Draft:The Animal Landscape and Man Simulation System (ALMaSS): Difference between revisions

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One of ALMaSS's distinctive features is its utilization of real weather data to drive farm management actions and biomass growth. The system has expanded its scope from its origins in Denmark to encompass countries such as [[Germany]], [[Poland]], [[Belgium]], [[Netherlands]], [[France]], [[Sweden]], and [[Finland]]. Ongoing efforts are aimed at further expansion into the UK, Ireland, Italy, and Portugal.
One of ALMaSS's distinctive features is its utilization of real weather data to drive farm management actions and biomass growth. The system has expanded its scope from its origins in Denmark to encompass countries such as [[Germany]], [[Poland]], [[Belgium]], [[Netherlands]], [[France]], [[Sweden]], and [[Finland]]. Ongoing efforts are aimed at further expansion into the UK, Ireland, Italy, and Portugal.


The system includes simulations for various species, encompassing both fauna and insects, with ongoing development efforts to expand the range. Some of the notable species include the [[Eurasian skylark|Eurasian Skylark]], [[Short-tailed field vole|Field Vole]]<ref>{{cite journal |last1=Topping |first1=Christopher J. |last2=Dalkvist |first2=Trine |last3=Grimm |first3=Volker |title=Post-Hoc Pattern-Oriented Testing and Tuning of an Existing Large Model: Lessons from the Field Vole |journal=PLOS ONE |date=25 September 2012 |volume=7 |issue=9 |pages=e45872 |doi=10.1371/journal.pone.0045872 |pmid=23049882 |pmc=3457952 |bibcode=2012PLoSO...745872T |doi-access=free }}</ref>, carabid beetles (e.g. [[Bembidion lampros]]<ref>{{cite journal |last1=Bilde |first1=Trine |last2=Topping |first2=Chris |title=Life history traits interact with landscape composition to influence population dynamics of a terrestrial arthropod: A simulation study |journal=Écoscience |date=January 2004 |volume=11 |issue=1 |pages=64–73 |doi=10.1080/11956860.2004.11682810|bibcode=2004Ecosc..11...64B |s2cid=88092229 }}</ref>), [[Erigone atra]]<ref>{{cite journal |last1=Thorbek |first1=P. |last2=Topping |first2=C.J. |title=The influence of landscape diversity and heterogeneity on spatial dynamics of agrobiont linyphiid spiders: An individual-based model |journal=BioControl |date=February 2005 |volume=50 |issue=1 |pages=1–33 |doi=10.1007/s10526-004-1114-8|bibcode=2005BioCo..50....1T |s2cid=21554814 }}</ref>, [[Roe deer|Roe Deer]]<ref>{{cite journal |last1=Jepsen |first1=J U |last2=Topping |first2=C J |title=Modelling roe deer ( Capreolus capreolus ) in a gradient of forest fragmentation: behavioural plasticity and choice of cover |journal=Canadian Journal of Zoology |date=1 September 2004 |volume=82 |issue=9 |pages=1528–1541 |doi=10.1139/z04-131}}</ref>, [[Grey partridge|Grey Partridge]]<ref>{{cite journal |last1=Topping |first1=Christopher John |last2=Høye |first2=Toke Thomas |last3=Odderskær |first3=Peter |last4=Aebischer |first4=Nicholas J. |title=A pattern-oriented modelling approach to simulating populations of grey partridge |journal=Ecological Modelling |date=March 2010 |volume=221 |issue=5 |pages=729–737 |doi=10.1016/j.ecolmodel.2009.11.004}}</ref>, [[European hare|European Brown Hare]]<ref>{{cite journal |last1=Topping |first1=Chris J. |last2=Høye |first2=Toke T. |last3=Olesen |first3=Carsten Riis |title=Opening the black box—Development, testing and documentation of a mechanistically rich agent-based model |journal=Ecological Modelling |date=January 2010 |volume=221 |issue=2 |pages=245–255 |doi=10.1016/j.ecolmodel.2009.09.014}}</ref>, [[European rabbit|European Rabbit]]<ref>{{cite journal |last1=Topping |first1=Christopher J. |last2=Weyman |first2=Gabriel S. |title=Rabbit Population Landscape-Scale Simulation to Investigate the Relevance of Using Rabbits in Regulatory Environmental Risk Assessment |journal=Environmental Modeling & Assessment |date=August 2018 |volume=23 |issue=4 |pages=415–457 |doi=10.1007/s10666-017-9581-3|bibcode=2018EMdAs..23..415T |s2cid=158439060 }}</ref>, [[Coccinella septempunctata|Seven-spotted Ladybird]], [[European Honey Bee]]<ref>{{cite journal |last1=Duan |first1=Xiaodong |last2=Wallis |first2=David |last3=Hatjina |first3=Fani |last4=Simon‐Delso |first4=Noa |last5=Bruun Jensen |first5=Annette |last6=Topping |first6=Christopher John |title=ApisRAM Formal Model Description |journal=EFSA Supporting Publications |date=February 2022 |volume=19 |issue=2 |doi=10.2903/sp.efsa.2022.EN-7184|s2cid=247143777 }}</ref>, and the [[Red mason bee|Red Mason Bee]][12]. Additionally, ALMaSS incorporates sub-population models for aphids, including the [[Black bean aphid]], [[Sitobion avenae|English grain aphid]], [[Myzus persicae|Peach-potato aphid]], and [[Acyrthosiphon pisum|Pea aphid]].
