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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: 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.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.


Sketch of the main processes involved in the bioenergetic budget of an individual of species i and parameters involved in each process (see the package vignette and Tables S1 and S2). Suitable prey are selected according to the species preference θij and the size preference parameters. Suitable prey are encountered and assimilated, and used for respiratory costs. The remaining energy is split between growth and reproduction depending on the individual.
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fig01: Sketch of the main processes involved in the bioenergetic budget of an individual of species i and parameters involved in each process (see the package vignette and Tables S1 and S2). Suitable prey are selected according to the species preference θij and the size preference parameters. Suitable prey are encountered and assimilated, and used for respiratory costs. The remaining energy is split between growth and reproduction depending on the individual.

Mentions: Size spectrum models are a subset of physiologically structured models (De Roos & Persson 2001) as growth and maturation are food-dependent, and processes are formulated at the individual level (Fig.1). All parameters in size spectrum models are related to individual size (weight), making it possible to formulate the model with a few general parameters. The model framework builds on two central assumptions. The first is that an individual can be characterized by its weight w and its species number i only. The model calculates the size and trait spectrum Ni(w) which is the density of individuals at a particular size. Scaling from individual-level processes of growth and mortality to the size spectrum is achieved by means of the McKendrick–von Foerster equation as follows:


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

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

Sketch of the main processes involved in the bioenergetic budget of an individual of species i and parameters involved in each process (see the package vignette and Tables S1 and S2). Suitable prey are selected according to the species preference θij and the size preference parameters. Suitable prey are encountered and assimilated, and used for respiratory costs. The remaining energy is split between growth and reproduction depending on the individual.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig01: Sketch of the main processes involved in the bioenergetic budget of an individual of species i and parameters involved in each process (see the package vignette and Tables S1 and S2). Suitable prey are selected according to the species preference θij and the size preference parameters. Suitable prey are encountered and assimilated, and used for respiratory costs. The remaining energy is split between growth and reproduction depending on the individual.
Mentions: Size spectrum models are a subset of physiologically structured models (De Roos & Persson 2001) as growth and maturation are food-dependent, and processes are formulated at the individual level (Fig.1). All parameters in size spectrum models are related to individual size (weight), making it possible to formulate the model with a few general parameters. The model framework builds on two central assumptions. The first is that an individual can be characterized by its weight w and its species number i only. The model calculates the size and trait spectrum Ni(w) which is the density of individuals at a particular size. Scaling from individual-level processes of growth and mortality to the size spectrum is achieved by means of the McKendrick–von Foerster equation as follows:

Bottom Line: 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.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.