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and Environmental Modeling","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"\n# Rpath \u003cimg src=\"man/figures/logo.png\" align=\"right\" width=\"120\" /\u003e \n\n\n\u003c!-- badges: start --\u003e\n[![gitleaks](https://github.com/NOAA-EDAB/Rpath/actions/workflows/secretScan.yml/badge.svg)](https://github.com/NOAA-EDAB/Rpath/actions/workflows/secretScan.yml)\n[![pkgdown](https://github.com/NOAA-EDAB/Rpath/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/NOAA-EDAB/Rpath/actions/workflows/pkgdown.yaml)\n[![R-CMD-check](https://github.com/NOAA-EDAB/Rpath/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NOAA-EDAB/Rpath/actions/workflows/R-CMD-check.yaml)\n\u003c!-- [![tests](https://github.com/NOAA-EDAB/Rpath/actions/workflows/tests.yml/badge.svg)](https://github.com/NOAA-EDAB/Rpath/actions/workflows/tests.yml) --\u003e\n\u003c!-- badges: end --\u003e\n\nPackage _Rpath_ is an R/Rcpp implementation of the Ecopath (mass-balance) and Ecosim (dynamic simulation) methods for the modeling of food webs. The _Rpath_ package includes sensitivity analysis tools, bioenergetics forcing, and the ability to\ndevelop adaptive dynamic simulations with annual adjustment/feedback for use\nin management strategy evaluations and similar analyses.\n\n## Installation\n\nTo install the package and build all of the vignettes locally\n\n```\nremotes::install_github(\"noaa-edab/Rpath\",build_vignettes=TRUE)\n```\n\nIf you experience issues installing the package using `remotes` or don't need the vignettes locally then please use this alternative\n\n```\npak::pak(\"noaa-edab/Rpath\")\n```\n\n# More details\n\nFor more background, please see:\n\n### For Rpath description and methods:\nLucey, S. M.,  Gaichas, S. K., \u0026 Aydin, K. Y. (2020). \nConducting reproducible ecosystem modeling using the open source mass balance model Rpath. \nEcological Modelling 427(2020), 109057. \nhttps://doi.org/10.1016/j.ecolmodel.2020.109057.\n\n### For use of Rpath for management strategy evaluations:\nLucey, S. M., Aydin, K. Y., Gaichas, S. K., Cadrin, S. X., Fay, G.,  Fogarty, M. J., \u0026 Punt, A. (2021).\nEvaluating fishery management strategies using an ecosystem model as an operating model.\nFisheries Research 234(2021), 105780.\nhttps://doi.org/10.1016/j.fishres.2020.105780.\n\n### For incorporation of bioenergetics into Rpath simulations:\nHeinichen, M., McManus, M. C., Lucey, S. M., Aydin, K. Y., Humphries, A., Innes-Gold, A., \u0026 Collie, J. (2022).\nIncorporating temperature-dependent fish bioenergetics into a Narragansett Bay food web model. \nEcological Modelling 466(2022), 109911.\nhttps://doi.org/10.1016/j.ecolmodel.2022.109911.\n\n### For use of Rpath sensitivity tools:\nWhitehouse, G.A., \u0026 Aydin, K.Y. (2020).\nAssessing the sensitivity of three Alaska marine food webs to perturbations: an example of Ecosim simulations using Rpath. \nEcological Modelling 429(2020), 109074. \nhttps://doi.org/10.1016/j.ecolmodel.2020.109074.\n\n### For original development of Ecopath and Ecosim:\nPolovina, J. J. (1984). \nModel of a coral reef ecosystem.\nCoral Reefs 3(1), 1–11. \nhttps://doi.org/10.1007/BF00306135.\n\nChristensen, V., \u0026 Walters, C. J. (2004). \nEcopath with Ecosim: Methods, capabilities and limitations. \nEcological Modelling 172(2), 109–139. \nhttps://doi.org/10.1016/j.ecolmodel.2003.09.003.\n\nWalters, C., Pauly, D., Christensen, V., \u0026 Kitchell, J. F. (2000). \nRepresenting Density Dependent Consequences of Life History Strategies in Aquatic Ecosystems: EcoSim II. \nEcosystems 3(1), 70–83. \nhttps://doi.org/10.1007/s100210000011.\n\n# Disclaimer\n\n*This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. 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