{"Package":"mizer","Title":"Multi-Species sIZE Spectrum Modelling in R","Type":"Package","Description":"A set of classes and methods to set up and run multi-species, trait\nbased and community size spectrum ecological models, focused on the marine\nenvironment.","Maintainer":"Gustav Delius ","Authors@R":"c(person(\"Gustav\", \"Delius\", email=\"gustav.delius@york.ac.uk\",\nrole=c(\"cre\", \"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-4092-8228\")),\nperson(\"Finlay\", \"Scott\", email=\"drfinlayscott@gmail.com\",\nrole=c(\"aut\", \"cph\")),\nperson(\"Julia\", \"Blanchard\", email=\"julia.blanchard@utas.edu.au\",\nrole=c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-0532-4824\")),\nperson(\"Ken\", \"Andersen\", email=\"kha@aqua.dtu.dk\",\nrole=c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-8478-3430\")),\nperson(\"Richard\", \"Southwell\", email=\"richard.southwell@york.ac.uk\",\nrole=c(\"ctb\", \"cph\")))","Version":"2.0.0","License":"GPL-3","Imports":"assertthat, deSolve, dplyr, ggplot2, grid, methods, plotly,\nplyr, progress, Rcpp, reshape2,","LinkingTo":"Rcpp","Depends":"R (>= 3.1)","Suggests":"testthat (>= 2.1.0), vdiffr, roxygen2, knitr, shinyBS,\nrmarkdown, pkgdown, covr, spelling","Collate":"'MizerParams-class.R' 'MizerSim-class.R' 'species_params.R'\n'setInteraction.R' 'setPredKernel.R' 'setSearchVolume.R'\n'setMaxIntakeRate.R' 'setMetabolicRate.R' 'setExtMort.R'\n'setReproduction.R' 'setResource.R' 'setFishing.R'\n'setInitialValues.R' 'upgrade.R' 'selectivity_funcs.R'\n'pred_kernel_funcs.R' 'resource_dynamics.R' 'project.R'\n'help.R' 'project_methods.R' 'rate_functions.R'\n'summary_methods.R' 'plots.R' 'newMultispeciesParams.R'\n'wrapper_functions.R' 'steady.R' 'extension.R' 'data.R'\n'RcppExports.R' 'deprecated.R'","RoxygenNote":"7.1.0","Encoding":"UTF-8","LazyData":"true","URL":"https://sizespectrum.org/mizer,\nhttps://github.com/sizespectrum/mizer","BugReports":"https://github.com/sizespectrum/mizer/issues","Language":"en-GB","NeedsCompilation":"yes","Packaged":"2020-04-04 09:37:49 UTC; gustav","Author":"Gustav Delius [cre, aut, cph] (),\nFinlay Scott [aut, cph],\nJulia Blanchard [aut, cph] (),\nKen Andersen [aut, cph] (),\nRichard Southwell [ctb, cph]","Repository":"CRAN","Date/Publication":"2020-04-04 10:10:09 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/mizer_2.0.0.tar.gz","jsonAuthors":[{"name":"Gustav Delius","email":"gustav.delius@york.ac.uk","maintainer":true},{"name":"Finlay Scott","email":"drfinlayscott@gmail.com","maintainer":false},{"name":"Julia Blanchard","email":"julia.blanchard@utas.edu.au","maintainer":false},{"name":"Ken Andersen","email":"kha@aqua.dtu.dk","maintainer":false},{"name":"Richard Southwell","email":"richard.southwell@york.ac.uk","maintainer":false}],"readme":"\n\n\n# mizer\n\n[![CRAN\nStatus](https://www.r-pkg.org/badges/version/mizer)](https://cran.r-project.org/package=mizer)\n[![Travis-CI Build\nStatus](https://travis-ci.org/sizespectrum/mizer.svg?branch=master)](https://travis-ci.org/sizespectrum/mizer)\n[![Coverage\nstatus](https://codecov.io/gh/sizespectrum/mizer/branch/master/graph/badge.svg)](https://codecov.io/github/sizespectrum/mizer?branch=master)\n[![CRAN\nDownloads](http://cranlogs.r-pkg.org/badges/grand-total/mizer)](https://cran.r-project.org/package=mizer)\n[![Rdoc](http://www.rdocumentation.org/badges/version/mizer)](http://www.rdocumentation.org/packages/mizer)\n\nMizer is an R package to run multi-species size-spectrum models of fish\ncommunities. The package has been developed to model marine ecosystems\nthat are subject to fishing. However, it may also be appropriate for\nother ecosystems.\n\nThe package contains routines and functions to allow users to set up an\necosystem model, and then project it through time under different\nfishing strategies. Methods are included to explore the results,\nincluding plots and calculation of community indicators such as the\nslope of the size spectrum. Size-based models can be complicated so\nmizer contains many default options that can be easily changed by the\nuser.\n\n\n\n\n\n\n\n\n\n\n\nMizer has been supporting research in marine ecology and fisheries\nscience since 2014 ([see\npublications](https://sizespectrum.org/mizer/articles/publications.html).\nIt is still under active development. The new version 2.0 has increased\nthe user-friendliness and the flexibility of the framework.\nContributions from the user community are very welcome. There is a\nsister package called\n[mizerExperimental](https://sizespectrum.org/mizerExperimental) where\nuser contributions can be checked out and receive feedback from the\ncommunity. Example mizer models can be contributed to\n[mizerExamples](https://sizespectrum.org/mizerExamples).\n\nDoes your project or publication use mizer? If so, we would love to\nknow. You can also join our Google Discussion group here:\n\n\nRecent work on mizer was funded by the European Commission Horizon 2020\nResearch and Innovation Programme under Grant Agreement No 634495 for\nthe project MINOUW () and the Australian\nResearch Council Discovery Project [Rewiring Marine Food\nWebs](http://marinesocioecology.org/rewiring-marine-food-webs/).\n\n## Installation\n\nThe package is on [CRAN](https://cran.r-project.org/package=mizer) and\ntherefore available from R’s built-in package manager.\n\n``` r\n# Install release version from CRAN\ninstall.packages(\"mizer\")\n\n# Alternatively, install development version from GitHub\ndevtools::install_github(\"sizespectrum/mizer\")\n```\n\n## Example\n\nThe following code loads the mizer package, loads some information about\nspecies in the North Sea that comes as an example with the package, sets\nup the parameters for the mizer model, and runs a simulation for 10\nyears.\n\n``` r\nlibrary(mizer)\nparams <- newMultispeciesParams(NS_species_params, inter)\nsim <- project(params, t_max = 10, effort = 0)\n```\n\nThe results of the simulation can then be analysed, for example via\nplots:\n\n``` r\nplot(sim)\n```\n\n![](man/figures/unnamed-chunk-4-1.png)\n\nSee the accompanying [Get\nstarted](https://sizespectrum.org/mizer/articles/mizer.html) page for\nmore details on how the package works, including detailed examples.","jobInfo":{"package":"mizer","version":"2.0.0","parsingStatus":"success","parserVersion":1,"parsedAt":"2020-05-05T22:29:56+0000"}}

Description

Usage

Arguments