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mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling.

Scott F, Blanchard JL, Andersen KH - Methods Ecol Evol (2014)

Bottom Line: A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size.The models we focus on are designed to capture fish community dynamics useful for assessing the community impacts of fishing.We present mizer, an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing.Multiple fishing gears can be defined and fishing mortality can change through time making it possible to simulate a range of exploitation strategies and management options.mizer implements three versions of the size spectrum modelling framework: the community model, where individuals are only characterized by their size; the trait-based model, where individuals are further characterized by their asymptotic size; and the multispecies model where additional trait differences are resolved.A range of plot, community indicator and summary methods are available to inspect the results of the simulations.

View Article: PubMed Central - PubMed

Affiliation: Maritime Affairs Unit, IPSC, European Commission Joint Research Centre Via Enrico Fermi 2749, I - 21027, Ispra (VA), Italy ; Centre for the Environment Fisheries and Aquaculture Science (CEFAS) Pakefield Road, Lowestoft, NR33 0HT, UK.

ABSTRACT

Size spectrum ecological models are representations of a community of individuals which grow and change trophic level. A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size. The models we focus on are designed to capture fish community dynamics useful for assessing the community impacts of fishing.We present mizer, an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing. Multiple fishing gears can be defined and fishing mortality can change through time making it possible to simulate a range of exploitation strategies and management options.mizer implements three versions of the size spectrum modelling framework: the community model, where individuals are only characterized by their size; the trait-based model, where individuals are further characterized by their asymptotic size; and the multispecies model where additional trait differences are resolved.A range of plot, community indicator and summary methods are available to inspect the results of the simulations.

No MeSH data available.


Comparing unfished and fished communities with the three model versions: (a) community, (b) trait-based and (c) multispecies based on the North Sea. Top row: biomass of the background resource (green), total community biomass (red) and individual species biomasses (black) in the unfished case; total community biomass in the fished case (blue dashed), all relative to the carrying capacity of the background resource at 10−3 g. In the trait-based model, the asymptotic weights of the 10 species in the model are evenly spread over a log scale, giving the parallel species biomass lines seen. In the multispecies model, the asymptotic weights are species-dependent and hence the species biomass lines are not parallel. Bottom row: relative total abundance of fished and unfished communities. Fishing is with knife-edge selectivity at 1000 g (vertical dashed line).
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fig02: Comparing unfished and fished communities with the three model versions: (a) community, (b) trait-based and (c) multispecies based on the North Sea. Top row: biomass of the background resource (green), total community biomass (red) and individual species biomasses (black) in the unfished case; total community biomass in the fished case (blue dashed), all relative to the carrying capacity of the background resource at 10−3 g. In the trait-based model, the asymptotic weights of the 10 species in the model are evenly spread over a log scale, giving the parallel species biomass lines seen. In the multispecies model, the asymptotic weights are species-dependent and hence the species biomass lines are not parallel. Bottom row: relative total abundance of fished and unfished communities. Fishing is with knife-edge selectivity at 1000 g (vertical dashed line).

Mentions: The first example simulates a trophic cascade using all three models (Fig.2). Here all species are fished with a knife-edge selectivity so that only individuals >1000 g are selected (a simplification as selectivity is normally species-specific, possible with mizer). The simulations are run to equilibrium to investigate equilibrium fished and unfished states (details can be found in the vignette). The fishing pressure lowers the relative abundance of fish >1000 g and reduces predation pressure on smaller prey, leading to an increase in their abundance. This in turn increases predation mortality on even smaller sizes, reducing their abundance and so on, causing a size-structured cascade.


mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling.

Scott F, Blanchard JL, Andersen KH - Methods Ecol Evol (2014)

Comparing unfished and fished communities with the three model versions: (a) community, (b) trait-based and (c) multispecies based on the North Sea. Top row: biomass of the background resource (green), total community biomass (red) and individual species biomasses (black) in the unfished case; total community biomass in the fished case (blue dashed), all relative to the carrying capacity of the background resource at 10−3 g. In the trait-based model, the asymptotic weights of the 10 species in the model are evenly spread over a log scale, giving the parallel species biomass lines seen. In the multispecies model, the asymptotic weights are species-dependent and hence the species biomass lines are not parallel. Bottom row: relative total abundance of fished and unfished communities. Fishing is with knife-edge selectivity at 1000 g (vertical dashed line).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384942&req=5

fig02: Comparing unfished and fished communities with the three model versions: (a) community, (b) trait-based and (c) multispecies based on the North Sea. Top row: biomass of the background resource (green), total community biomass (red) and individual species biomasses (black) in the unfished case; total community biomass in the fished case (blue dashed), all relative to the carrying capacity of the background resource at 10−3 g. In the trait-based model, the asymptotic weights of the 10 species in the model are evenly spread over a log scale, giving the parallel species biomass lines seen. In the multispecies model, the asymptotic weights are species-dependent and hence the species biomass lines are not parallel. Bottom row: relative total abundance of fished and unfished communities. Fishing is with knife-edge selectivity at 1000 g (vertical dashed line).
Mentions: The first example simulates a trophic cascade using all three models (Fig.2). Here all species are fished with a knife-edge selectivity so that only individuals >1000 g are selected (a simplification as selectivity is normally species-specific, possible with mizer). The simulations are run to equilibrium to investigate equilibrium fished and unfished states (details can be found in the vignette). The fishing pressure lowers the relative abundance of fish >1000 g and reduces predation pressure on smaller prey, leading to an increase in their abundance. This in turn increases predation mortality on even smaller sizes, reducing their abundance and so on, causing a size-structured cascade.

Bottom Line: A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size.The models we focus on are designed to capture fish community dynamics useful for assessing the community impacts of fishing.We present mizer, an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing.Multiple fishing gears can be defined and fishing mortality can change through time making it possible to simulate a range of exploitation strategies and management options.mizer implements three versions of the size spectrum modelling framework: the community model, where individuals are only characterized by their size; the trait-based model, where individuals are further characterized by their asymptotic size; and the multispecies model where additional trait differences are resolved.A range of plot, community indicator and summary methods are available to inspect the results of the simulations.

View Article: PubMed Central - PubMed

Affiliation: Maritime Affairs Unit, IPSC, European Commission Joint Research Centre Via Enrico Fermi 2749, I - 21027, Ispra (VA), Italy ; Centre for the Environment Fisheries and Aquaculture Science (CEFAS) Pakefield Road, Lowestoft, NR33 0HT, UK.

ABSTRACT

Size spectrum ecological models are representations of a community of individuals which grow and change trophic level. A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size. The models we focus on are designed to capture fish community dynamics useful for assessing the community impacts of fishing.We present mizer, an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing. Multiple fishing gears can be defined and fishing mortality can change through time making it possible to simulate a range of exploitation strategies and management options.mizer implements three versions of the size spectrum modelling framework: the community model, where individuals are only characterized by their size; the trait-based model, where individuals are further characterized by their asymptotic size; and the multispecies model where additional trait differences are resolved.A range of plot, community indicator and summary methods are available to inspect the results of the simulations.

No MeSH data available.