August 2016 - MARMAM - devlists.uvic.ca

'Applied Bayesian modelling for ecologists and epidemiologists' - STATS COURSE
by Oliver Hooker 24 Aug '16

24 Aug '16

Applied Bayesian modelling for ecologists and epidemiologists (ABME) Delivered by Dr. Matt Denwood and Prof. Jason Matthiopoulos http://prstatistics.com/course/applied-bayesian-modelling-for-ecologists-an… This 6 day course will run from 24th -29th October 2016 at SCENE field station, Loch Lomond national park, Scotland. This application-driven course will provide a founding in the basic theory & practice of Bayesian statistics, with a focus on MCMC modelling for ecological & epidemiological problems. Starting from a refresher on probability & likelihood, the course will take students all the way to cutting-edge applications such as state-space population modelling & spatial point-process modelling of which both methods are relevant to population and spatial data collected on marine mammals. By the end of the week, you should have a basic understanding of how common MCMC samplers work and how to program them, and have practical experience with the BUGS language for common ecological and epidemiological models. The experience gained will be a sufficient foundation enabling you to understand current papers using Bayesian methods, carry out simple Bayesian analyses on your own data and springboard into more elaborate applications such as dynamical, spatial and hierarchical modelling. Course content is as follows Day 1 • Revision of likelihoods using full likelihood profiles and an introduction to the theory of Bayesian statistics. o Probability and likelihood o Conditional, joint and total probability, independence, Baye’s law o Probability distributions o Uniform, Bernoulli, Binomial, Poisson, Gamma, Beta and Normal distributions – their range, parameters and common use of Likelihood and parameter estimation by maximum likelihood o Numerical likelihood profiles and maximum likelihood • Introduction to Bayesian statistics o Relationship between prior, likelihood & posterior distributions o Summarising a posterior distribution; The philosophical differences between frequentist & Bayesian statistics, & the practical implications of these o Applying Bayes’ theorem to discrete & continuous data for common data types given different priors o Building a posterior profile for a given dataset, & compare the effect of different priors for the same data Day 2 • An introduction to the workings of mcmc, and the potential dangers of mcmc inference. Participants will program their own (basic) mcmc sampler to illustrate the concepts and fully understand the strengths and weaknesses of the general approach. The day will end with an introduction to the bugs language. o Introduction to MCMC. o The curse of dimensionality & the advantages of MCMC sampling to determine a posterior distribution. o Monte Carlo integration, standard error, & summarising samples from posterior distributions in R . o Writing a Metropolis algorithm & generating a posterior distribution for a simple problem using MCMC. o Markov chains, autocorrelation & convergence. o Definition of a Markov chain. o Autocorrelation, effective sample size and Monte Carlo error. o The concept of a stationary distribution and burning. o Requirement for convergence diagnostics, and common statistics for assessing convergence. o Adapting an existing Metropolis algorithm to use two chains, & assessing the effect of the sampling distribution on the autocorrelation. o Introduction to BUGS & running simple models in JAGS. o Introduction to the BUGS language & how a BUGS model is translated to an MCMC sampler during compilation. o The difference between deterministic & stochastic nodes, & the contribution of priors & the likelihood. o Running, extending & interpreting the output of simple JAGS models from within R using the runjags interface. Day 3 • This day will focus on the common models for which jags/bugs would be used in practice, with examples given for different types of model code. All aspects of writing, running, assessing and interpreting these models will be extensively discussed so that participants are able and confident to run similar models on their own. There will be a particularly heavy focus on practical sessions during this day. The day will finish with a discussion of how to assess the fit of mcmc models using the deviance information criterion (dic) and other methods. o Using JAGS for common problems in biology. o Understanding and generating code for basic generalised linear mixed models in JAGS. o Syntax for quadratic terms and interaction terms in JAGS. o Essential fitting tips and model selection. o The need for minimal cross-correlation and independence between parameters and how to design a model with these properties. o The practical methods and implications of minimizing Monte Carlo error and autocorrelation, including thinning. o Interpreting the DIC for nested models, and understanding the limitations of how this is calculated. o Other methods of model selection and where these might be more useful than DIC. o Most commonly used methods Rationale and use for fixed threshold, ABGD, K/theta, PTP, GMYC with computer practicals. o Other methods, Haplowebs, bGMYC, etc. with computer practicals Day 4 • Day 4 will focus on the flexibility of mcmc, and precautions required for using mcmc to model commonly encountered datasets. An introduction to conjugate priors and the potential benefits of exploiting gibbs sampling will be given. More complex types of models such as hierarchical models, latent class models, mixture models and state space models will be introduced and discussed. The practical sessions will follow on from day 3. o General guidance for model specification. o The flexibility of the BUGS language and MCMC methods. o The difference between informative and diffuse priors. o Conjugate priors and how they can be used. o Gibbs sampling. o State space models. o Hierarchical and state space models. o Latent class and mixture models. o Conceptual application to animal movement. o Hands-on application to population biology. o Conceptual application to epidemiology Day 5 • Day 5 will give some additional practical guidance for the use of Bayesian methods in practice, and finish with a brief overview of more advanced Bayesian tools such as INLA and stan. o Additional Bayesian methods. o Understand the usefulness of conjugate priors for robust analysis of proportions (Binomial and Multinomial data). o Be aware of some methods of prior elicitation. o Advanced Bayesian tools. o Strengths and weaknesses of Integrated Nested Laplace Approximation (INLA) compared to BUGS. o Strengths and weaknesses of Stan compared to BUGS Day 6 • Round table discussions and problem solving with final Q and A round table discussion and problem solving with final Q and A. o The final day will consist of round table discussions, the class will be split in to smaller groups to discuss set topics/problems. This will include participants own data where possible. After an early lunch there will be a general question and answer time until approx. 2pm as a whole group before transport to Balloch train station. There will be a 15 minute morning coffee break, an hour for lunch, and a15 minute afternoon coffee break. We keep the timing of these flexible depending how the course advances. Breakfast is from 08:00-08:45 and dinner is at 18:00 each day. Please email any inquiries to oliverhooker(a)prstatistics.com or visit our website www.prstatistics.com Please feel free to distribute this material anywhere you feel is suitable. Upcoming courses - email for details oliverhooker(a)prstatistics.com 1. INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (August) 2. INTRODUCTION TO PYTHON FOR BIOLOGISTS (October) 3. LANDSCAPE GENETIC DATA ANALYSIS USING R (October) 4. PHYLOGENETIC DATA ANALYSIS USING R (October/November) 5. SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R (November) 6. ADVANCING IN STATISTICAL MODELLING USING R (December) 7. MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R (January) 8. ADVANCED PYTHON FOR BIOLOGISTS (February) 9. NETWORK ANALYSIS FOR ECOLOGISTS USING R (March) 10. INTRODUCTION TO GEOMETRIC MORPHOMETRICS USING R (June) Dates still to be confirmed - email for details oliverhooker(a)prstatistics.com • STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R • INTRODUCTION TO R AND STATISTICS FOR BIOLOGISTS • BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS Oliver Hooker PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/

