diff --git a/joss.07475/10.21105.joss.07475.crossref.xml b/joss.07475/10.21105.joss.07475.crossref.xml new file mode 100644 index 000000000..3a264e4e8 --- /dev/null +++ b/joss.07475/10.21105.joss.07475.crossref.xml @@ -0,0 +1,247 @@ + + + + 20250121194633-9c07f7b87776b5574e6bf3a7d38fe4331d98445b + 20250121194633 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 01 + 2025 + + + 10 + + 105 + + + + dia: An R package for the National Oceanic and Atmospheric Administration dam impact analysis + + + + Daniel S. + Stich + + Biology Department and Biological Field Station, State University of New York at Oneonta, NY 13280 USA + + https://orcid.org/0000-0002-8946-1115 + + + Julie L. + Nieland + + National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, Woods Hole, MA 02543 USA + + + + Timothy F. + Sheehan + + National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, Woods Hole, MA 02543 USA + + https://orcid.org/0000-0002-9689-1180 + + + + 01 + 21 + 2025 + + + 7475 + + + 10.21105/joss.07475 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.14708353 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/7475 + + + + 10.21105/joss.07475 + https://joss.theoj.org/papers/10.21105/joss.07475 + + + https://joss.theoj.org/papers/10.21105/joss.07475.pdf + + + + + + Dam impact analysis model for Atlantic salmon in the Penobscot River, Maine + Nieland + Northeast Fisheries Science Center Reference Document 13-09 + 2013 + Nieland, J. L., Sheehan, T. F., Saunders, R., Murphy, J. S., Trinko Lake, T., & Stevens, J. R. (2013). Dam impact analysis model for Atlantic salmon in the Penobscot River, Maine. In Northeast Fisheries Science Center Reference Document 13-09. National Oceanic; Atmospheric Administration. https://repository.library.noaa.gov/view/noaa/4559 + + + National Marine Fisheries Service Endangered Species Act Biological Opinion Amendment of License for the Mattaceunk Project f/NER/2013/9640 + National Marine Fisheries Service + 2013 + National Marine Fisheries Service. (2013). National Marine Fisheries Service Endangered Species Act Biological Opinion Amendment of License for the Mattaceunk Project f/NER/2013/9640. National Oceanic and Atmospheric Administration. https://repository.library.noaa.gov/view/noaa/55737 + + + Quantifying the effects of dams on Atlantic salmon in the Penobscot River watershed, with a focus on Weldon Dam + Nieland + Northeast Fisheries Science Center Reference Document 19-16 + 10.25923/v67x-kk62 + 2020 + Nieland, J. L., & Sheehan, T. F. (2020). Quantifying the effects of dams on Atlantic salmon in the Penobscot River watershed, with a focus on Weldon Dam. In Northeast Fisheries Science Center Reference Document 19-16. National Oceanic and Atmospheric Administration. https://doi.org/10.25923/v67x-kk62 + + + Dramatic declines in North Atlantic diadromous fishes + Limburg + BioScience + 11 + 59 + 10.1525/bio.2009.59.11.7 + 0006-3568 + 2009 + Limburg, K. E., & Waldman, J. R. (2009). Dramatic declines in North Atlantic diadromous fishes. BioScience, 59(11), 955–965. https://doi.org/10.1525/bio.2009.59.11.7 + + + What have we lost? Modeling dam impacts on American shad populations through their native range + Zydlewski + Frontiers in Marine Science + 8 + 10.3389/fmars.2021.734213 + 2296-7745 + 2021 + Zydlewski, J., Stich, D. S., Roy, S., Bailey, M., Sheehan, T., & Sprankle, K. (2021). What have we lost? Modeling dam impacts on American shad populations through their native range. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.734213 + + + dia: Atlantic salmon dam impact analysis (DIA) for R + Stich + GitHub repository + 10.5281/zenodo.13376045 + 2021 + Stich, D. S., Nieland, J. L., & Sheehan, T. F. (2021). dia: Atlantic salmon dam impact analysis (DIA) for R. In GitHub repository. GitHub. https://doi.org/10.5281/zenodo.13376045 + + + Assessing demographic effects of dams on diadromous fish: a case study for Atlantic salmon in the Penobscot River, Maine + Nieland + International Council for the Exploration of the Sea Journal of Marine Science + 8 + 72 + 10.1093/icesjms/fsv083 + 1054-3139 + 2015 + Nieland, J. L., Sheehan, T. F., & Saunders, R. (2015). Assessing demographic effects of dams on diadromous fish: a case study for Atlantic salmon in the Penobscot River, Maine. International Council for the Exploration of the Sea Journal of Marine Science, 72(8), 2423–2437. https://doi.org/10.1093/icesjms/fsv083 + + + A dam passage performance standard model for American shad + Stich + Canadian Journal of Fisheries and Aquatic Sciences + 5 + 76 + 10.1139/cjfas-2018-0008 + 2019 + Stich, D. S., Sheehan, T. F., & Zydlewski, J. D. (2019). A dam passage performance standard model for American shad. Canadian Journal of Fisheries and Aquatic Sciences, 76(5), 762–779. https://doi.org/10.1139/cjfas-2018-0008 + + + Does what goes up also come down? Using a recruitment model to balance alewife nutrient import and export + Barber + Marine and Coastal Fisheries + 2 + 10 + 10.1002/mcf2.10021 + 2018 + Barber, B. L., Gibson, A. J., O’Malley, A. J., & Zydlewski, J. (2018). Does what goes up also come down? Using a recruitment model to balance alewife nutrient import and export. Marine and Coastal Fisheries, 10(2), 236–254. https://doi.org/10.1002/mcf2.10021 + + + shiny: Web application framework for R + Chang + 10.32614/CRAN.package.shiny + 2024 + Chang, W., Cheng, J., Allaire, J., Sievert, C., Schloerke, B., Xie, Y., Allen, J., McPherson, J., Dipert, A., & Borges, B. (2024). shiny: Web application framework for R. https://doi.org/10.32614/CRAN.package.shiny + + + R: A language and environment for statistical computing + R Core Team + 2024 + R Core Team. (2024). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org/ + + + ggplot2: Elegant graphics for data analysis + Wickham + 10.32614/CRAN.package.ggplot2 + 978-3-319-24277-4 + 2016 + Wickham, H. (2016). ggplot2: Elegant graphics for data analysis. Springer-Verlag New York. https://doi.org/10.32614/CRAN.package.ggplot2 + + + Welcome to the tidyverse + Wickham + Journal of Open Source Software + 43 + 4 + 10.21105/joss.01686 + 2019 + Wickham, H., Averick, M., Bryan, J., Chang, W., D’Agostino McGowan, L., Françoi, R., Grolemun, G., Haye, A., Henr, L., Heste, J., Kuh, M., Lin Pederse, T., Mille, E., Bach, S. M., Müll, K., Jeroen Oo, D., Seid, D. P., V., … Yutani, H. (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686. https://doi.org/10.21105/joss.01686 + + + FLR: An open-source framework for the evaluation and development of management strategies + Kell + ICES Journal of Marine Science + 64 + 10.1093/icesjms/fsm012 + 2007 + Kell, L. T., Mosqueira, I., Grosjean, P., Fromentin, J.-M., Garcia, D., Hillary, R., Jardim, E., Mardle, S., Pastoors, M. A., Poos, J. J., Scott, F., & Scott, R. D. (2007). FLR: An open-source framework for the evaluation and development of management strategies. ICES Journal of Marine Science, 64, 640–646. https://doi.org/10.1093/icesjms/fsm012 + + + FSA: Fisheries stock analysis + Ogle + 10.5281/zenodo.597719 + 2022 + Ogle, D. H., Doll, J. C., Wheeler, P., & Dinno, A. (2022). FSA: Fisheries stock analysis. https://doi.org/10.5281/zenodo.597719 + + + fishStan: Hierarchical Bayesian models for fisheries + Erickson + Journal of Open Source Software + 71 + 7 + 10.21105/joss.03444 + 2022 + Erickson, R. A., Stich, D. S., & Hebert, J. L. (2022). fishStan: Hierarchical Bayesian models for fisheries. Journal of Open Source Software, 7(71), 3444. https://doi.org/10.21105/joss.03444 + + + + + + diff --git a/joss.07475/10.21105.joss.07475.pdf b/joss.07475/10.21105.joss.07475.pdf new file mode 100644 index 000000000..d1bebb52c Binary files /dev/null and b/joss.07475/10.21105.joss.07475.pdf differ diff --git a/joss.07475/paper.jats/10.21105.joss.07475.jats b/joss.07475/paper.jats/10.21105.joss.07475.jats new file mode 100644 index 000000000..73b76e2c1 --- /dev/null +++ b/joss.07475/paper.jats/10.21105.joss.07475.jats @@ -0,0 +1,555 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +7475 +10.21105/joss.07475 + +dia: An R package for the National Oceanic and +Atmospheric Administration dam impact analysis + + + +https://orcid.org/0000-0002-8946-1115 + +Stich +Daniel S. + + +* + + + +Nieland +Julie L. + + + + +https://orcid.org/0000-0002-9689-1180 + +Sheehan +Timothy F. + + + + + +Biology Department and Biological Field Station, State +University of New York at Oneonta, NY 13280 USA + + + + +National Oceanic and Atmospheric Administration, National +Marine Fisheries Service, Northeast Fisheries Science Center, Woods +Hole, MA 02543 USA + + + + +* E-mail: + + +22 +10 +2024 + +10 +105 +7475 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2025 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +R +fisheries +dams +population dynamics +life history models + + + + + + Summary +

