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1st Edition of Stochastic Individual-Based Models and Simulations Course

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Casa Morgado do Esporão

Rua Dona Isabel, 6

7000-880 Évora


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Science Retreats and InBIO-CIBIO at the University of Évora are jointly organising the 1st edition of the course “Individual-based modelling for ecology, evolution and conservation: concepts, methods, applications, and challenges” taught by Professors Justin Travis, Greta Bocedi and Steve Palmer.

This course will introduce key concepts in individual-based modelling, highlighting both the opportunities that this modelling approach provides as well as discussing the challenges.

The course will cover the use of individual-based models for developing novel theory as well as how the approach can be used for a broad range of applied questions. Examples will be drawn from a range of topics including the use of individual-based models in landscape ecology (e.g. to model functional connectivity), their use in simulating range expansions under alternative potential future scenarios, the evolution of life history strategies (including dispersal and mating system).

During the course, the students will have the opportunity to learn how to use RangeShifter (Bocedi et al. 2014 Methods in Ecology and Evolution), a platform developed by the teaching team for individual-based modelling of ecological and evolutionary processes. There will additionally be the opportunity to develop new code in R or C++, depending upon the participants’ interests and expertise. The course will be structured with lectures and tutorials during the mornings and project work in the afternoons. Participants will be supported in working individually or in small groups in developing models to address questions related to systems or questions that they work on. They will be guided, where appropriate, in making use of environmental and ecological data from their system. Training will be provided in effectively dealing with the different sources of uncertainty present within output generated from individual-based models. The course is the first to be run in this format in Evora but it builds upon several successful shorter format courses that have been run to introduce participants to RangeShifter and on an Advanced Modelling for Ecology and Conservation course that is part of a Masters programme at University of Aberdeen.

Course Objectives

In the end of the course, our aim is that students will be equipped to:

1. Understand the key features of individual-based models for use within ecology, evolution and conservation.

2. Understand the roles that individual-based models can play in developing theory and also in application.

3. Effectively specify a research question and then design an individual-based simulation study to address that question.

4. Get started with stochastic individual based modelling using the software platform RangeShifter, or by developing new code in R.

5. Effectively analyse and communicate the outcomes from individual-based models.

*RangeShifter 2.0 is being developed and at this course we will introduce the participants to the new functionality that is included. Most notably, it includes the capability for simulating neutral and adaptive genetics.


The course targets posgraduate students but also established researchers wanting to extend or update their knowledge in individual based modelling for applications to their specific lines of research.



Fees and cancelation policy

20% discounts on the registration fee are available to students and researchers from InBIO-CIBIO and to students from the University of Évora (contact us by email to obtain the promotional code). When paying through a non-Portuguese EU institution you will be exempt of VAT (value added tax) if you provide the adequate VAT tax code. If you come from outside the EU you are also exempt of VAT. Should you prefer paying the registration fee via wire transfer let us know and we'll provide you with the necessary information.

If you wish to cancel your participation in this course, cancellations up to 20 days before the course start date will incur a 30% cancellation fee. For later cancellations, or non-attendance, the full course fee will be charged. In the unlikely event that the course is cancelled due to unforeseen circumstances, accepted candidates will either be entitled to a full refund of the course fee, or the fee can be credited toward a future course. The organisation is not responsible for travel costs, or any other expenses incurred by the candidate as a result of such cancellation. Every effort will be made to avoid the cancellation of the planned course.


The course accepts a minimum of 10 students and maximum of 20 students.


The course fee includes participation in the course, provision of course material and the certificate of participation in the end of the course, as well as daily coffee breaks (offering assortment of coffees, teas, fruit juices and cookies).

There will be limited accommodation at the “Casa Morgado Esporão”. 10% discounts on announced rates will be offered to registered students. Should they wish, students can share double rooms and apartments in the house. Alternatively, there is also a wide range of accommodation options in the city centre. Once registered let us know what your preferred options for accommodation are and we’ll be more than happy to provide assistance.

About the instructor: Professors Justin Travis, Greta Bocedi and Steve Palmer

Prof Justin Travis has interests across a broad range of ecological and evolutionary questions. The common theme across his group’s work is the development and application of individual-based models. He has more than 20 years of experience developing these models for addressing theoretical questions and increasingly for ecological forecasting and for informing management. A major focus of his group’s activity over the last few years has been developing the RangeShifter software, providing a platform that facilitates the running of individual-based simulations across complex landscapes. This software is now central to many of the group’s collaborations on projects related to landscape design, connectivity, population viability, range-shifting and invasions. Prof Travis also has many years of experience teaching individual-based modelling approaches and over the last 10 years has run an Advanced Modelling Master’s course at Aberdeen.

Dr Steve Palmer has wide-ranging experience in ecological modelling, advanced statistical analysis and computer programming. His ecological research is underpinned by a strong interest in systems analysis and programming skills initially developed in the business sector. Much of his research career has been conducted in collaborative teams with experts in diverse aspects of ecology, including habitat utilisation, woodland regeneration, fisheries management and the development of ecological theory. He currently focuses principally on the role of dispersal in demography and range-shifting, developing object-oriented, spatially-explicit, individual-based models for predicting how environmental change affects species’ distributions, the influence of movement behaviour on dispersal success in heterogeneous landscapes and the application of Bayesian methods to estimate model parameters.

Dr Greta Bocedi is a post-doctoral research fellow at the University of Aberdeen. Her research aims to understand the evolution of species’ life histories and behaviours, and species’ responses to environmental changes, by combining ecological and evolutionary modelling to generate new eco-evolutionary theory and theory-grounded applications. Bocedi developed the RangeShifter software as part of her PhD with the aim of bringing ecological and evolutionary theory into a user-friendly application for understanding, and eventually predicting, species’ responses to changes at different spatial scales. More recently, she has started developing genetically-explicit individual-based models for evolution of mating systems. Her research ranges from dispersal and mating system evolution, to the role of dispersal behaviours and local adaptation in range expansion and shifting, to evolution of genetic architecture. In 2015 Bocedi won an MCED Award for innovative contributions to ecological modelling.

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Casa Morgado do Esporão

Rua Dona Isabel, 6

7000-880 Évora


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