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Student leadership opportunities with the American Cetacean Society
by Sabena Siddiqui 24 Aug '16

24 Aug '16

Dear MARMAM subscribers, The American Cetacean Society Student Coalition (ACSSC) is the student arm of the American Cetacean Society (ACS), the world's oldest whale conservation organization. After 50 years ACS continues to be a leader in the field of cetacean education, conservation, policy, and education ( http://acsonline.org/) The ACSSC is a community of aspiring researchers, policy makers, and enthusiasts committed to protecting the marine environment and the lives of cetaceans. Through direct action informed by science, ACSSC groups act as forums where students can learn more about cetaceans and their marine environment to carry out the most effective, research-based responses to the perils that cetaceans face. The ACSSC serves as a much needed bridge between the scientific community and the public. Our student groups use community education and citizen science to encourage conservation and scientific literacy in their communities. The Coalition works to provide students of all skill sets with support and access to a community of other young professionals, as well as guidance from established researchers and professionals. Student members of the ACSSC are provided with an opportunity to feel inspired, engaged, and empowered among an active community through a web of regional student groups across the country. We invite US university students to lead their own groups, whether they are coastal or landlocked. One of the benefits of joining the ACS National Student Coalition is the ability to network and collaborate with your peers in different disciplines and institutions to address the challenges that cetaceans face today. Leading your own ACS student coalition group can be very rewarding and fun. ACSSC activities have included: citizen science projects, water quality testing, cetacean research, oyster reef restoration, beach clean ups, guest speakers, panel discussions, documentary screenings, lobbying, fundraisers, and many social events. ACSSC groups have implemented campaigns focusing upon issues such as sustainable seafood and its impacts upon cetaceans, marine debris and entanglement, issues related to the captive industry, and more. ACSSC groups have successfully engaged with their local communities on region specific issues as well. For more information regarding what is involved in starting your own student coalition visit our website: http://acsonline.org/who-we-are/our-governance/chapters/student-coalition/ Like us on facebook to see our latest updates and campaign activities: ACSSC facebook: https://www.facebook.com/American-Cetacean-Society-Student-Coalition-ACSSC-… If you are interested in starting your own group, email us at: acssc.national(a)gmail.com Scientists, supervisors, professors, etc., please refer your promising students to us. *Sabena Siddiqui * *MSc student University of Hawaii-Hilo* Student Chair American Cetacean Society *"P**rotecting whales, dolphins, porpoises, and their habitats through public education, research grants, and conservation actions.*" ACS website <http://acsonline.org/> ACS Student Coalition website <http://acsonline.org/who-we-are/our-governance/chapters/student-coalition/>

