Abteilung Ökoinformatik, Biometrie und Waldwachstum

[["dc.bibliographiccitation.firstpage","691"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Oikos"],["dc.bibliographiccitation.lastpage","696"],["dc.bibliographiccitation.volume","124"],["dc.contributor.author","Thiele, Jan Christoph"],["dc.contributor.author","Grimm, Volker"],["dc.date.accessioned","2018-11-07T09:56:32Z"],["dc.date.available","2018-11-07T09:56:32Z"],["dc.date.issued","2015"],["dc.description.abstract","There are two major limitations to the potential of computational models in ecology for producing general insights: their design is path-dependent, reflecting different underlying questions, assumptions, and data, and there is too little robustness analysis exploring where the model mechanisms explaining certain observations break down. We here argue that both limitations could be overcome if modellers in ecology would more often replicate existing models, try to break the models, and explore modifications. Replication comprises the re-implementation of an existing model and the replication of its results. Breaking models means to identify under what conditions the mechanisms represented in a model can no longer explain observed phenomena. The benefits of replication include less effort being spent to enter the iterative stage of model development and having more time for systematic robustness analysis. A culture of replication would lead to increased credibility, coherence and efficiency of computational modelling and thereby facilitate theory development."],["dc.identifier.doi","10.1111/oik.02170"],["dc.identifier.isi","000356010600003"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/36975"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1600-0706"],["dc.relation.issn","0030-1299"],["dc.relation.orgunit","Abteilung Ökoinformatik, Biometrie und Waldwachstum"],["dc.title","Replicating and breaking models: good for you and good for ecology"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","9"],["dc.bibliographiccitation.journal","Tagung (Deutscher Verband Forstlicher Forschungsanstalten, Sektion Forstliche Biometrie und Informatik)"],["dc.bibliographiccitation.lastpage","19"],["dc.contributor.author","Thiele, Jan Christoph"],["dc.contributor.author","Lanwert, D."],["dc.date.accessioned","2022-01-13T09:09:06Z"],["dc.date.available","2022-01-13T09:09:06Z"],["dc.date.issued","2009"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/98111"],["dc.relation.issn","1860-4064"],["dc.title","E-Assessment - Erfahrungen aus der Praxis am Beispiel \"Raumbezogene Informationssysteme\""],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","480"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Methods in Ecology and Evolution"],["dc.bibliographiccitation.lastpage","483"],["dc.bibliographiccitation.volume","3"],["dc.contributor.author","Thiele, Jan C."],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Grimm, Volker"],["dc.date.accessioned","2018-11-07T09:09:50Z"],["dc.date.available","2018-11-07T09:09:50Z"],["dc.date.issued","2012"],["dc.description.abstract","1. NetLogo is a free software platform for implementing individual-based and agent-based models. However, NetLogos support of systematic design, performance and analysis of simulation experiments is limited. The statistics software R includes such support. 2. RNetLogo is an R package that links R and NetLogo: any NetLogo program can be controlled and run from R and model results can be transferred back to R for statistical analyses. RNetLogo includes 16 functions, which are explained and demonstrated in the user manual and tutorial. The design of RNetLogo was inspired by a similar link between Mathematica and NetLogo. 3. RNetLogo is a powerful tool for making individual-based modelling more efficient and less ad hoc. It links two fast growing user communities and constitutes a new interface for integrating descriptive statistical analyses and individual-based modelling."],["dc.identifier.doi","10.1111/j.2041-210X.2011.00180.x"],["dc.identifier.isi","000304902500005"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/26354"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","2041-210X"],["dc.title","RNetLogo: an R package for running and exploring individual-based models implemented in NetLogo"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Journal of Statistical Software"],["dc.bibliographiccitation.lastpage","41"],["dc.bibliographiccitation.volume","58"],["dc.contributor.author","Thiele, Jan Christoph"],["dc.date.accessioned","2019-07-10T08:11:53Z"],["dc.date.available","2019-07-10T08:11:53Z"],["dc.date.issued","2014"],["dc.description.abstract","The RNetLogo package delivers an interface to embed the agent-based modeling platform NetLogo into the R environment with headless (no graphical user interface) or interactive GUI mode. It provides functions to load models, execute commands, push values, and to get values from NetLogo reporters. Such a seamless integration of a widely used agent-based modeling platform with a well-known statistical computing and graphics environment opens up various possibilities. For example, it enables the modeler to design simulation experiments, store simulation results, and analyze simulation output in a more systematic way. It can therefore help close the gaps in agent-based modeling regarding standards of description and analysis. After a short overview of the agent-based modeling approach and the software used here, the paper delivers a step-by-step introduction to the usage of the RNetLogo package by examples."],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11712"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60814"],["dc.language.iso","en"],["dc.notes.intern","Migrated from goescholar"],["dc.relation.issn","1548-7660"],["dc.relation.orgunit","Abteilung Ökoinformatik, Biometrie und Waldwachstum"],["dc.rights","CC BY 3.0"],["dc.rights.access","openAccess"],["dc.rights.uri","https://creativecommons.org/licenses/by/3.0"],["dc.subject","NetLogo; R; agent-based modeling; ABM; individual-based modeling; IBM; statistics; graphics."],["dc.subject.ddc","570"],["dc.title","R Marries NetLogo: Introduction to the RNetLogo Package"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.journal","Computers and Electronics in Agriculture"],["dc.bibliographiccitation.lastpage","8"],["dc.bibliographiccitation.volume","92"],["dc.contributor.author","Hemmerling, Reinhard"],["dc.contributor.author","Evers, Jochem B."],["dc.contributor.author","Smolenova, Katarina"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.contributor.author","Kurth, Winfried"],["dc.date.accessioned","2018-11-07T09:27:26Z"],["dc.date.available","2018-11-07T09:27:26Z"],["dc.date.issued","2013"],["dc.description.abstract","In simulation models of plant development, physiological processes taking place in plants are typically described in terms of ODEs (Ordinary Differential Equations). On the one hand, those processes drive the development of the plant structure and on the other hand, the developed structure again influences these processes (e.g., photosynthesis, hormone synthesis and transport, and allocation of carbon, nitrogen, etc.). To study this dependence, simulation models, termed functional-structural plant models (FSPMs), are developed. Such models usually operate at the organ scale, considering the topology and the geometry of organs, while being validated at the scale of the plant individual. The open source modelling platform GroIMP was designed for the purpose of creating FSPMs. In GroIMP, the structure of a plant is described by the eXtended L-system language (XL) which is an extension of the Java programming language and works on a general graph structure. It is general enough to be used for many biological problems that can be described by graphs. Until now, to specify and solve ODEs, Java code had to be used and there was no general solution for doing this easily and conveniently in XL Here we propose an extension to the XL language that allows the user to easily specify ODEs in terms of rule applications. Furthermore, their specification is separated from the numerical solution, with the possibility to choose between different integration methods. The new framework is illustrated with examples of auxin transport in Arabidopsis and gibberellic acid signal transduction in barley and compared with the conventional approach in FSPMs (Euler method). We show that besides the user-friendly specification of ODEs within rules by using a special operator, the results are computed faster, are more stable and accurate. The new framework is also compared with the mathematical formalism of differential L-systems (dL-systems). (C) 2013 Elsevier B.V. All rights reserved."],["dc.description.sponsorship","DFG [Ku 847/8-1]"],["dc.identifier.doi","10.1016/j.compag.2012.12.007"],["dc.identifier.isi","000316592000001"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/30538"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Elsevier Sci Ltd"],["dc.relation.issn","0168-1699"],["dc.title","Extension of the GroIMP modelling platform to allow easy specification of differential equations describing biological processes within plant models"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","11"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Journal of Artificial Societies and Social Simulation"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Thiele, Jan Christoph"],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Grimm, Volker"],["dc.date.accessioned","2018-11-07T09:38:43Z"],["dc.date.available","2018-11-07T09:38:43Z"],["dc.date.issued","2014"],["dc.description.abstract","Agent-based