A primer on POMDPs
POMDPs (Partially observable Markov decision processes) are powerful decision models that allow users to make decisions under imperfect observations over time. This primer provides a much-needed entry point to ecologists.
Posts by iadine
Mar 21
Congratulations Martin! Outstanding doctoral thesis award
Martin was awarded an outstanding doctoral thesis award (top 5% of PhD graduate).
Martin first joined the team as an internship student from the French engineering school “Ecole des Ponts”. After 6 months discovering our research environment, Martin decided to embark onto a PhD.
During his PhD, Martin published 4 papers. I am particularly fond of two papers he led, because they exemplify the type of AI research needed to tackle challenging problems in applied ecology: Read more
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Can we do better with our funds to manage biodiversity’s key threats?
Nations, regions, governments, organisations and communities around the world are increasingly concerned about declines and losses of biodiversity. For many, there are important moral and legal requirements to improve the outlook for biodiversity and avoid species extinctions. However, understanding how to best invest resources in management to improve biodiversity is far from simple. Unless we are considering the right information in a logical way, we won’t be able to make the best use of the resources we have. Read more
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Apply now! 3-year Postdoc on building trusted AI for environmental decisions
We are seeking a highly motivated and dynamic postdoctoral research fellow to work on developing AI specifically designed to deliver interpretable and explainable solutions to environmental decision problems.
Jun 29
The changing life of Antarctica’s ice-free ‘islands’ – ECOS
Warmer temperatures mean more ice-free areas and increasing terrestrial habitat in Antarctica, but that’s not necessarily good news for Antarctic natives.
Source: The changing life of Antarctica’s ice-free ‘islands’ – ECOS
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Prioritising the value of information for the management of Moira Grass (Report now available)
We have led a value of information project to help managers of Moira Grass determine which information should be collected as a priority. The team worked very closely with domain experts to design and complete this project. Our findings indicate that management strategies targeting grazing (61% increase in total extent; 46% increase in Moira grass cover; 42% increase in thatch depth) and flood duration and depth are most likely to improve the restoration of Moira grass at the Barmah Forest (See Executive Summary below for more information).
The report:
Nicol, Sam; Stratford, Danial; Joehnk, Klaus; Chades, Iadine. Prioritising the value of information for the management of Moira grass at Barmah forest. Brisbane: CSIRO; 2017. csiro:EP17815. (CSIRO PDF report)
We have learned a lot during this project on the strengths and weaknesses of Value of Information. We will aim to publish these lessons learned in the academic literature.
Executive summary:
Barmah Forest is a Ramsar listed wetland complex in the Murray–Darling Basin of Australia. Barmah Forest supports the largest area of Moira grass (Pseudoraphis spinescens) plains in the Murray-Darling Basin and is amongst the most southerly distribution of the species in Australia.
Feral horse (Barmah, 2016)
The plains are recognised as part of the Ramsar ecological character description of the forest. Reduction in the area of Moira grass plains has been one of the most significant long-term ecological changes within the forest. The causes of decline are uncertain Read more
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The Conservation Decisions team selected for ON Prime!
Sam, Josie, Iadine, Nicole and Stephanie will test and strengthen their Conservation Technology idea through ON Prime 2!
We are very excited and can’t wait to start! We can’t say much at this stage, however we will use our social media platforms to share the different stage of our adventure.
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Fast and accurate MARXAN: the return of the ILP (Integer Linear Programming)
In Beyer et al (Ecological Modelling, 2016), Yann and co-authors propose an efficient integer linear program (ILP) to solve conservation planning problems for MARXAN and MARXAN with zones.
Because conservation planning problems are not linear, an accurate linearization was required to get an efficient ILP model, i.e. running in a good computing time. Yann’s contribution was to propose an efficient linearization, and to clarify the advantages of using ILP compared to the current heuristic used in MARXAN (simulated annealing). ILP is an exact method so it always provides optimal solutions. Moreover, ILP allows to easily integrate multiple objectives and to deal with unknown instances by using robust approaches.
In conservation, ILP has been avoided for the past decades because of long computational running times. However, recent versions of linear programming software solutions include new algorithms such as new branch-and-cuts / dynamic search processes, reducing the computation time required to solve ILP problems by millions compared to the first versions.