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Advanced PAMGuard course
by PAMTech 23 Aug '16

23 Aug '16

PAMTech Advanced PAMGuard PAMTech (pamtech.org) is offering an Advanced PAMGuard course, teaching the advanced use of the leading research and industry software, PAMGuard ( pamguard.org) for offline analysis. We are a small UK-based company made up of PAMGuard developers and experienced field acousticians who can enable you to get the most out of PAM applications. A high tutor-to-student ratio on our courses ensures participants can get individual assistance with their training requirements. Our next course is running on: 21/10/2016 and 22/10/2016 This two-day classroom-based course allows those with previous PAMGuard experience to get to grips with more advanced features, focusing on offline analysis and data management. The course will include some core analysis modules, but participants will also be able to tailor training to their particular needs by selecting from a range of optional modules including complex classifiers and localisation techniques, and the PAMGuard MATLAB library. There is also the opportunity to bring your own datasets and explore ways they can be analysed using PAMGuard. The course will take place on the Vine Trust Barge, Prince of Wales Dock, Edinburgh, EH6 7DX, Scotland, UK. Cost £350 Participants must bring their own laptop running Linux or Windows (not OSX). We would recommend Windows 7/8.1/10 or Ubuntu 12.10+. For those wishing to follow the MATLAB module, a copy of MATLAB version 2012 or above is required. Course costs do not include accommodation, travel or food. To find out more, contact: pamtech.acoustics(a)gmail.com Or go to: pamtech.org To book go to: http://advancedpamguardpamtech.eventzilla.net (50% non-refundable deposit required)

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Job Opening: Alaska Marine Mammal Acoustic Impact Assessment
by Jobs.Ocean.Associates 22 Aug '16

22 Aug '16

Ocean Associates Inc. is seeking a candidate who will provide professional supportto the National Marine Fisheries Service in Anchorage, Alaska, in assessing acoustic impacts to marine mammals.Please see http://www.oceanassoc.com/Jobs/jobslist.html for more details.

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JOB POSTING: Lead Animal Caretaker- Marine Mammals
by Heather Down 22 Aug '16

22 Aug '16

Dear colleagues, The Oklahoma City Zoo (OKC Zoo) is seeking an enthusiastic Lead Animal Caretaker for the Marine Mammal Department. This is a new position for the department and is an excellent opportunity for an experienced Senior Trainer looking to get into leadership or for a seasoned Lead. The OKC Zoo is financially strong and actively implementing an exciting master plan. Oklahoma City is progressive and economically robust. It was voted by National Geographic in the Top 20 places to visit in 2015 and that interest translates into what it is like to live here. The position posting link is below and is open until filled on AZA.org, IMATA.org, and OKCZoo.org. https://www.aza.org/jobs?job=3191 Thank you, Heather R. Down Assistant Zoological Curator- Marine Mammals Oklahoma City Zoo and Botanical Garden 2101 NE 50th Street Oklahoma City, OK 73111 hdown(a)okczoo.org http://www.okczoo.org CONFIDENTIALITY NOTE: This e-mail message and any attachments are intended solely for the person to which it is addressed and may contain privileged and confidential information protected by law. If you have received this communication in error, please notify the sender immediately by telephone or e-mail, destroy this message and delete any copies held in your electronic files. Unauthorized use and/or re-disclosure may subject you to penalties under applicable state and federal laws.