The system includes simulations for various species, encompassing both fauna and insects, with ongoing development efforts to expand the range. Some of the notable species include the [[Eurasian skylark|Eurasian Skylark]], [[Short-tailed field vole|Field Vole]]<ref>{{cite journal |last1=Topping |first1=Christopher J. |last2=Dalkvist |first2=Trine |last3=Grimm |first3=Volker |title=Post-Hoc Pattern-Oriented Testing and Tuning of an Existing Large Model: Lessons from the Field Vole |journal=PLOS ONE |date=25 September 2012 |volume=7 |issue=9 |pages=e45872 |doi=10.1371/journal.pone.0045872 |pmid=23049882 |pmc=3457952 |bibcode=2012PLoSO...745872T |doi-access=free }}</ref>, carabid beetles (e.g. [[Bembidion lampros]]<ref>{{cite journal |last1=Bilde |first1=Trine |last2=Topping |first2=Chris |title=Life history traits interact with landscape composition to influence population dynamics of a terrestrial arthropod: A simulation study |journal=Écoscience |date=January 2004 |volume=11 |issue=1 |pages=64–73 |doi=10.1080/11956860.2004.11682810|bibcode=2004Ecosc..11...64B |s2cid=88092229 }}</ref>), [[Erigone atra]]<ref>{{cite journal |last1=Thorbek |first1=P. |last2=Topping |first2=C.J. |title=The influence of landscape diversity and heterogeneity on spatial dynamics of agrobiont linyphiid spiders: An individual-based model |journal=BioControl |date=February 2005 |volume=50 |issue=1 |pages=1–33 |doi=10.1007/s10526-004-1114-8|bibcode=2005BioCo..50....1T |s2cid=21554814 }}</ref>, [[Roe deer|Roe Deer]]<ref>{{cite journal |last1=Jepsen |first1=J U |last2=Topping |first2=C J |title=Modelling roe deer ( Capreolus capreolus ) in a gradient of forest fragmentation: behavioural plasticity and choice of cover |journal=Canadian Journal of Zoology |date=1 September 2004 |volume=82 |issue=9 |pages=1528–1541 |doi=10.1139/z04-131}}</ref>, [[Grey partridge|Grey Partridge]]<ref>{{cite journal |last1=Topping |first1=Christopher John |last2=Høye |first2=Toke Thomas |last3=Odderskær |first3=Peter |last4=Aebischer |first4=Nicholas J. |title=A pattern-oriented modelling approach to simulating populations of grey partridge |journal=Ecological Modelling |date=March 2010 |volume=221 |issue=5 |pages=729–737 |doi=10.1016/j.ecolmodel.2009.11.004}}</ref>, [[European hare|European Brown Hare]]<ref>{{cite journal |last1=Topping |first1=Chris J. |last2=Høye |first2=Toke T. |last3=Olesen |first3=Carsten Riis |title=Opening the black box—Development, testing and documentation of a mechanistically rich agent-based model |journal=Ecological Modelling |date=January 2010 |volume=221 |issue=2 |pages=245–255 |doi=10.1016/j.ecolmodel.2009.09.014}}</ref>, [[European rabbit|European Rabbit]]<ref>{{cite journal |last1=Topping |first1=Christopher J. |last2=Weyman |first2=Gabriel S. |title=Rabbit Population Landscape-Scale Simulation to Investigate the Relevance of Using Rabbits in Regulatory Environmental Risk Assessment |journal=Environmental Modeling & Assessment |date=August 2018 |volume=23 |issue=4 |pages=415–457 |doi=10.1007/s10666-017-9581-3|bibcode=2018EMdAs..23..415T |s2cid=158439060 }}</ref>, [[Coccinella septempunctata|Seven-spotted Ladybird]], [[European Honey Bee]]<ref>{{cite journal |last1=Duan |first1=Xiaodong |last2=Wallis |first2=David |last3=Hatjina |first3=Fani |last4=Simon-Delso |first4=Noa |last5=Bruun Jensen |first5=Annette |last6=Topping |first6=Christopher John |title=ApisRAM Formal Model Description |journal=EFSA Supporting Publications |date=February 2022 |volume=19 |issue=2 |doi=10.2903/sp.efsa.2022.EN-7184|s2cid=247143777 }}</ref>, and the [[Red mason bee|Red Mason Bee]][12]. Additionally, ALMaSS incorporates sub-population models for aphids, including the [[Black bean aphid]], [[Sitobion avenae|English grain aphid]], [[Myzus persicae|Peach-potato aphid]], and [[Acyrthosiphon pisum|Pea aphid]].