Populations of anadromous (sea-run) fishes such as Atlantic salmon + Salmo salar have experienced severe global declines + as a result of pollution, overfishing, and construction of dams + (Limburg + & Waldman, 2009). Life-history-based simulation models are + commonly used for planning and implementing fisheries recovery + activities for many diadromous species + (Barber + et al., 2018; e.g., + Nieland + et al., 2013; + Stich + et al., 2019; + Zydlewski + et al., 2021). Before open-source tools became prevalent, many + institutionalized decision-support tools utilizing such models relied + on closed-source or paid software. For example, the National Oceanic + and Atmospheric Administration (NOAA) Dam Impact Analysis (DIA) was + originally created as a stochastic life cycle model for Atlantic + salmon in the @RISK add-in within Microsoft + Excel + (Nieland + et al., 2013). This tool differs from those hosted in similar R + packages for non-salmonid species (e.g. + Stich + et al., 2019; + Zydlewski + et al., 2021) in that it incorporates homing behavior + (probability of adults returning to natal streams or straying to + others) and integrates results of physical modeling to inform + population dynamics + (Nieland + et al., 2013; + Nieland + & Sheehan, 2020). This class of tools, in general, provides + advantages for decision making related to anadromous species because + it allows integration of geographically and temporally explicit stock + dynamics (e.g., influences of dams) that are not readily implemented + in classical fisheries stock assessment tools such as those available + in existing R packages + (Erickson + et al., 2022; e.g. + Kell et + al., 2007; + Ogle et + al., 2022). We created the dia package + (Stich et + al., 2021) for the R programming language + (R Core + Team, 2024) as a freely accessible, open-source implementation + of these tools that will promote transparency in planning and decision + making.