models are increasingly used to address questions regarding real-world phenomena and mechanisms; therefore, the calibration of model parameters to certain data sets and patterns is often needed. Furthermore, sensitivity analysis is an important part of the development and analysis of any simulation model. By exploring the sensitivity of model output to changes in parameters, we learn about the relative importance of the various mechanisms represented in the model and how robust the model output is to parameter uncertainty. These insights foster the understanding of models and their use for theory development and applications. Both steps of the model development cycle require massive repetitions of simulation runs with varying parameter values. To facilitate parameter estimation and sensitivity analysis for agent-based modellers, we show how to use a suite of important established methods. Because NetLogo and R are widely used in agent-based modelling and for statistical analyses, we use a simple model implemented in NetLogo as an example, packages in R that implement the respective methods, and the RNetLogo package, which links R and NetLogo. We briefly introduce each method and provide references for further reading. We then list the packages in R that may be used for implementing the methods, provide short code examples demonstrating how the methods can be applied in R, and present and discuss the corresponding outputs. The Supplementary Material includes full, adaptable code samples for using the presented methods with R and NetLogo. Our overall aim is to make agent-based modellers aware of existing methods and tools for parameter estimation and sensitivity analysis and to provide accessible tools for using these methods. In this way, we hope to contribute to establishing an advanced culture of relating agent-based models to data and patterns observed in real systems and to foster rigorous and structured analyses of agent-based models."],["dc.identifier.isi","000339121300018"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/33127"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relatedmaterial.fulltext","https://www.jasss.org/17/3/11.html"],["dc.relation.issn","1460-7425"],["dc.relation.orgunit","Abteilung Ökoinformatik, Biometrie und Waldwachstum"],["dc.title","Facilitating Parameter Estimation and Sensitivity Analysis of Agent-Based Models: A Cookbook Using Net Logo and R"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","813"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Annals of Botany"],["dc.bibliographiccitation.lastpage","827"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Ong, Yongzhi"],["dc.contributor.author","Streit, Katarina"],["dc.contributor.author","Henke, Michael"],["dc.contributor.author","Kurth, Winfried"],["dc.date.accessioned","2018-11-07T09:35:41Z"],["dc.date.available","2018-11-07T09:35:41Z"],["dc.date.issued","2014"],["dc.description.abstract","Background and Aims Functional-structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs. Methods A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow(from macro-to micro-scale) is catered for in the framework. The methods are implemented within the programming language XL. Key Results Three example models are implemented using the proposed multiscale graph model and framework. The first illustrates the fundamental usage of the graph data structure and grammar, the second uses probabilistic modelling for organs at the fine scale in order to derive crown growth, and the third combines multiscale plant topology with ozone trends and metabolic network simulations in order to model juvenile beech stands under exposure to a toxic trace gas. Conclusions The graph data structure supports data representation and grammar operations at multiple scales. The results demonstrate that multiscale modelling is a viable method in FSPM and an alternative to correlation-based modelling. Advantages and disadvantages of multiscale modelling are illustrated by comparisons with single-scale implementations, leading to motivations for further research in sensitivity analysis and run-time efficiency for these models."],["dc.identifier.doi","10.1093/aob/mcu155"],["dc.identifier.isi","000343039600018"],["dc.identifier.pmid","25134929"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/32443"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1095-8290"],["dc.relation.issn","0305-7364"],["dc.title","An approach to multiscale modelling with graph grammars"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","117"],["dc.bibliographiccitation.issue","2-3"],["dc.bibliographiccitation.journal","Tree