The results are impressive and you should definitely have a look if your conservation planning problem takes too long to solve or you are uncertain about the quality of the solutions! Congratulations Yann and team!
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Small data call for big ideas
Urgent decision making can’t wait for big data!
In this week Nature’s correspondence, Iadine and Sam raise that the shift of private and public funding towards big data problems could impact our ability to solve some of our most urgent decision problems – for which we have no or very little amount of data available: biodiversity, health and biosecurity issues to cite a few. Sam and Iadine also provide some solutions and call for big ideas. It’s free for all to read.
Chades, I. & Nicol, S. (2016) Information: Small data call for big ideas. Nature, 539, 31-31.
Iadine and Sam wrote a bigger piece on the topic. We welcome your comments: Chades, I. & Nicol, S. (2016, November 2). Small data, big ideas. Zenodo. http://doi.org/10.5281/zenodo.164443
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UPDATE: Getting our priority right: 9 publications on Priority Threat Management
Perhaps the most impactful decision support tool we have developed to date, Priority Threat Management (PTM) is a team adventure where a dedicated bunch of interdisciplinary scientists and kick ass facilitator work alongside stakeholders to establish the best strategies to manage threats to biodiversity. Stay tuned as we have grand plans to improve PTM and make it available to the entire world.
I was asked to provide a list of reference on priority threat management, sharing it with you here:
Freely accessible material:
- Ponce Reyes, R., Firn, J., Nicol, S., Chadès, I., Stratford, D.S., Martin, T.G., Whitten, S., Carwardine, J. (2016) Priority Threat
Management for Imperilled Species of the Queensland Brigalow Belt CSIRO, Brisbane. (PDF) (see The Conversation article, CSIRO website) - Firn, J., Maggini, R., Chadès, I., Nicol, S., Walters, B., Reeson, A., Martin, T. G., Possingham, H. P., Pichancourt, J.-B., Ponce-Reyes, R. and Carwardine, J. (2015), Priority threat management of invasive animals to protect biodiversity: Lake Eyre Basin ( see the Conversation article, CSIRO website with PDFs)
- Carwardine J., Nicol S., van Leeuwen S.,Walters B., Firn J., Reeson A., Martin T.G., Chades I. (2014) Priority threat management for Pilbara species of conservation significance, CSIRO Ecosystems Sciences, Brisbane. (PDF) (see The Conversation article, blog post, CSIRO website)
- Firn, J., Martin, T.G., Walters, B., Hayes, J.,Nicol, S., Chadès, I., and Carwardine, J. (2013) Priority Threat Management of invasive plants species in the Lake Eyre Basin. CSIRO Climate Adaptation Flagship Working Paper No. 17 (QUT and CSIRO) (PDF) (blog post)
- Carwardine, J., O’Connor, T., Legge, S., Mackey, B., Possingham, H.P., Martin, T.G. (2011) Priority threat management to protect Kimberley wildlife CSIRO Ecosystem Sciences, Brisbane. (PDF)
Journal paper (PDF available upon request):
- Firn, J., Maggini, R., Chadès, I., Nicol, S., Walters, B., Reeson, A., Martin, T. G., Possingham, H. P., Pichancourt, J.-B., Ponce-Reyes, R. and Carwardine, J. (2015), Priority threat management of invasive animals to protect biodiversity under climate change. Global Change Biology. doi: 10.1111/gcb.13034
- Firn, J., Martin, T. G., Chadès, I., Walters, B., Hayes, J., Nicol, S., Carwardine, J. (2015), Priority threat management of non-native plants to maintain ecosystem integrity across heterogeneous landscapes. Journal of Applied Ecology. doi: 10.1111/1365-2664.12500
- Chadés, I., Nicol, S., van Leeuwen, S., Walters, B., Firn, J., Reeson, A., Martin, T. G. and Carwardine, J. (2015), Benefits of integrating complementarity into priority threat management. Conservation Biology, 29: 525–536. doi: 10.1111/cobi.12413
- Carwardine, J., O’Connor, T., Legge, S., Mackey, B., Possingham, H.P., Martin, T.G. (2012). Prioritizing threat management for biodiversity conservation. Conservation Letters. 5:196–204 doi: 10.1111/j.1755-263X.2012.00228.x
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Targeting threats alone “won’t save our wildlife” … so what would?