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JNCC MMO & PAM TRAINING - UK, SEPTEMBER 2016
by Sam Nichols 22 Aug '16

22 Aug '16

Seiche Training is taking last bookings for its JNCC MMO and PAM courses 19-20 and 21-23 September taking place in Devon, UK: *JNCC MMO course - 19-20 September* This two day JNCC-accredited MMO course provides the skills needed to become a Marine Mammal Observer. Highest quality training, both in the classroom and on board a vessel, allows delegates to gain experience with marine mammal identification while at sea. Certificate for offshore work awarded upon successful completion of the course. *PAM Level 1 course - 21-23 September* This three day PAM course provides the skills needed to become an offshore PAM operator. Run by Seiche's highly experienced team with thorough support material, interactive PAMGuard workshops and a boat session, this course will expand delegates' knowledge of acoustic monitoring and provide insight into industry requirements for environmental mitigation. Certificate for offshore work awarded upon successful completion of the course. Please contact us for further information by email (training(a)seiche.com) or look at our website ( *www.seichetraining.com <http://www.seichetraining.com/>* ). Thanks.

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Hunstanton SEA LIFE Sanctuary
by Hunstanton ACT 22 Aug '16

22 Aug '16

Hunstanton SEA LIFE Sanctuary is offering a unique opportunity to gain hands on work experience with the rescue and rehabilitations our marine mammals, alongside gaining experience working with our aquarium and resident sanctuary animals. The placement requires a full-time commitment of 40 hours per week, over 12 consecutive weeks starting mid-December. Following our busiest year ever for common seal pups rescues we are launching our new winter internship which will allow candidates to work with our rescued grey seals. The type of work varies depending on the number of pups brought into the centre but typical duties will include: - Preparing the daily feeds, including nutritional supplements - Cleaning out the rehab pens and pools, and maintaining high standards in the hospital. - Daily feeding and rehabilitation husbandry of the pups - Assisting in medical examinations, treatments and sampling - Assisting with rescues &/or releases of seal pup - Assisting in the husbandry of the resident seals - Maintaining animal clinical and husbandry records - Maintaining equipment, facilities and supplies - Visitor interactions & giving presentations - General duties in the day to day running of the Sanctuary All applicants must have achieved 5 GCSE’s including Maths, English and Science and should be in full time education. We do take mature students and those looking at getting into the industry with relevant interest and experience. The placements are unpaid and housing is not provided, successful candidates will be required to live within 20 minutes of the Sanctuary due to night feeds for seals. To apply please submit a CV and cover letter, including relevant experience to Hollie Stephenson at Hunstanton.ACT(a)merlinentertainments.biz<mailto:Hunstanton.ACT@merlinentertainments.biz> Merlin Entertainments plc. Registered office: 3 Market Close, Poole, Dorset, BH15 1NQ. Registered number 08700412. Registered in England & Wales. 'This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email.'

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New publication: measuring ambient and flow noise on DTAGs attached to marine mammals
by Benda-Beckmann, A.M. (Sander) von 22 Aug '16

