This is a new project starting as of today. The main aim is to develop a tool for adaptive management of goose populations during their stay in Denmark. The primary focus species is the Pink-Footed Goose, although we will probably also take Greylag and Barnacle Goose into the model on a more or less equal footing.

Primary drivers to be implemented are the physical map, weather, hunting (and other human related mortalities), food resource dynamics and inter- and intra-specific competition, and a cognitive memory module to handle learning about foraging experiences and hunting impacts.

The focus area for the model will be North Jutland, but it may be necessary to extend this to a wider geographic area to incorporate regional dynamics.

With this project I aim to document the development process using the CCPForge forum, so look under 'Goose Management Modelling' over the next few weeks, for news on progresss.

 

The long awaited vole POM paper has been published by PLoS ONE. I have uploaded a copy to the research papers directory.

Citation:

Topping CJ, Dalkvist T, Grimm V (2012) Post-Hoc Pattern-Oriented Testing and Tuning of an Existing Large Model: Lessons from the Field Vole. PLoS ONE 7(9): e45872. doi:10.1371/journal.pone.0045872

Abstract

Pattern-oriented modeling (POM) is a general strategy for modeling complex systems. In POM, multiple patterns obse...(see more)

Welcome to Keith Porter who has kindly agreed to help with the biological basis for the Marsh Fritillary model. Keith did his PhD study on this species and continues to work with it today so we are very lucky that he is interested in helping with this project.

Høye TT, Skov F and Topping CJ (2012) Interpreting outputs of agent-based models using abundance-occupancy relationships. Ecological Indicators, 20, 221-227 Abstract Reliable assessments of how human activities affect wild populations are essential for effective natural resource management. Agent-based models provide a powerful tool for integration of multiple drivers of ecological systems, but selecting and interpreting their output is often challenging. Here, we develop an indicator (the AOR-index) based on the abundance-occupancy relationship to facilitate the interpretation of agent-based model outputs. The AOR-index is based on the distribution of individuals in the landscape translated into the number of individuals in each cell of a regular grid. The proportion of grid cells with at least one individual is used to quantify occupancy and the mean number of individuals in occupied cells is used to quantify abundance. The AOR-index is a two-dimensional index giving the relat...(see more)

A new ALMaSS model for the spread of rodenticide via poisoned small mammals has been started. This project is related to the high incidence and high concentration of rodenticides found in Danish predators, often with concentrations above the lethal dose. The project will initially develop a simple model for spread based on assumptions of small mammal dispersal and the spatio-temporal dynamics of bait locations. Contact Chris Topping for details New classes for Rodenticide and RodenticideManager will shortly be added to the code.

Topping, C.J. & Lagisz, M. (2012) Spatial Dynamic Factors Affecting Population-Level Risk Assessment for a Terrestrial Arthropod: An Agent-Based Modeling Approach. Human and Ecological Risk Assessment, 18, 168-180. Summary: Agent-based models (ABMs) explicit handling of space and time and integration of nonlinear interactions between system components to create a system response could facilitate realistic risk assessmentmodeling.We used this approach to evaluate the impact of spatial dynamic factors on a theoretical risk assessment of an insecticide on a carabid beetle population (based on Bembidion lampros). Results indicated that both impacts and recovery were dependent on period of application, area treated, spatial distribution of stressor, beetle dispersal, and underlying habitat suitability. The impact of the stressor was detected far outside the area to which it was applied, and the extent of this impact was affected by beetle dispersal and landscape structure. T...(see more)

A warm welcome to the ALMaSS project to Philippe Thomas from Environment Canada. Phil is going to use ALMaSS as part of his study to evaluate the use of field trials and models for small mammal pesticide risk assessment.

The eagle-eyed of you might have noticed a new branch appearing in the SVN repository. This is for the Marsh Fritillary (Euphydryas aurinia). This species differs from the rest of the ALMaSS species in that it will require detailed modelling of the habitat and its larval food plants, providing some new challenges. The initial model will assume fixed food plant densities and suitability and concentrate on modelling the butterfly's ecology and behaviour on this basis. Later work should increase the environmental dynamics of the model by incorporating habitat heterogeneity and food plant quality dynamics at a fine resolution. The project is funded by 5.Juni fund and will be carried out primarily by myself and Toke Hoye.

