[news]


starwars

August 7, 2016. Having fun with R by analysing the social Star Wars network in The Attack of the Clones. I adapted two clever analyses made by others here and here. Check it out on RPubs. The data and R codes are available on GitHub.


ImpressionJuly 21, 2016. Wow, another good news, our project « Climate and management effects on COMmunity dynamics – Developing multi-species DEMOgraphy » will be funded by ANR! I submitted it in April for the third time. I originally submitted it (just once) to the ERC back in 2011, it was rejected. Over the years, we received constructive comments from the referees that helped improving the project, and made it more solid. In DEMOCOM, we will develop an integrated statistical framework for estimation and inference about community dynamics via the development of a multispecies demography, bringing together concepts, predictions and tools from both fields of demography and community ecology. We will apply this new framework to case studies on fishes, mammals and birds. The methods will be made available through R packages. This is a collaborative project with many partners involved, and people to be hired (stay tuned). The project will start early 2017, more soon.


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June 1, 2016. Great news! Our project on « Scenarios for coexistence between men and dolphins on the Mediterranean French littoral » will be funded by Fondation de France. In this project, we will propose management strategies for human activities and populations of bottlenose dolphins to coexist. Building on the GDEGeM project, we will adopt an ecological approach to infer the spatio-temporal distribution of dolphins and their interactions with human activities, and a sociological approach to explore the attitudes and perceptions of local actors towards dolphins. We will resort to participatory modeling to build, test and use a model to assess  management strategies collectively. In passing, I kind of liked the selection procedure: we first submitted a written application, then were asked to come for an interview. I could answer the questions of the committee and have a direct feeling of what they were thinking of our project. We will start this project officially by the end of the year, more soon.


cartoon-science-communicationSummer 2016. I decided to teach myself how to do proper reproducible research. Many reasons to that: save time on the mid/long term, make my analyses open and criticizable, share with others, … There are tons of resources on  the web. I use the tutorials provided by guru Karl Broman. For people like me who learned S-plus, he has some advice to switch to modern tools. Among others, I try and use more and more RStudio in connection with KnitR and R Markdown and share my codes on GitHub. I am more a Fortran guy, but Rcpp makes me wonder about C++. Version control, piping and the tidy universe are not yet entirely familiar to me, I’m making baby steps (or grandpa steps I should say). Let’s see how it goes.


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June 28 – July 1, 2016. I attended the International Statistical Ecology Conference in Seattle. I don’t go often to conferences, but I do my best not to miss that one. This year, clearly, hidden Markov models (HMM) were on the lips of everyone. Well, it was cool to realize that I wasn’t too ‘has been’ by giving a 1-day workshop on fitting occupancy models with HMM and program E-SURGE developed in our team 😉
I also gave a talk on the use of PCA to deal with many correlated covariated in capture-recapture models. I also co-authored a talk that Ian Renner (see below) gave on combining sources of information on species distribution.


big_fish_og

May 30, 2016. My post-doc Sarah Cubaynes and I went to visit our colleague Jon Aars in Tromso, Norway. We are working together on the demography of polar bears using an amazing dataset the Norwegian Polar Institute has been collecting for decades. It was also the opportunity to catch up with Nigel (Gilles) Yoccoz who’s being very helpful with this project. Jon took us fishing; I was luckier than with fly-fishing 😉


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26-27 May 2016. We organised the second conference of the GdR EcoStat. We spent two lovely days in Montpellier talking about ecological statistics with the hundred people who attended. The talks are available here. If you’d like to know more about our acitivities in the GdR, check out our website.


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March 12, 2016. Fishing season is open 😉


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December 1-2, 2015. The GIS3M held an international workshop in Marseille on the conservation of Bottlenose dolphin conservation and monitoring in the North-Western Mediterranean Sea. This was the opportunity to discuss the results of the GDEGeM project on the same topic. I mostly contributed by analysing the tons of photo-IDs that were collected during the program to estimate abundance and analyze the social structure. My talk is here.


Lebreton

November 13.  Jean-Dominique Lebreton went on retirement, and we could not let him go without organizing something in his honor. Jean-Do had a tremendous influence in the field of statistical ecology with important contributions in (among others) multivariate analyses, software developments, population dynamics, and capture-recapture methods. On a personal side, I would simply not be here in science without him. Many friends and colleagues came or sent a message for the occasion. These interventions were filmed, see here and enjoy.


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November 3, 2016. Taking the opportunity of Ian Renner’s visit, we organized thanks to the GdR EcoStat a conference on the recent advances in the modeling of species distribution. We were lucky to have the cream of researchers in the domain with Julien Papaïx, Joseph Chipperfield, Ian Renner, Joern Pagel, Bob O’Hara, Laura Pollock and Damaris Zurell. The talks are available here.


