SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias

Detalhes bibliográficos
Autor(a) principal: Quaglietta, Lorenzo
Data de Publicação: 2019
Outros Autores: Porto, Miguel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.5/17750
Resumo: Software article
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spelling SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape biasconnectivitydendritic ecological networkslandscape heterogeneitylinear habitatshidden Markov modelsmechanistic movement modelsindividual-based movement simulationmovement ecologyriver networksresistanceSoftware articleBackground: Lack of suitable analytical software and computational power constrains the comprehension of animal movement. In particular, we are aware of no tools allowing simulating spatially-explicit multistate Markovian movements constrained to linear features or conditioned by landscape heterogeneity, which hinders movement ecology research in linear/dendritic (e.g. river networks) and heterogeneous landscapes. SiMRiv is a novel, fast and intuitive R package we designed to fill such gap. It does so by allowing continuous-space mechanistic spatially-explicit simulation of multistate Markovian individual movements incorporating landscape bias on local behavior. Results: We present SiMRiv and its main functionalities, illustrate its simulation capabilities and easy-of-use, and discuss its limitations and potential improvements. We further provide examples of use and a preliminary evaluation, using real and simulated data, of a parameter approximation experimental method. SiMRiv allowed us to generate increasingly complex movements of three theoretical species (aquatic, semiaquatic and terrestrial), showing the effects of input parameters and water-dependence on emerging movement patterns, and to parameterize a high-frequency simulation model from real, low-frequency movement (telemetry) data. Typical running times for conducting 1000 simulations with 10,000 steps each, of two-state movement trajectories in a river network, were of ca. 3 min in an Intel Core i7 CPU X990 @ 3.47 GHz Conclusions: SiMRiv allows simulation of movements constrained to linear habitats or conditioned by landscape heterogeneity, therefore enhancing the application of movement ecology to linear/dendritic and heterogeneous landscapes. Importantly, the software is flexible enough to be used in linear, heterogeneous, as well as homogeneous landscapes. Using the same software, algorithm and approach, one can therefore use SiMRiv to study the movement of different organisms in a variety of landscapes, facilitating comparative research. SiMRiv balances ease and speed with high realism of the movement models obtainable, constituting a fast, powerful, yet intuitive tool, which should contribute exploring several movement-related questions. Its applications depart from the generation of mechanistic null movement models, up to population level (e.g. landscape connectivity) analyses, holding potential for all fields requiring the simulation of random trajectoriesBMCRepositório da Universidade de LisboaQuaglietta, LorenzoPorto, Miguel2019-04-29T14:15:54Z20192019-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.5/17750engQuaglietta and Porto Movement Ecology (2019) 7:11https://doi.org/10.1186/s40462-019-0154-8info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-03-06T14:47:24Zoai:www.repository.utl.pt:10400.5/17750Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T17:02:55.689461Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
title SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
spellingShingle SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
Quaglietta, Lorenzo
connectivity
dendritic ecological networks
landscape heterogeneity
linear habitats
hidden Markov models
mechanistic movement models
individual-based movement simulation
movement ecology
river networks
resistance
title_short SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
title_full SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
title_fullStr SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
title_full_unstemmed SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
title_sort SiMRiv: an R package for mechanistic simulation of individual, spatially-explicit multistate movements in rivers, heterogenous and homogenous spaces incorporating landscape bias
author Quaglietta, Lorenzo
author_facet Quaglietta, Lorenzo
Porto, Miguel
author_role author
author2 Porto, Miguel
author2_role author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Quaglietta, Lorenzo
Porto, Miguel
dc.subject.por.fl_str_mv connectivity
dendritic ecological networks
landscape heterogeneity
linear habitats
hidden Markov models
mechanistic movement models
individual-based movement simulation
movement ecology
river networks
resistance
topic connectivity
dendritic ecological networks
landscape heterogeneity
linear habitats
hidden Markov models
mechanistic movement models
individual-based movement simulation
movement ecology
river networks
resistance
description Software article
publishDate 2019
dc.date.none.fl_str_mv 2019-04-29T14:15:54Z
2019
2019-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.5/17750
url http://hdl.handle.net/10400.5/17750
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Quaglietta and Porto Movement Ecology (2019) 7:11
https://doi.org/10.1186/s40462-019-0154-8
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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