gómez JM, Heitmann BL, Kent-Smith L, Melchior J-C, Pirlich M (2004). “Bioelectrical impedance analysis—part I: review of principles and methods.” Clinical Nutrition 23(5): 1226-1243. pdf

Mollie Attended an ADMB Developers’ Workshop in Iceland

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After the ADMB Developers' Meeting, I investigated the thermal activity in Iceland.

This photo has nothing to do with the workshop. I did some hiking after the workshop and found this huge boiling cauldron of water in the land of fire and ice. The landscapes were amazing with so much geothermal activity, old lava fields, and water falls.

The main purpose of my trip to Iceland was to work September 18-22 with eleven other developers on the statistical software Automatic Differentiation Model Builder (ADMB) at the University of Iceland and the Marine Research Institute in Reykjavik, Iceland. ADMB is useful for fitting nonlinear models and has the flexibility to fit random effects. It’s nearly as flexible as MCMC methods like WinBUGS, but much faster and without the need for specifying prior information (it’s really cool!).

It’s so much easier to get everyone engaged in a discussion and making decisions when we’re all working in the same room, rather than over email when we’re spread out over the corners of the earth. Since we had developers coming from North America and Europe, Iceland was a good midway point, and we had an excellent Icelandic host.

We discussed many important decisions for how to move forward with the software including documentation, parallelization, the most efficient linear algebra libraries, optimizers, links to R, and potentially moving to Github. We’re working to make the documentation easier for new users and writing an introduction aimed especially at R users. We discussed teaching workshops in the near future. We have one scheduled at the International Statistical Ecology Conference and we’re interested in teaching to other groups as well. Let me know if you’re interested.

Moving forward – Animal Movement Ecology Summer School

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The last week of August could not have been more hectic and inspiring for some of the people of our lab. The first Animal Movement Ecology Summer School held at the University of Zurich as part of the PhD Program in Ecology of the Life Science Zurich Graduate School has been a great success. We managed to bring together 30 highly dedicated and motivated participants from UZH/ETHZ and from overseas as well as seven top lecturers for what has been an intense and dynamic week.

Participants had the opportunity to alternate high-quality lectures – covering a wide range of topics, such as remote sensing, home-range and movement analysis, patch occupancy models, population dynamics – with some social activities, such has bbq and the long-sought-after jump in the Limmat, the local river. The scope of such activities was to quickly create a cohesive group and promote interactions among the participants and with the lecturers to establish future collaborations. A great success has been the day organised at the Tierpark Goldau, where we had the possibility to follow lectures in a natural and inspiring environment.

 

Participants interacting during one exercise in the suggestive class room at the Tierpark Goldau
Participants interacting during one exercise in the suggestive class room at the Tierpark Goldau

We, organizers, received very positive feedbacks from all participants, which is very encouraging, and we are therefore keen to offer a similar, and even more exciting, course during the summer 2014! Stay tuned on this blog if you do not want to miss-out and want to…keep moving forward!

Animal Movement Ecology Summer School

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Our group is proud to announce the upcoming Animal Movement Ecology Summer School held at the University of Zurich (August 26–30 2013) and for which we already secured the contribution of leading scientist: Dr. Luca Börger, Dr. John Fieberg, Dr. Patrick Laube, Dr. Gabriela Schaepman-Strub, Dr. Dennis Hansen, Dr. Marc Kery, Prof. Arpat Ozgul.

This one-week course covers several aspects of animal movement ecology and includes both theoretical/conceptual and practical sessions.
The course builds on analytical complexity and leads the participant through several steps: from sourcing landscape information through available remote sensing imagery; to import and represent geographical data into R; to the calculation of home ranges; and finally to the characterisation and investigation of animal movement modes in a spatially explicit landscape matrix. The participants will furthermore be given an overview on patch occupancy models and how to treat and analyse presence/absence and abundance data. Fundamental aspects such as study design, spatial autocorrelation, sources of error and time varying covariates will be discussed.
Data sets will be provided but the participants are encouraged to bring their own data. Basic knowledge in R is required. Participants should bring their own laptop with the latest version of R installed. Active participation during the course is required to obtain the credit points.

Eco-evolutionary Dynamics Workshop in Leiden

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This week, Cindy and I participated in the “Eco-evolutionary Dynamics in a Changing World” workshop at Lorentz Center, Leiden.

The organisers, Stephanie Jenouvrier, Thomas Reed and Marcel Visser, brought together a select group of researchers working at the interface of ecology and evolution, from both theoretical and empirical backgrounds, to brainstorm on our current understanding of eco-evolutionary dynamics. Unlike most other workshops, this one had quite an interesting format. There were only a few plenary talks, and most of the time participants held smaller break-out sessions on their own research area. Although there were no final road-maps or even a clear definition of eco-evolutionary semantics, these break-out sessions, I think, worked very well for tossing around ideas and discussing more specialised topics among those with shared interests. For our part, we received great input on our two projects.