Physiology"],["dc.bibliographiccitation.lastpage","128"],["dc.bibliographiccitation.volume","21"],["dc.contributor.author","Oppelt, A. L."],["dc.contributor.author","Kurth, W."],["dc.contributor.author","Godbold, Douglas L."],["dc.date.accessioned","2018-11-07T09:26:35Z"],["dc.date.available","2018-11-07T09:26:35Z"],["dc.date.issued","2001"],["dc.description.abstract","Aspects of root architecture, including topology, link length, diameter and scaling relations, were analyzed in excavated coarse root systems of three field-grown fruit tree species (Strychnos cocculoides Bak., Strychnos spinosa Lam. and Vangueria infausta Burch) and the fruit-bearing shrub Grewia flava DC. We investigated the root systems using semi-automatic digitizing and computer-based 3-D reconstruction techniques. Topological analysis was carried out to investigate branching patterns as basic determinants of root architecture. New topological indices were developed and revealed significant differences among the species. The different architectural strategies can be explained in terms of cost-benefit relations and efficiency in soil resource exploration and exploitation. In addition, some well-known hypotheses about geometry and scaling, most of them previously unverified by empirical observations on root systems, were tested. For practical applications, the main emphasis is on the relationship between proximal root diameter, an easily determined parameter, and several parameters describing the size of the whole root system. We also tested the \"pipe stem\" theory, essentially dating back to Leonardo da Vinci, which underlies many models and which we found conformed to our measurement data with reasonable accuracy. A physiological consequence of the \"constant cross-sectional area rule\" may be a certain homogeneity of hydraulic architecture throughout root systems."],["dc.identifier.isi","000166829300007"],["dc.identifier.pmid","11303642"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/30333"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Heron Publishing"],["dc.publisher.place","Victoria"],["dc.relation.conference","2nd IUFRO International Symposium on Dynamics of Physiological Processes in Woody Roots"],["dc.relation.eventlocation","NANCY, FRANCE"],["dc.relation.issn","0829-318X"],["dc.title","Topology, scaling relations and Leonardo's rule in root systems from African tree species"],["dc.type","conference_paper"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1103"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Frontiers of Computer Science"],["dc.bibliographiccitation.lastpage","1117"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Henke, Michael"],["dc.contributor.author","Kurth, Winfried"],["dc.contributor.author","Buck-Sorlin, Gerhard H."],["dc.date.accessioned","2018-11-07T10:05:36Z"],["dc.date.available","2018-11-07T10:05:36Z"],["dc.date.issued","2016"],["dc.description.abstract","In the last decade, functional-structural plant modelling (FSPM) has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse (by modularisation), combination and comparison, and the enhancement of existing models. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization. Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim (e.g., photosynthesis, organ formation and growth). Simulation runs with several general parameter sets adopted from the literature show that the present prototypewas able to reproduce a plausible output range for different crops (rapeseed, barley, etc.) in terms of both the dynamics and final values (at harvest time) of model state variables such as assimilate production, organ biomass, leaf area and architecture."],["dc.identifier.doi","10.1007/s11704-015-4472-8"],["dc.identifier.isi","000385137600011"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/38926"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","2095-2236"],["dc.relation.issn","2095-2228"],["dc.relation.orgunit","Abteilung Ökoinformatik, Biometrie und Waldwachstum"],["dc.title","FSPM-P: towards a general functional-structural plant model for robust and comprehensive model development"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.contributor.advisorcorporation","Fakultät für Forstwissenschaften und Waldökologie, Universität Göttingen"],["dc.contributor.author","Thiele, Jan Christoph"],["dc.date.accessioned","2022-01-13T09:16:17Z"],["dc.date.available","2022-01-13T09:16:17Z"],["dc.date.issued","2007"],["dc.format.extent","179"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/98117"],["dc.relation.orgunit","Fakultät für Forstwissenschaften und Waldökologie"],["dc.title","Ein individuenbasiertes Modell zur Populationsdynamik von Daphnia magna in Laborexperimenten"],["dc.type","thesis"],["dc.type.internalPublication","yes"],["dc.type.subtype","master"],["dspace.entity.type","Publication"]]