9608687-15452173October 26 – November 6, 2015. Ian Renner from the University of Newcastle in Australia spent some time with us while on a sabbatical. We worked together on developing a method to combine sources of information on species distribution. Ian brought his sound expertise on the Lasso for covariate selection and point processes that provide a nice integrated framework. It was fun to program in R in parallel. I wish I could do that more often. We even managed (credit goes to Ian) to present something at the International Statistical Ecology Conference (see above). On a personal side, Ian has become a friend, his kindness and interest in other people are amazing.

Update: Excellent news! Ian will be back with us for 2 weeks or so early 2017. More soon.


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Autumn 2015. I had the visit of  Raluca Bancilla a research scientist from Romania. We investigated spatio-temporal environmental variation in and individual heterogeneity on emigration/immigration rates of the troglophile harvestmen species Paranemastoma silli with capture-recapture models. We used two P. silli populations inhabiting two caves, Closani and Lazului Caves, located in the Mehedinti Mountains in southwestern Romania. Yes, we do not only work on big emblematic mammal species 😉
On a personal side, Raluca is always smiling and laughing – ‘la banane’ like we say in French, it was so good to have her in the team. I’m looking forward to hosting her again!

Update: Excellent news! Raluca will be with us again for a short 2-week visit in October 2016. We will resume a project we started one year ago on the evaluation of demographic parameters of two related species of spadefoot toads (Pelobates syriacus and P. fuscus) from the Danube Delta Biosphere Reserve, Romania, using capture-recapture models.


hirAugust 12-14, 2015. We visited our colleagues from Dolphin Biology and Conservation (Giovanni Bearzi, Silvia Bonizzoni, Nina Santostasi ‎and‎‎ Eva Greene). Lots of discussions on future projects about the estimation of striped, bottlenose and common dolphins abundance, their distribution in the gulf of Corinth (Greece) and their interactions with fishermen. Nina will be visiting us in Ocotber-March to work on the abundance project. We also went out for a survey and spotted several groups of striped dolphins, and two common dolphins. Thanks to Giovanni and Silvia for their hospitality and kindness. The beginning of a new adventure in Greece!


hirAugust 2-6, 2015. I attended the International Congress on Biological Conservation that was held in my home town Montpellier. The students of our team were on fire and talked about their exciting work. Gilles presented a bio-economic model to study the population dynamics of Asian captive elephants, a nice example of how to explicitly incorporate interactions between captive and wild populations in species management. Julie talked about her use of opportunistic data to map the colonisation of the wolf in France; this is a neat example of how to generate non-detections by carefully assessing the observation efforts to use dynamic occupancy models. Anne-Sophie presented an application of Poisson point process modeling to map the presence of brown bear presence in Greece using citizen science data with possible observer bias. Blaise presented his results on a sociological survey to assess the attitudes of local residents towards the presence of Brown bears in the Pyrenees. Last, Laetitia had a poster on the use of a spatially explicit individual-based model to explore the best strategies (reintroductions and / or corridors) to restore the population of lynx in the Vosges mountains. I gave a talk on a review of the methods to analyse citizen science data. This was part of a symposium (nicely summarised by Muki Haklay here) organised by Karine Princé and Wes Hochachka. Stay tuned, a paper is on its way! Overall, the program of this conference was dense, the talks and discussions between sessions were stimulating, I’m looking forward to attending the next one!


hirJuly 20, 2015. Just submitted a big proposal to the Biodiversa call. It was great to write this project with Hervé Fritz who, without a doubt, knows how to write grant applications! If successful, we’ll be working on the social and ecological dimensions of connectivity in lynx habitats. This is joint work with French, Swiss, German, Norwegian and Swedish colleagues. More soon hopefully.

Update: On May 2016, I received the news that our project was rejected. Big disappointment. But hey, that’s life, and this project is awesome, we’ll find other ways to implement it!


hirEarly July 2015. I had the visit of Sarah Benhaim and Lucile Marescot (a former PhD student of mine), both post-doc at the Leibniz Institute in Berlin supervised by Stephanie Kramer-Schadt. It was an exciting week that we spent discussing and analyzing data on the spotted hyenas from the Serengeti National Park with questions at the interface of demography, sociality and epidemiology. This is joint work with Heribert Hofer and Marion East.


