Literature DB >> 23565336

Computational ecology as an emerging science.

Sergei Petrovskii1, Natalia Petrovskaya.   

Abstract

It has long been recognized that numerical modelling and computer simulations can be used as a powerful research tool to understand, and sometimes to predict, the tendencies and peculiarities in the dynamics of populations and ecosystems. It has been, however, much less appreciated that the context of modelling and simulations in ecology is essentially different from those that normally exist in other natural sciences. In our paper, we review the computational challenges arising in modern ecology in the spirit of computational mathematics, i.e. with our main focus on the choice and use of adequate numerical methods. Somewhat paradoxically, the complexity of ecological problems does not always require the use of complex computational methods. This paradox, however, can be easily resolved if we recall that application of sophisticated computational methods usually requires clear and unambiguous mathematical problem statement as well as clearly defined benchmark information for model validation. At the same time, many ecological problems still do not have mathematically accurate and unambiguous description, and available field data are often very noisy, and hence it can be hard to understand how the results of computations should be interpreted from the ecological viewpoint. In this scientific context, computational ecology has to deal with a new paradigm: conventional issues of numerical modelling such as convergence and stability become less important than the qualitative analysis that can be provided with the help of computational techniques. We discuss this paradigm by considering computational challenges arising in several specific ecological applications.

Keywords:  computational ecology; conceptual modelling; predictive modelling

Year:  2012        PMID: 23565336      PMCID: PMC3293204          DOI: 10.1098/rsfs.2011.0083

Source DB:  PubMed          Journal:  Interface Focus        ISSN: 2042-8898            Impact factor:   3.906


  25 in total

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3.  Finite-difference schemes for reaction-diffusion equations modeling predator-prey interactions in MATLAB.

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Journal:  Bull Math Biol       Date:  2007-02-01       Impact factor: 1.758

4.  Dynamics of age-structured and spatially structured predator-prey interactions: individual-based models and population-level formulations.

Authors:  E McCauley; W G Wilson; A M de Roos
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5.  Random dispersal in theoretical populations.

Authors:  J G SKELLAM
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Review 6.  Forests and climate change: forcings, feedbacks, and the climate benefits of forests.

Authors:  Gordon B Bonan
Journal:  Science       Date:  2008-06-13       Impact factor: 47.728

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Authors:  T M Powell; P J Richerson; T M Dillon; B A Agee; B J Dozier; D A Godden; L O Myrup
Journal:  Science       Date:  1975-09-26       Impact factor: 47.728

8.  Bayesian methods for analyzing movements in heterogeneous landscapes from mark-recapture data.

Authors:  Otso Ovaskainen; Hanna Rekola; Evgeniy Meyke; Elja Arjas
Journal:  Ecology       Date:  2008-02       Impact factor: 5.499

9.  Mountain pine beetle and forest carbon feedback to climate change.

Authors:  W A Kurz; C C Dymond; G Stinson; G J Rampley; E T Neilson; A L Carroll; T Ebata; L Safranyik
Journal:  Nature       Date:  2008-04-24       Impact factor: 49.962

10.  Computational ecology: from the complex to the simple and back.

Authors:  Mercedes Pascual
Journal:  PLoS Comput Biol       Date:  2005-07       Impact factor: 4.475

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  8 in total

1.  Towards a simplification of models using regression trees.

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Journal:  J R Soc Interface       Date:  2013-02       Impact factor: 4.118

2.  Towards the marriage of theory and data.

Authors:  Simon A Levin
Journal:  Interface Focus       Date:  2012-02-01       Impact factor: 3.906

3.  Geomagnetic imprinting predicts spatio-temporal variation in homing migration of pink and sockeye salmon.

Authors:  Nathan F Putman; Erica S Jenkins; Catherine G J Michielsens; David L G Noakes
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4.  Increased adoption of best practices in ecological forecasting enables comparisons of forecastability.

Authors:  Abigail S L Lewis; Whitney M Woelmer; Heather L Wander; Dexter W Howard; John W Smith; Ryan P McClure; Mary E Lofton; Nicholas W Hammond; Rachel S Corrigan; R Quinn Thomas; Cayelan C Carey
Journal:  Ecol Appl       Date:  2021-12-14       Impact factor: 6.105

Review 5.  Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists.

Authors:  Marco D Visser; Sean M McMahon; Cory Merow; Philip M Dixon; Sydne Record; Eelke Jongejans
Journal:  PLoS Comput Biol       Date:  2015-03-26       Impact factor: 4.475

6.  Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab).

Authors:  Constantinos Varsos; Theodore Patkos; Anastasis Oulas; Christina Pavloudi; Alexandros Gougousis; Umer Zeeshan Ijaz; Irene Filiopoulou; Nikolaos Pattakos; Edward Vanden Berghe; Antonio Fernández-Guerra; Sarah Faulwetter; Eva Chatzinikolaou; Evangelos Pafilis; Chryssoula Bekiari; Martin Doerr; Christos Arvanitidis
Journal:  Biodivers Data J       Date:  2016-11-01

7.  Sensitivity analysis of Repast computational ecology models with R/Repast.

Authors:  Antonio Prestes García; Alfonso Rodríguez-Patón
Journal:  Ecol Evol       Date:  2016-11-21       Impact factor: 2.912

8.  Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students.

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Journal:  PLoS Comput Biol       Date:  2021-01-14       Impact factor: 4.475

  8 in total

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