How Predation and Landscape Fragmentation Affect Vole Population Dynamics Trine Dalkvist, Richard M. Sibly, Chris J. Topping Background: Microtine species in Fennoscandia display a distinct north-south gradient from regular cycles to stable populations. The gradient has often been attributed to changes in the interactions between microtines and their predators. Although the spatial structure of the environment is known to influence predator-prey dynamics of a wide range of species, it has scarcely been considered in relation to the Fennoscandian gradient. Furthermore, the length of microtine breeding season also displays a north-south gradient. However, little consideration has been given to its role in shaping or generating population cycles. Because these factors covary along the gradient it is difficult to distinguish their effects experimentally in the field. The distinction is here attempted using realistic agent-based modelling. Methodology/Principal Findings: By us...(see more)

Evaluation of wildlife management through organic farming. Chris J. Topping Ecological Engineering 37 (2011): 2009-2017 Abstract: Organic farming has often been suggested as a way of increasing biodiversity in agricultural landscapes, but literature reports a variable success. The drivers in play are multi-factorial and include the particular species groups under consideration, the precise form of organic management, the landscape structural and management context, the area and scale considered, and the historical context. Here ALMaSS, a comprehensive agent-based model simulation system, was used to produce an assessment of the impact of organic and conventional farm types, landscape structure, and management context for six common agricultural wildlife species. ALMaSS outputs can be expressed as a simple index of relative change in abundance and distribution, allowing easy comparison between scenarios. Results indicate that organic farming generally had a beneficial effect, but ...(see more)

Welcome to Yolanda! Yolanda is from the Department of Zoology, Otago University, NZ and is interested in developing the domestic cat model. She has supplied the training data set for the cat model from her NZ studies.

Welcome to Lene. Lene is in fact one of the earliest ALMaSS folk from back when the first ALMaSS models were being developed when she carried out her masters project using the roe deer model. Since then she has been developing ABMs of white tailed deer primarily for epidemiological studies in the USA and Canada. With Lene joining the project we will be looking at re-integrating the roe deer model into the current ALMaSS code base.

Nick is interested in combining elements of FASSET, a farm assessment tool into ALMaSS to increase the farming realism. More on FASSET here: http://www.fasset.dk

A new ALMaSS paper is available as online first from GCB Bioenergy. I've uploaded a pdf into the ALMaSS Research papers section of Docs: Biodiversity and the mitigation of climate change through bioenergy: impacts of increased maize cultivation on farmland wildlife JANA GEVERS, TOKE THOMAS HØYE, CHRIS JOHN TOPPING, MICHAEL GLEMNITZ and BORIS SCHRODER Abstract The public promotion of renewable energies is expected to increase the number of biogas plants and stimulate energy crops cultivation (e.g. maize) in Germany. In order to assess the indirect effects of the resulting land-use changes on biodiversity, we developed six land-use scenarios and simulated the responses of six farmland wildlife species with the spatially explicit agent-based model system ALMaSS. The scenarios differed in composition and spatial configuration of arable crops. We implemented scenarios where maize for energy production replaced 15% and 30% of the area covered by other cash crops. Biogas maize ...(see more)

Welcome to Hazel who is currently working at CSIRO in Australia. Hazel has been using ALMaSS to look at the impact of changes in set-aside management on skylarks in the UK as an example of an ABM for policy use.

Tommy Dalgaard has a long history of working with ALMaSS and has been involved in providing data and expertise to develop the farming and landscape classes since the beginning of ALMaSS in 1998.

Welcome to Tommy Asferg who will be working together with Jannick and Chris to develop the cat model. Tommy is the brains behind our cat's ecology and behaviour.

Two new project applications have been added to the Forums, one intiating domestic cat modelling in ALMaSS, the other on applying ALMaSS to evaluate the effect of changes in set-aside in Denmark. See the Projects and applications forum for details.

Richard Sibly is interested in using Agent Based Models (ABMs) and experiments with invertebrates to develop new Population Ecology theory applicable to real landscapes. Classic theory does not take account of spatial heterogeneity, but real landscapes consist of fragments of patches of different types. Developing theory to take proper account of heterogeneity is challenging but important because today's landscapes are increasingly fragmented. He has been exploring these issues with Dr Chris Topping, Dr Jacob Nabe-Nielsen, Dr Valery Forbes, Dr Mads Forchhammer, Dr Annemette Palmqvist, Trine Dalkvist and other members of the Danish Centre of Integrated Population Ecology. He is now working with several research students and research fellows to produce and validate simple ABMs of species vulnerable to pesticides for use in regulatory risk assessment http://cream-itn.eu/work-packages-and-projects/wp-3-vertebrates/bird-1-modelling-the-importance-of-landscape-structure-and-life-history-tr...(see more)

Tomasz Kułakowski joins the project. Tom is working with modelling skylark and woodpigeon and is currently carrying out his PhD study at Reading University as part of the CREAM project.

Trine Dalkvist joins the ALMaSS project on CCPForge today. Trine is working with the field vole model towards her PhD study.

Jannick Hansen joined the ALMaSS project. Jannick is doing his MSc research project on modelling domestic cat behaviour in ALMaSS

Anna Malawska, PhD student at Aarhus University has joined the project. Anna will be working with the problem of building farmer decision making behaviour into ALMaSS

The current version of the ALMaSS documentation in ODdox format is now available as a .zip file from Docs. Unzip the contents to a clean directory and find index.html with your browser to start to explore this.

As of today I have started the process of hosting ALMaSS code and documentation to CCPForge. This will be an ongoing process and may take some time.