22 Aug '16

Dear MARMAM-readers, We are pleased to inform you that our paper 'Separating underwater ambient noise from flow noise recorded on stereo acoustic tags attached to marine mammals', by A.M. von Benda-Beckmann, P. J. Wensveen, F. I.P. Samara, S. P. Beerens, P. J. O. Miller, is now available online at the Journal of Experimental Biology, 219, 2271-2275, 2016. http://jeb.biologists.org/content/early/2016/05/25/jeb.133116 Abstract: Sound recording acoustic tags attached to marine animals are commonly used in behavioural studies. Measuring ambient noise is of interest to understand responses of marine mammals to anthropogenic underwater sound, or to assess their communication space. Noise of water flowing around the tag reflects the speed of the animal, but hinders ambient noise measurement. Here we describe a correlation-based method for stereo acoustic tags to separate the relative contributions of flow and ambient noise. The uncorrelated part of the noise measured in DTAG recordings related well to animal swim speed of a humpback whale (Megaptera novaeangliae), thus providing a robust measure of flow noise over a wide frequency bandwidth. By removing measurements affected by flow noise, consistent ambient noise estimates were made for two killer whales (Orcinus orca) with DTAGs attached simultaneously. The method is applicable to any multi-channel acoustic tag, enabling application to a wide range of marine species. For any inquiries or requests please contact me at: sander.vonbenda(a)tno.nl<mailto:sander.vonbenda@tno.nl>. Kind regards, Sander von Benda-Beckmann Netherlands Organisation for Applied Scientific Research (TNO) Acoustics & Sonar Department Oude Waalsdorperweg 63 2597 AK The Hague The Netherlands This message may contain information that is not intended for you. If you are not the addressee or if this message was sent to you by mistake, you are requested to inform the sender and delete the message. TNO accepts no liability for the content of this e-mail, for the manner in which you use it and for damage of any kind resulting from the risks inherent to the electronic transmission of messages.

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JNCC MMO (UK) and BOEM PSO (Gulf of Mexico) and PAM Training Courses - September 2016
by Alison Gill 20 Aug '16

20 Aug '16

Intelligent Ocean Ltd (http://www.intelligentocean.com/) is running the following training courses during September in Kings Lynn, Norfolk, UK for which we have spaces available. Introduction to Passive Acoustic Monitoring 12th September 2016 - £150 (please note there is an online training component to this course that must be completed before this practical day) Joint Nature Conservation Committee (JNCC) Marine Mammal Observer (MMO) Training for UK - 13th September 2016 - £130 Bureau of Ocean Energy Management (BOEM) Protected Species Observer (PSO) Training for Gulf of Mexico, USA - 14th September 2016 - £60 (when taken in conjunction with the JNCC MMO course). To book a place please use our online booking system at this link http://www.intelligentocean.com/booking.php Alison Gill Intelligent Ocean Ltd http://www.intelligentocean.com/

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New paper: Net loss of humpback dolphins
by Shanan Atkins 19 Aug '16

19 Aug '16

Dear Marmam community We’re pleased to tell you about our recently published study on how bycatch can potentially influence populations. Atkins S, Cantor M, Pillay N, Cliff G, Keith M, Parra G (2016) Net loss of endangered humpback dolphins: integrating residency, site fidelity, and bycatch in shark nets. Mar Ecol Prog Ser 555:249–260 ABSTRACT: Fisheries bycatch—the incidental catch of non-target species during fishing—is problematic for large marine vertebrates. Bather protection programmes that use gillnets to kill sharks cause the incidental mortality of humpback dolphins *Sousa *spp., potentially impacting the long-term survival of these threatened species. Understanding dolphins’ spatial and temporal use of gillnetted areas is critical for designing effective mitigation strategies. We photo-identified dolphins over 8 yr in a high-bycatch area (Richards Bay, South Africa) to assess the residency, site fidelity, and movement patterns of Indian Ocean humpback dolphins *S. plumbea *and evaluate how emigration, immigration, and mortality rates influence the use of Richards Bay at various temporal scales. Overall, residency was low but site fidelity was high, leading to high population turnover in the short term but low turnover over 6 mo and longer. There was clear individual variation in visitation but no evidence of seasonality. By considering such movements, the net loss of dolphins from the area became evident. While dolphins naturally emigrate from the area, the recognition of several catalogued individuals among the bycaught dolphins indicated that mortality in the shark nets contributes to the permanent loss of both residents and transients. Richards Bay may represent an ecological trap: high site fidelity indicates dolphins perceived the area as ecologically attractive, but high mortality due to shark nets makes it risky. We examined these results relative to gillnet bycatch mitigation methods and recommend that stakeholders collaborate as a mitigation team to prioritise management actions to reduce bycatch without compromising bather safety. The paper can be found http://www.int-res.com/abstracts/meps/v555/p249-260/ or send a request to me: shananatkins(a)gmail.com <shananatkins(a)vgmail.co.za> . Kind regards Shanan Shanan Atkins shananatkins(a)gmail.com <shananatkins(a)vgmail.co.za> Source-toSea Programme, Endangered Wildlife Trust School of Animal, Plant and Environmental Sciences, University of Witwatersrand SOUTH AFRICA

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