hirMay/June 2015 – Among the papers we had published lately, I’d like to emphasize two contributions on the conservation of brown bears with some eminent colleagues:
– Karamanlidis, A.A., M. de Gabriel Hernando, L. Krambokoukis, O. Gimenez (2015). Evidence of a large carnivore population recovery: counting bears in Greece. Journal for Nature Conservation. This is a joint venture with Alex and the Greek Arcturos NGO in which we provide the first reliable abundance estimates for brown bears in Greece.
– Bischof, R., H. Broseth, O. Gimenez (2015). Wildlife in a politically divided world: insularism inflates estimates of brown bear abundance. Conservation Letters. Richard had this very clever idea to use spatially-explicit capture-recapture models to assess to what extent abundance estimates are affected by double-counting animals that move across borders – see here for a nice summary of our work.


hirEnd of June, 2015. I’m so delighted to announce that Julie will start a PhD in October with me, jointly working with Eric Marboutin and Christophe Duchamp from ONCFS. There will be also collaborations with John Linnell from NINA. She’ll be studying the various ways to assess the distribution of large carnivores and methods to optimise the associated monitoring protocols.


hirEnd of May – early June, 2015. My 2 master students finished their internships. I was so lucky to have them and work with them. Iago worked on the estimation of abundance using bilateral photo-identification capture-recapture data, with an application to bottlenose dolphins. He made a very neat contribution to the field by greatly improving existing algorithms (here and here) to fit capture-recapture models to these non-standard data. Julie worked on inferring the distribution of wolves in France from the beginning of its recolonization in the early 90’s. Her main contribution was to show that by carefully describing observers’ characteristics and properly quantify the prospection effort, citizen science data can be used to map the range dynamics of species with large dispersal distances and home ranges. Iago will spend next year improving his (already largely above the average) skills in informatics, AI, programming, agent-based modelling… Hopefully, we’ll work again together. Julie is applying for PhD grants, more soon.


hirMay 21, 2015. We had our annual department day; for the occasion, we invited Anne-Caroline Prévot. Anne-Caro is having a fascinating scientific pathway, as she started with a PhD in bird population dynamics and now she’s working on topics requiring skills in environmental psychology. Google her, you’ll see for yourself, her work is awesome. For this special day, we opted for a particular format, with less science than usual, the idea being to show what’s going on behind the scenes. We had a roundtable on the link between research, managers and citizens. We also had several short unorthodox talks where we tried to analyse why some of our papers/projects were successful, but also why we failed at being read or funded. Interestingly, Rob Salguero-Gomez, a colleague of ours, wrote a nice piece on the topic here. Last, we gathered several persons with various professional profiles so that our students could ask them all the questions they wanted. Overall, I think it went amazingly well, and all the attendees found something to take home with them.


hirMay 13, 2015. As one of our always excellent department seminar, we had the chance to welcome Heath Smith from University of Washington, Center for Conservation Biology. Heath, together with his dog Chester with whom I became friend during the talk, is working with detection dogs on all sorts of important questions and organisms in conservation biology. Heath then headed to the Pyrénées with Nathalie Espuno to meet with our colleagues from the ONCFS bear (dream)team with whom we’re working on Blaise’s PhD. They’re gonna try this technique there, no doubt the results will be of interest for our work on large carnivores!


hirMay 7, 2015. I acted as the “president” on the PhD committee of Sophie Monsarrat who, with her supervisor Ana Rodrigues, kindly invited me. It was about the reconstruction of marine mammal’s historical distribution and abundance using historical data. Sophie did an amazing job during her PhD, have a look to her recent paper on the topic. Her presentation was just awesome, I wish I could give such vivid and fascinating talks, irrespective of the topic. Otherwise, her work reminded me of my current work on monk seals with Alex Karamanlidis from the MoM NGO and the talk I’m supposed to give at the ICCB2015 on the analysis of citizen science data. More soon.


hirEarly May 2015: I was on a committee that hired 3 junior permanent researchers for INRA. Everything went smoothly mostly due to the friendly atmosphere between people of the committee. It had me thinking about what works and what doesn’t work in job applications and interviews. Here are my 2 cents suggestions, I’m sure you can find plenty of more clever and relevant recommendations on the internet.

