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23.155Z","avatar_url":"https://github.com/sizespectrum.png","language":"R","category":"Biosphere","sub_category":"Marine Life and Fishery","monthly_downloads":386,"total_dependent_repos":6,"total_dependent_packages":0,"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/\"\n)\n```\n\n\n\u003cdiv style=\"text-align: center;\"\u003e\n\u003cimg src=\"man/figures/mizer.png\" style='height: 50%; width: 50%; object-fit: contain' title=\"mizer logo created by Kira Askaroff (www.kiraaskaroff.com)\"/\u003e\n\n[![CRAN Status](https://www.r-pkg.org/badges/version-ago/mizer)](https://cran.r-project.org/package=mizer)\n[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/grand-total/mizer)](https://cran.r-project.org/package=mizer)\n[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/mizer)](https://cran.r-project.org/package=mizer)\n[![Coverage status](https://codecov.io/gh/sizespectrum/mizer/branch/master/graph/badge.svg)](https://app.codecov.io/github/sizespectrum/mizer?branch=master)\n\u003c/div\u003e\n\nMizer is an R package to run \n[dynamic multi-species size-spectrum models](#dynamic-multi-species-size-spectrum-models) \nof fish communities. The package has been developed to model marine ecosystems\nthat are subject to fishing. However, it may also be appropriate for other aquatic\necosystems. By providing a framework for multi-species fisheries modelling as an R package, mizer enhances the accessibility, usability, and reproducibility of models, and thus aims to facilitate collaboration and innovation. \n\nThe package contains functions that allow you to set up an ecosystem \nmodel and then project it through time under different fishing strategies.\nMethods are included to explore the results, including plots and calculations of\ncommunity indicators such as the slope of the size spectrum. Size-based models\ncan be complicated, so mizer contains many default options that you can however\nchange when needed.\n\n\u003ca href=\"https://sizespectrum.org/mizer/reference/figures/mizer_workflow.png\" target=\"_blank\"\u003e\n\u003cimg src=\"man/figures/mizer_workflow.png\" style='height: 100%; width: 100%; object-fit: contain' title=\"mizer workflow\"/\u003e\n\u003c/a\u003e\n\n\u003c!-- Mizer can also be used to create web apps that allow users to explore models --\u003e\n\u003c!-- without the need to install R. An [example of such an --\u003e\n\u003c!-- app](https://mizer.shinyapps.io/selectivity/) investigates the effect of --\u003e\n\u003c!-- switching to a gear with a T90 extension net to reduce the catches of undersize --\u003e\n\u003c!-- hake and red mullet --\u003e\n\nMizer has been supporting research in marine ecology and fisheries science \nsince 2014 \n([see publications](https://sizespectrum.org/mizer/articles/publications.html)). \nMizer is still under active\ndevelopment. Version 2.0 has increased the user-friendliness and the\nflexibility of the framework. Contributions from the user community are very\nwelcome. There is a sister package called \n[mizerExperimental](https://sizespectrum.org/mizerExperimental/) where user\ncontributions can be checked out and receive feedback from the community. \nExample mizer models can be contributed to \n[mizerExamples](https://sizespectrum.org/mizerExamples/). Follow us on\n[twitter](https://x.com/mizer_model) and read our \n[blog](https://blog.mizer.sizespectrum.org) to stay up-to-date with new\ndevelopments. \nDoes your project or publication use mizer? If so, we would love to know. \n\nRecent work on mizer was funded by the European\nCommission Horizon 2020 Research and Innovation Programme under Grant Agreement\nNo 634495 for the project MINOUW (http://minouw-project.eu/) and the Australian\nResearch Council Discovery Project [Rewiring Marine Food Webs](https://marinesocioecology.org/projects/rewiring-marine-food-webs-predicting-consequences-of-species-distribution-shifts-on-marine-communities/).\n\n\n## Installation\n\nThe package is on [CRAN](https://cran.r-project.org/package=mizer) and therefore\navailable from R's built-in package manager.\n```{r, eval = FALSE}\n# Install latest released version from CRAN\ninstall.packages(\"mizer\")\n\n# Alternatively, install the development version from GitHub\nremotes::install_github(\"sizespectrum/mizer\")\n```\n\n## Example\nThe following code loads the mizer package, loads some information about species\nin the North Sea that comes as an example with the package, sets up the \nparameters for the mizer model, and runs a simulation for 10 years.\n```{r, message = FALSE}\nlibrary(mizer)\nparams \u003c- newMultispeciesParams(NS_species_params, NS_interaction)\nsim \u003c- project(params, t_max = 10, effort = 0)\n```\nThe results of the simulation can then be analysed, for example via plots:\n```{r}\nplot(sim)\n```\n\nSee the accompanying\n[Get started](https://sizespectrum.org/mizer/articles/mizer.html) page\nfor more details on how the package works, including detailed examples.\n\n\u003ca href=\"https://sizespectrum.org/mizer/reference/figures/size_spectrum.png\" target=\"_blank\"\u003e\n\u003cimg src=\"man/figures/size.png\" style='height: 95%; width: 95%; object-fit: contain' title=\"Size spectrum dynamics\"/\u003e\n\u003c/a\u003e\n\n## Dynamic multi-species size-spectrum model\n\nSize-based multi-species models are important for fisheries science because they provide a more realistic and accurate representation of the dynamics of fish populations and the ecosystems in which they live. In contrast to traditional single-species models, which consider a single fish stock as an isolated unit, size-based multi-species models account for the fact that fish populations are part of a larger ecosystem and interact with other species through predation, competition, and other ecological processes.