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SPOTting Model Parameters Using a Ready-Made Python Package

The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optim...

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Detalles Bibliográficos
Autores principales: Houska, Tobias, Kraft, Philipp, Chamorro-Chavez, Alejandro, Breuer, Lutz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682995/
https://www.ncbi.nlm.nih.gov/pubmed/26680783
http://dx.doi.org/10.1371/journal.pone.0145180
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author Houska, Tobias
Kraft, Philipp
Chamorro-Chavez, Alejandro
Breuer, Lutz
author_facet Houska, Tobias
Kraft, Philipp
Chamorro-Chavez, Alejandro
Breuer, Lutz
author_sort Houska, Tobias
collection PubMed
description The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function.
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spelling pubmed-46829952015-12-31 SPOTting Model Parameters Using a Ready-Made Python Package Houska, Tobias Kraft, Philipp Chamorro-Chavez, Alejandro Breuer, Lutz PLoS One Research Article The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function. Public Library of Science 2015-12-17 /pmc/articles/PMC4682995/ /pubmed/26680783 http://dx.doi.org/10.1371/journal.pone.0145180 Text en © 2015 Houska et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Houska, Tobias
Kraft, Philipp
Chamorro-Chavez, Alejandro
Breuer, Lutz
SPOTting Model Parameters Using a Ready-Made Python Package
title SPOTting Model Parameters Using a Ready-Made Python Package
title_full SPOTting Model Parameters Using a Ready-Made Python Package
title_fullStr SPOTting Model Parameters Using a Ready-Made Python Package
title_full_unstemmed SPOTting Model Parameters Using a Ready-Made Python Package
title_short SPOTting Model Parameters Using a Ready-Made Python Package
title_sort spotting model parameters using a ready-made python package
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682995/
https://www.ncbi.nlm.nih.gov/pubmed/26680783
http://dx.doi.org/10.1371/journal.pone.0145180
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