I was fortunate to be a co-author on the paper recently published in Frontiers in Ecology and the Environment led by Viv and Ayesha Tulloch, “Why do we map threats? Linking threat mapping with actions to make better conservation decisions.” (see media release PDF).
This is a great thinking piece about why we should probably not use threat maps “as is” to inform conservation decisions and how threat maps should be included as part of the decision process. I would recommend reading this paper if you are new to structured decision making and would like an easy read. The authors have done a fantastic job at explaining the risk of not following a transparent decision making process.
As a side note, our priority threat management work in the Pilbara was highlighted as a good example of making transparent decisions (No doubts they are other good examples in the literature!). It’s always a privilege to be acknowledged by our peers, it’s even better when these are esteemed close collaborators. Thanks for your support!
The paper:
Vivitskaia JD Tulloch, Ayesha IT Tulloch, Piero Visconti, Benjamin S Halpern, James EM Watson, Megan C Evans, Nancy A Auerbach, Megan Barnes, Maria Beger, Iadine Chadès, Sylvaine Giakoumi, Eve McDonald-Madden, Nicholas J Murray, Jeremy Ringma, and Hugh P Possingham 2015. Why do we map threats? Linking threat mapping with actions to make better conservation decisions. Frontiers in Ecology and the Environment 13: 91–99. http://dx.doi.org/10.1890/140022
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Complementarity saves more species, simple stuff!
Our manuscript on how complementarity can help saving more species per dollar spent is available online. If you are interested in cost-effectiveness analysis, PPP, priority threat management, expert elicitations, or the Pilbara, have a look:
Chades, I., Nicol, S., van Leeuwen, S., Walters, B., Firn, J., Reeson, A., Martin, T. G. . and Carwardine, J. (2014), Benefits of integrating complementarity into priority threat management. Conservation Biology. doi: 10.1111/cobi.12413 (abstract) (request PDF)
This paper presents the science behind our beautiful Pilbara report.
Photo: Northern Quoll at Red Hill Homestead. Credit: Leanne Corker, Red Hill Station.
Abstract:
Conservation decision tools based on cost-effectiveness analysis are used to assess threat management strategies for improving species persistence. These approaches rank alternative strategies by their benefit to cost ratio but may fail to identify the optimal sets of strategies to implement under limited budgets because they do not account for redundancies. We devised a multiobjective optimization approach in which the complementarity principle is applied to identify the sets of threat management strategies that protect the most species for any budget. We used our approach to prioritize threat management strategies for 53 species of conservation concern in the Pilbara, Australia. We followed a structured elicitation approach to collect information on the benefits and costs of implementing 17 different conservation strategies during a 3-day workshop with 49 stakeholders and experts in the biodiversity, conservation, and management of the Pilbara. We compared the performance of our complementarity priority threat management approach with a current cost-effectiveness ranking approach. A complementary set of 3 strategies: domestic herbivore management, fire management and research, and sanctuaries provided all species with >50% chance of persistence for $4.7 million/year over 20 years. Achieving the same result cost almost twice as much ($9.71 million/year) when strategies were selected by their cost-effectiveness ranks alone. Our results show that complementarity of management benefits has the potential to double the impact of priority threat management approaches.
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CDT x EDG seminar series #13: Dr Virginia Matzek
Friday 7th of November, from 3-4 pm in room GA604, ESP, Dr. Virginia Matzek (Santa Clara University, California) will present her research on “Bringing managers’ perspectives to bear on habitat restoration and ecosystem services in California and Australia”.
(beers and snacks available afterwards-as part of the social club!)