== The Theoretical Approach of ALMaSS ==
== The Theoretical Approach of ALMaSS ==
The development of ALMaSS represented a significant departure from conventional ecological modeling paradigms. In contrast to the creation of simplistic models tailored for specific purposes, ALMaSS embraced a comprehensive and detailed approach. Leveraging advancements in [[computer technology]], it introduced a paradigm shift by prioritizing the intricate modeling of both the environment and animals. This approach was designed to cater to diverse scenarios, marking a departure from traditional, limited-use models.
The development of ALMaSS represented a significant departure from conventional ecological modeling paradigms. In contrast to the creation of simplistic models tailored for specific purposes, ALMaSS embraced a comprehensive and detailed approach. Leveraging advancements in [[computer technology]], it introduced a paradigm shift by prioritizing the intricate modeling of both the environment and animals. This approach was designed to cater to diverse scenarios, marking a departure from traditional, limited-use models.


At the core of ALMaSS's innovative methodology are reflective agent models<ref>{{cite journal |last1=Malawska |first1=Anna |last2=Topping |first2=Christopher John |date=May 2018 |title=Applying a biocomplexity approach to modelling farmer decision‐making and land use impacts on wildlife |journal=Journal of Applied Ecology |volume=55 |issue=3 |pages=1445–1455 |doi=10.1111/1365-2664.13024 |s2cid=91025437}}</ref>, a key component that sets it apart. These models delve into the intricacies of the ecological system, providing a level of detail crucial for creating accurate and reliable predictive models<ref>{{cite journal |last1=Topping |first1=Christopher J. |last2=Alrøe |first2=Hugo Fjelsted |last3=Farrell |first3=Katharine N. |last4=Grimm |first4=Volker |date=November 2015 |title=Per Aspera ad Astra: Through Complex Population Modeling to Predictive Theory |journal=The American Naturalist |volume=186 |issue=5 |pages=669–674 |doi=10.1086/683181 |pmid=26655779 |s2cid=21232891}}</ref>. By adopting reflective agent models, ALMaSS ensures a nuanced understanding of the interplay between the environment and animal behaviors, leading to the development of robust predictive models that find application across various scenarios
At the core of ALMaSS's innovative methodology are reflective agent models<ref>{{cite journal |last1=Malawska |first1=Anna |last2=Topping |first2=Christopher John |date=May 2018 |title=Applying a biocomplexity approach to modelling farmer decision-making and land use impacts on wildlife |journal=Journal of Applied Ecology |volume=55 |issue=3 |pages=1445–1455 |doi=10.1111/1365-2664.13024 |bibcode=2018JApEc..55.1445M |s2cid=91025437}}</ref>, a key component that sets it apart. These models delve into the intricacies of the ecological system, providing a level of detail crucial for creating accurate and reliable predictive models<ref>{{cite journal |last1=Topping |first1=Christopher J. |last2=Alrøe |first2=Hugo Fjelsted |last3=Farrell |first3=Katharine N. |last4=Grimm |first4=Volker |date=November 2015 |title=Per Aspera ad Astra: Through Complex Population Modeling to Predictive Theory |journal=The American Naturalist |volume=186 |issue=5 |pages=669–674 |doi=10.1086/683181 |pmid=26655779 |s2cid=21232891}}</ref>. By adopting reflective agent models, ALMaSS ensures a nuanced understanding of the interplay between the environment and animal behaviors, leading to the development of robust predictive models that find application across various scenarios


ALMaSS is built using an [[object-oriented design]] and is implemented in [[C++]]. The current visual interface utilizes [[Qt (software)|Qt]] technology. Since its inception, ALMaSS has been widely utilized and presented in numerous scientific publications, covering areas such as population genetics, ecology, pesticide impacts, and risk assessment on wildlife. See the ALMaSS Outputs RIO collection for a full bibliography.
ALMaSS is built using an [[object-oriented design]] and is implemented in [[C++]]. The current visual interface utilizes [[Qt (software)|Qt]] technology. Since its inception, ALMaSS has been widely utilized and presented in numerous scientific publications, covering areas such as population genetics, ecology, pesticide impacts, and risk assessment on wildlife. See the ALMaSS Outputs RIO collection for a full bibliography.