In disorder, read and stick to the guidelines (not that obvious sometimes), and do not hesitate to include figures and boxes in the document. Structure does not hurt, well articulated sections are welcome. In contrast with CNRS, but like universities, INRA hires people based on the quality of fit to profiles proposed by the INRA teams (but it also has non-thematic positions), hence the importance to project yourself in the team/lab where the researcher will be hosted, and the job itself. Have your applications read by one or two colleagues, if possible someone who has experience in being on the kind of hiring committee you will have to face.

asieFor the interview, appearances matter, whether you like it or not, therefore pick something neutral and comfortable (my opinion). Don’t use slides with too much text or complex figures (no tables please!), and point at your slides so that your visual support is part of your speech. Don’t look at the screen or the walls, try to look at the members of the jury. Occupy the space, don’t always stay at the same spot, but do not move too much (I’m useless at that). Don’t rush when you talk, and give short answers so that every member of the committee gets a chance to ask you a question. Be honest: if you don’t know something, or if you don’t understand a question (which most likely means that members of the hiring committee do not understand this question either), say it. Last, but not least: rehearse, rehearse and rehearse again, there will be a moment where you do no longer sound like you know your text by heart, but rather, like saying it has become natural. From my experience, the round of questions is more determinant than the talk itself, but we have very rare opportunities to train on how to answer questions. Try to have sessions of questions with your colleagues to get better at it; it comes with experience, no secret. For short talks, my advice is to write your text, at least for the first slides so that you’re confident you won’t get stuck when you start giving your speech.


asie23 April 2015: Great news! Gilles Maurer will soon start his PhD on the links between wild and captive populations of Asian elephants using an interdisciplinary approach. This is a joint venture with the Beauval zoo and B. Mulot through the CIFRE framework that funds applied PhDs with non-academic partners.


hir9 April 2015: Paméla Lagrange successfully defended her PhD co-supervised with M. Bélisle from the University of Sherbrooke on the ‘Drivers of survival and breeding dispersal using a capture-recapture framework in Tree Swallows – Québec’. The members of the committee (M. Festa-Bianchet, G. Gauthier, C. Barbraud, E. Cam) were unanimously amazed by both the ecological and methodological contribution of Paméla to the field. Congrats Pam!


corinth7-10 April 2015: I had the visit of Nina Santostasi from Italy to work for a few days on the estimation of striped dolphin abundance in the gulf of Corinth (in Greece). Nina is working with Giovanni Bearzi and Silvia Bonizzoni from the NGO Dolphin Biology and Conservation. Hopefully our collaboration will provide elements for the conservation of the species.


demo2-3 April 2015: As part of the GdR EcoStat and our evolutionary demography group, we had a stimulating workshop on the quantification of individual heterogeneity in survival of wild populations using an approach recently developed by Hal Caswell. Hal attended the workshop with Lotte de Vries her new PhD student who will be leading the study.


logoGdR12-13 March 2015: We organised the first conference of the GdR EcoStat (check out the logo on the left, thanks Pierre Lopez for the design!). We spent two lovely days in Lyon talking about ecological statistics with the hundred people who attended. The talks are available here. If you’d like to know more about our activities in the GdR, check out our website.


lynx6 February 2015: Laetitia Blanc succesfully defended her PhD on the conservation of lynx in France. Congrats Laeti! She had very nice feedbacks by the members of committee (X. Lambin, E. Marboutin, J. Linnell, M. Schaub and F. Bonadonna). Laetitia will be working for a few months with us on the estimation of lynx abundance in Norway (with J. Linnell) and with ONCFS to finish up a chapter of her thesis.


February 2015: Welcome to our new master students Iago Bonnici and Julie Louvrier and Tamar Lok our new post-doc. More about their work here.


paillassonJanuary 2015: Our team has recently joined the department Biodiversity & Conservation at CEFE, a department that I have the pleasure to head now. We have moved offices and are now on the second floor. I have an office with a brand new parquet floor and red walls (that I chose and installed/painted myself, can you believe it?!). We had our office-warming party early March. Do not hesitate to come by and visit our new offices!


isec24 December 2014: Our meeting report on ISEC2014 has appeared in Biology Letters just before Christmas eve, nice gift! Check it out, it’s in open access.


alaska16 December 2014: Jim Sedinger, professor at the University of Nevada (Reno), said goodbye to the team after 3 months with us on a sabbatical. It’s been great to have Jim here analyzing data collected as part of the amazing Black Brant monitoring initiated in the 40s. More soon on our joint project on senescence and individual heterogeneity.


espitemo15 December 2014: I acted as president of the examining committee of Sarah Calba who defended her PhD in epistemology of sciences with the predictions in community ecology as a case study. The thesis was supervised by two clever colleagues of mine, Virginie Maris and Vincent Devictor. Sarah did more than well, and the discussions were lively and the debate vivid. As a general comment, I wish we, as ecologists, had more time as part of our training to think of why and how we conduct our scientific activities. Sarah has a nice paper showing that the identification of patterns and processes linking species diversity to functional or phylogenetic diversity depends on the methodological choices we make as analysts. This reminds me of the discussion about ‘Researcher Degrees of Freedom’ on Gelman’s blog.