Title: Bringing managers’ perspectives to bear on habitat restoration and ecosystem services in California and Australia
Summary: This talk highlights some of the recent work my lab has done in California, as well as our planned work in Australia. The first part of the talk will treat a survey of managers’ research needs for invasive plant management in the state. As a follow-up to this work, we went to the literature to see what had actually been published relevant to California invasive plant management, and documented some mismatches in the topic, scope, and approach of scientific research, when compared with managers’ needs. The second part of the talk discusses whether managers can expect to recoup the cost of restoration of riparian forest in California via the state’s new compliance market for carbon credits. Both of these themes–the potential mismatch of perspectives, and the need to measure ecosystem services resulting from restoration–turn up in the work I’m planning to do here in Australia. I’ll close with a brief account of our proposed work surveying Australian managers and members of the general public for their perspectives on the desirability of ecosystem services as a project goal for restoration.
Bio: Virginia Matzek is an assistant professor in the Department of Environmental Studies and Sciences at Santa Clara University in California, USA. The primary focus of her lab is on linking ecosystem services to ecological restoration. A plant ecologist and biogeochemist by training, she now finds herself interested as much by why people restore ecosystems as by how they do it. She will be at CEED working with Kerrie Wilson and Marit Kragt until mid-December 2014.
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Free toolbox to solve stochastic dynamic programming problems in R, MATLAB, OCTAVE and SciLab
If you are interested in finding the best decisions over time to save or eradicate the cutest species, then you are probably interested in using Stochastic Dynamic Programming (SDP) or its mathematical model Markov Decision Process (MDP). If you have a burning problem ready to be solved but not sure how to, then good news we have released the MDPToolbox (ver. 4) in R, Matlab, Octave and Scilab. Please spread the word, the toolbox is free! Thanks to Ecography, you can now support our efforts by citing our paper:
To download the toolbox: http://www7.inra.fr/mia/T/MDPtoolbox/
If you are still unsure about SDP, try: Marescot, L., G. Chapron, I. Chadès, P. Fackler, C. Duchamp, E. Marboutin, and O. Gimenez. 2013. Complex decisions made simple: a primer on stochastic dynamic programming. Methods in Ecology and Evolution 4:872-884.
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Pilbara shows how to save the most species per dollar: report now available!
We are pleased to announce the release of our report on ‘Prioritising threat management for Pilbara species of conservation significance’ (PDF, 10Mo)(The Conversation). This was a very rewarding collaborative project with scientists from CSIRO, QUT, UQ, and WA Dept Parks and Wildlife, with input from 49 experts across land management, policy, industrial, agricultural, indigenous and academic sectors, and was funded by Atlas Iron through the Dept of Environment Pilbara Taskforce.
The work comes at an important time in the Pilbara’s history and we hopeful that it will have a positive impact.
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Prioritising species for monitoring conservation actions: Combining cost-effectiveness with complementarity
We have a decision point article that just came out this month! A great opportunity to communicate on how we can use complementarity between species to improve our monitoring efficiency, and of course remain cost-effective. In Tulloch et al (2013), we used network theory and a lot of ecology to find the best way of modelling and solving this problem. In the end, we were very pleased to show that it is possible to increase your monitoring power by selecting the most complementary species and also reducing the cost. A win-win situation that is rarely available in conservation. Read more
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Complex decisions made simple: a primer on stochastic dynamic programming
Do you need to find the best decisions to maximize your chances of protecting a threatened species today but also in the future? Yes? Then you might be interested by our primer on stochastic dynamic programming (SDP). Stochastic Dynamic Programming (SDP) is an essential tool in conservation biology and natural resources management.
Marescot L., Chapron G., Chadès I., Fackler P., Duchamp C., Marboutin E. & Gimenez O. (2013). Complex decisions made simple: a primer on stochastic dynamic programming. Methods in Ecology and Evolution, 4, 872-884.
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Weeds in the Lake Eyre Basin? Listen to Jennifer Firn on Radio National
Jennifer Firn was on Radio National speaking (Bush Telegraph) about our priority threat management work targeting weeds in the Lake Eyre Basin. You can check our previous blog post on the subject and the report (PDF). Well done Jennifer!
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What’s up with wildflowers in the Wheatbelt? Novel plant communities in agricultural landscapes
What’s up with wildflowers in the Wheatbelt? Novel plant communities in agricultural landscapes – By our very own John Dwyer @MayfieldLabUQ Read more
The Conservation Decisions Team 