Revision as of 19:33, 5 February 2024

  • Comment: Not enough significant, independent coverage. WikiOriginal-9 (talk) 22:06, 5 November 2023 (UTC)


ALMaSS, short for the Animal Landscape and Man Simulation System.[1][2], is a comprehensive family of interconnected landscape-scale simulations designed to explore the impacts of landscape management on animal populations. Developed in 1996 by Chris J. Topping, ALMaSS integrates Geographic Information System (GIS)-generated landscapes with country-specific farm data and management practices. This integration results in detailed dynamic simulations of landscapes, providing a robust environment for running various models. ALMaSS primarily hosts two types of models: Agent-based models (ABM) and spatial stage-structured population models, also known as sub-population models. The latter are employed for species with vast populations where ABM simulations are unfeasible, relying on a conceptual basis rooted in Leslie matrix models.

One of ALMaSS's distinctive features is its utilization of real weather data to drive farm management actions and biomass growth. The system has expanded its scope from its origins in Denmark to encompass countries such as Germany, Poland, Belgium, Netherlands, France, Sweden, and Finland. Ongoing efforts are aimed at further expansion into the UK, Ireland, Italy, and Portugal.

The system includes simulations for various species, encompassing both fauna and insects, with ongoing development efforts to expand the range. Some of the notable species include the Eurasian Skylark, Field Vole[3], carabid beetles (e.g. Bembidion lampros[4]), Erigone atra[5], Roe Deer[6], Grey Partridge[7], European Brown Hare[8], European Rabbit[9], Seven-spotted Ladybird, European Honey Bee[10], and the Red Mason Bee[12]. Additionally, ALMaSS incorporates sub-population models for aphids, including the Black bean aphid, English grain aphid, Peach-potato aphid, and Pea aphid.

The Theoretical Approach of ALMaSS

The development of ALMaSS represented a significant departure from conventional ecological modeling paradigms. In contrast to the creation of simplistic models tailored for specific purposes, ALMaSS embraced a comprehensive and detailed approach. Leveraging advancements in computer technology, it introduced a paradigm shift by prioritizing the intricate modeling of both the environment and animals. This approach was designed to cater to diverse scenarios, marking a departure from traditional, limited-use models.

At the core of ALMaSS's innovative methodology are reflective agent models[11], a key component that sets it apart. These models delve into the intricacies of the ecological system, providing a level of detail crucial for creating accurate and reliable predictive models[12]. By adopting reflective agent models, ALMaSS ensures a nuanced understanding of the interplay between the environment and animal behaviors, leading to the development of robust predictive models that find application across various scenarios

ALMaSS is built using an object-oriented design and is implemented in C++. The current visual interface utilizes Qt technology. Since its inception, ALMaSS has been widely utilized and presented in numerous scientific publications, covering areas such as population genetics, ecology, pesticide impacts, and risk assessment on wildlife. See the ALMaSS Outputs RIO collection for a full bibliography.

Main Components of ALMaSS

Regarding model design, ALMaSS integrates detailed GIS-based landscapes that incorporate physical habitats, farms, and farm management practices. The system retains individual farms and their fields, utilizing geolocated data to calculate farm rotations, vegetation growth models, as well as patterns of nectar and pollen, and pesticide loads. These calculations dynamically adjust based on hourly weather data and temporal considerations within the year.

To simulate the living landscapes, ALMaSS employs agent-based models, incorporating animal species with varying temporal resolutions, either on a daily or 10-minute timescale depending on the species. For modeling intricate behaviors, ALMaSS adopts a state-transition approach, enabling individuals to transition between different states or behaviors, contributing to a more nuanced representation of ecological dynamics.

Documentation

To address the complexity of ALMaSS modelling, a new documentation paradigm has been proposed. This approach involves publishing a Formal Model article format paper[13], followed by the creation of Doxygen-based documentation and model evaluation papers. This method ensures a high level of quality assurance for complex models like ALMaSS. The Food and Ecological Systems Modelling Journal accepts these model documentation formats.

Use

The development of ALMaSS led to the establishment of the Social-Ecological Systems Simulation Centre (SESS) at Aarhus University in 2020. SESS serves as the hub for ALMaSS development and collaborates with researchers and institutions across Europe. ALMaSS continues to be a vital tool for researchers and institutions, providing valuable insights into the intricate interactions between landscape management and animal populations, feeding into key Horizon Europe research projects (e.g. EcoStack, B-GOOD, PollinERA).