\n\nOne of the key advantages of size-based multi-species models is that they provide a more comprehensive understanding of the impacts of fishing on fish populations and ecosystems. By considering the size distribution of different fish species, these models can capture the effects of fishing on both target and non-target species, and on different life stages of a species. This is particularly important for species that are caught as bycatch or that are indirectly affected by fishing through changes in their food web.\n\nAnother advantage of size-based multi-species models is that they can be used to investigate the effects of environmental changes and other perturbations on fish populations and ecosystems. For example, these models can be used to explore the impacts of climate change on the distribution and abundance of fish populations, or the effects of habitat loss or pollution on fish communities.\nBecause mizer is a mechanistic model, it can deduce the\ncomplex population-level changes that we are interested in from the simpler\nchanges in the physiological rates and feeding interactions of individual fish\nspecies.\n\nOverall, size-based multi-species models provide a more comprehensive and realistic framework for understanding the dynamics of fish populations and ecosystems, and for developing effective fisheries management strategies that account for the complex interactions among species and their environment.\n\n\u003cimg src=\"man/figures/size_selective_fishing.png\" style='height: 95%; width: 95%; object-fit: contain' title=\"Effect of size-selective fishing\"/\u003e\n\nA mizer model captures the interactions between species. The growth\nrates of fish are determined by the availability of prey and the death rates\nare influenced by the abundance of predators, as well as fishing. The model\nstarts with the individual-level physiological rates for each species, as well\nas the predation preferences, and deduces the population-level dynamics from\nthese. Thus quantities like fish diets and fisheries yields emerge dynamically\nand can be projected into the future.\n\nBecause a mizer model tracks the size of individuals as they grow up over\nseveral orders of magnitude from their egg size to their maximum size, it\ncorrectly tracks the ontogenetic diet shifts. An individual typically moves \nthrough several trophic levels during its life time. This is often not \ncorrectly captured in other multi-species models.\n\nA mizer model can be set up with only a small amount of information\nbecause it uses allometric scaling relations and size-based feeding rules to\nchoose sensible defaults for unknown parameters.\n\nSetting up a new multi-species mizer model is a two-step process, similar to\nwhat may be familiar from Ecopath with Ecosim: First one calibrates the model\nto describe a steady state that is in agreement with current observations\n(as in Ecopath), then one chooses the additional parameters that determine the\ndynamics away from the steady state (as in Ecosim). This model can then be\nused to investigate future effects of changes in fishing policy or of \nenvironmental stressors.\n\n\n## A strong theoretical basis\n\nOne big advantage of a mizer model is that it is based on a strong mathematical\nfoundation. This allows a degree of a priori understanding of the behaviour of\nthe model that is absent in many other multi-species models. This theoretical\nfoundation is well presented in the book \"Fish Ecology, Evolution, and\nExploitation\" by Ken Andersen.\n\nIt is interesting to think of the marine ecosystem as a transport system that\nmoves biomass from the size of primary producers (mostly unicellular\nplankton) up to the sizes of fish that humans like to consume.\nEach fish that grows up from egg size to maturity by eating smaller\nindividuals is like a car on this biomass highway. The yield of our\nfisheries depend on this traffic flowing smoothly and without traffic jams.\n\nAn analogy with road traffic may be helpful:\n\n\u003ca href=\"https://sizespectrum.org/mizer/reference/figures/traffic_jam.png\" target=\"_blank\"\u003e\n\u003cimg src=\"man/figures/traffic.png\" style='height: 95%; width: 95%; object-fit: contain' title=\"Fish growth traffic jam\"/\u003e\n\u003c/a\u003e\n\nIn road traffic, if traffic density gets too high in a section of the highway,\ndrivers slow down, which leads to a pile-up producing even higher traffic\ndensity, leading to further slow-down in a potentially vicious cycle known as a\ntraffic jam. Traffic management that ignores how the traffic density affects\ntraffic speed fails. Luckily our mathematical understanding of transport\nequations has made practical contributions to managing traffic in ways that\nproduce smoother traffic flow and hence higher throughput.\n\nMizer implements the transport equations for marine ecosystems. The\npotential for traffic jams is the same: if for example there is a high density\nof predators of a particular size, which all have preference for prey of a\nparticular smaller size, then due to competition for that prey the growth of\nthose predators slows down, leading to a pile-up which leads to further \ndepletion of prey, leading to further slow-down, in a potentially vicious cycle.\n\nLuckily, the natural ecosystem has evolved to facilitate very smooth traffic\non this biomass highway, with resultant high productivity. This state is\ncharacterised by an approximate power-law shape of the biomass size spectrum.\nThe purpose of mizer is to allow us to understand how various stressors, like\nfishing or climate change, affect the size spectrum and hence the flow of biomass\nand the productivity and resilience of the marine ecosystem. Mizer allows us to\ninvestigate how size-based fisheries management strategies can be used to keep\nthe ecosystem close to its natural productive state.\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["mizer"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/20806","html_url":"https://ost.ecosyste.ms/projects/20806"}