applibugs28 November 2014: We held AppliBugs in Montpellier, with the idea to stimulate exchanges and to share information on Bayesian methods and applications (programme here). The day went well despite a rainstorm falling on Montpellier. All talks were great, and I was particularly interested in Adrien Todeschini’s presentation of Biips, a software allowing the implementation of state-space models using particle filtering and a R/BUGS-like syntax.


demo20-21 November 2014: We had a lovely 2-day workshop in Lyon on individual heterogeneity in demography as part of our research group on Statistical Ecology. I gave a short talk providing an overview of heterogeneous capture-recapture models. We agreed on meeting again early April 2015 to carry out a comparative analysis of individual heterogeneity using the datasets shared by the group and the method developed by Hal Caswell (check it out here).


citizenscience16-17 October 2014: After a month off, I’m back to work starting with a 2-day workshop on citizen sciences I’ve co-organised with Romain Julliard and Pascal Monestiez (programme here) as part of our research group on Statistical Ecology and our group on citizen sciences CiSStats. The discussions were stimulating with a nice balance between talks given by data providers on the first day and modelers on the second day. I gave a short talk based on Anne-Sophie’s work on mapping brown bear distribution in Greece using opportunistic data. Check out Anne-Sophie’s talk she gave at the 2014 International Conference on Bear Research and Management in Thessaloniki (Greece) and at the joint BES-SFE Ecology conference in Lille.


Waterfall3-1140x610July 2014: I attended Daniel Turek’s talk at ISEC about NIMBLE a neat alternative to WinBUGS and JAGS. It is developed by Perry de Valpine’s group at Berkeley and ‘lets you use BUGS models natively in R, program functions that use them, and compile everything via C++ for faster computing’. I played around with NIMBLE a bit, here is an example of fitting a classic capture-recapture model to simulated data – thanks to Perry and Daniel for their help! NIMBLE seems a lot faster than its competitors, and much more flexible. I’ll continue my investigations with more complex models – stay tuned.


group-pix-isec2014July 2014: ISEC 2014 is now closed. Organising this conference has been a fantastic adventure; hopefully the participants liked it.


July 2014: My talk at ISEC 2014 on fitting occupancy models with hidden-Markov models using E-SURGE; check out Laetitia‘s and Blaise‘s talks too on how to improve the estimation of abundance by using presence-absence data and informative priors.


June 2014: Sending questionnaires for Blaise’s PhD to study the local perception of the presence of brown bears in the Pyrénées. On the left, the 3000 questionnaires to be sent; in the middle, those questionnaires once packed in boxes; on the right, the nice guy from the mail company La Poste comes and picks them up. Now the question is how many of them will we get back?…

before after bye


June 2014: The team is leading the organisation of ISEC2014. We’re getting ready by, among many other things, preparing the delegates’ packs. Of course, these efforts cannot go without some relaxing time.

preparing-delegate-pack relaxing-planche-de-la-mer relaxing


June 2014: Ben Rashford and Thomas Foulke from the University of Wyoming visited us. They gave a great talk on ‘Wolf Re-Introduction in the Northern Rockies, USA: From Population and Predation Trends to Policy and Economics’.


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June 2014: Rachel Guénon successfully defended her Master internship on the Dalmatian pelican and life-history tradeoffs.


April 2014: Dave and Lise are going back home to the US after a 6-month sabbatical with us. It’s been awesome to have you here!


2014-04-28 18.35.12April 2014: Relaxing after finishing up writing a big grant proposal. Tedeschi and Truck concert at the mytic Olympia Paris with Jonny Lang as the opening act.


logo_cefeMarch 2014: The team run two 1-week workshops on capture-recapture models and matrix models. We’re grateful to all the attendees who came, with fascinating research topics and stimulating questions. No need to say that your presence means a lot to us! We hope to see again many people next year! Warm and special thanks to Dave Koons, Lise Aubry and Pamela Lagrange!


January 2014 The French research group in Statistical Ecology (GDR EcoStat) is born. Funded by CNRS, the objective is to structure the research in statistical ecology at a national (French) level. Check out our website, and sign up for our mailing list!


May 2013: My plenary talk at the 2013 EURING meeting on individual variability in capture-recapture models. I couldn’t attend, but the organizers were kind enough to run my presentation to the audience. I had to be a bit imaginative for the attendees not to fall asleep…


cnrs2012: CNRS interview to get a senior research scientist position


2010: Habilitation – Talk and manuscript in French or English

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