References

  1. ^ Topping, Christopher John (7 July 2022). "The Animal Landscape and Man Simulation System (ALMaSS): a history, design, and philosophy". Research Ideas and Outcomes. 8. doi:10.3897/rio.8.e89919.
  2. ^ Topping, Chris J.; Hansen, Tine S.; Jensen, Thomas S.; Jepsen, Jane U.; Nikolajsen, Frank; Odderskær, Peter (September 2003). "ALMaSS, an agent-based model for animals in temperate European landscapes". Ecological Modelling. 167 (1–2): 65–82. doi:10.1016/S0304-3800(03)00173-X.
  3. ^ Topping, Christopher J.; Dalkvist, Trine; Grimm, Volker (25 September 2012). "Post-Hoc Pattern-Oriented Testing and Tuning of an Existing Large Model: Lessons from the Field Vole". PLOS ONE. 7 (9): e45872. Bibcode:2012PLoSO...745872T. doi:10.1371/journal.pone.0045872. PMC 3457952. PMID 23049882.
  4. ^ Bilde, Trine; Topping, Chris (January 2004). "Life history traits interact with landscape composition to influence population dynamics of a terrestrial arthropod: A simulation study". Écoscience. 11 (1): 64–73. Bibcode:2004Ecosc..11...64B. doi:10.1080/11956860.2004.11682810. S2CID 88092229.
  5. ^ Thorbek, P.; Topping, C.J. (February 2005). "The influence of landscape diversity and heterogeneity on spatial dynamics of agrobiont linyphiid spiders: An individual-based model". BioControl. 50 (1): 1–33. Bibcode:2005BioCo..50....1T. doi:10.1007/s10526-004-1114-8. S2CID 21554814.
  6. ^ Jepsen, J U; Topping, C J (1 September 2004). "Modelling roe deer ( Capreolus capreolus ) in a gradient of forest fragmentation: behavioural plasticity and choice of cover". Canadian Journal of Zoology. 82 (9): 1528–1541. doi:10.1139/z04-131.
  7. ^ Topping, Christopher John; Høye, Toke Thomas; Odderskær, Peter; Aebischer, Nicholas J. (March 2010). "A pattern-oriented modelling approach to simulating populations of grey partridge". Ecological Modelling. 221 (5): 729–737. doi:10.1016/j.ecolmodel.2009.11.004.
  8. ^ Topping, Chris J.; Høye, Toke T.; Olesen, Carsten Riis (January 2010). "Opening the black box—Development, testing and documentation of a mechanistically rich agent-based model". Ecological Modelling. 221 (2): 245–255. doi:10.1016/j.ecolmodel.2009.09.014.
  9. ^ Topping, Christopher J.; Weyman, Gabriel S. (August 2018). "Rabbit Population Landscape-Scale Simulation to Investigate the Relevance of Using Rabbits in Regulatory Environmental Risk Assessment". Environmental Modeling & Assessment. 23 (4): 415–457. Bibcode:2018EMdAs..23..415T. doi:10.1007/s10666-017-9581-3. S2CID 158439060.
  10. ^ Duan, Xiaodong; Wallis, David; Hatjina, Fani; Simon-Delso, Noa; Bruun Jensen, Annette; Topping, Christopher John (February 2022). "ApisRAM Formal Model Description". EFSA Supporting Publications. 19 (2). doi:10.2903/sp.efsa.2022.EN-7184. S2CID 247143777.
  11. ^ Malawska, Anna; Topping, Christopher John (May 2018). "Applying a biocomplexity approach to modelling farmer decision-making and land use impacts on wildlife". Journal of Applied Ecology. 55 (3): 1445–1455. Bibcode:2018JApEc..55.1445M. doi:10.1111/1365-2664.13024. S2CID 91025437.
  12. ^ Topping, Christopher J.; Alrøe, Hugo Fjelsted; Farrell, Katharine N.; Grimm, Volker (November 2015). "Per Aspera ad Astra: Through Complex Population Modeling to Predictive Theory". The American Naturalist. 186 (5): 669–674. doi:10.1086/683181. PMID 26655779. S2CID 21232891.
  13. ^ Topping, Christopher John; Kondrup Marcussen, Luna; Thomsen, Peet; Chetcuti, Jordan (4 October 2022). "The Formal Model article format: justifying modelling intent and a critical review of data foundations through publication". Food and Ecological Systems Modelling Journal. 3. doi:10.3897/fmj.3.91024.
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