+ + + Statement of need +

dia is an R-based implementation of a + previously closed-source life cycle model of Atlantic salmon + population dynamics that is used to understand population response to + natural and anthropogenic influences in freshwater and marine + environments. It was developed to assess the sensitivity of + restoration outcomes to uncertainty in life-history inputs alongside + the impacts of dams and restoration activities. The DIA model uses + empirical life-history estimates (e.g., survival), predictive flow and + resulting flow-specific dam survival modeling, and other empirical + data in freshwater and marine environments to simulate consecutive + generations of Atlantic salmon in the Penobscot River (Maine, USA) + under varying environmental conditions or management decisions. As the + largest remaining population of this critically endangered species in + the USA, the population is intensively managed. Management decisions + include fish passage rates at dams, fishery harvest rates, and numbers + and locations for hatchery stocking of fish + (Nieland + et al., 2013). Since development, it has been used for + mechanistic exploration of key life-history uncertainties within the + context of species recovery + (Nieland + et al., 2015) and to support decision-making at federally + regulated hydropower dams on the Penobscot River (e.g., + National + Marine Fisheries Service, 2013; + Nieland + & Sheehan, 2020).

+

We created dia for use by fisheries + researchers, managers, and practitioners interested in understanding + population dynamics of intensively managed endangered Atlantic salmon + in the USA. The R package maintains the core routines from the + original closed-source version of the model by replicating + spreadsheet-based calculations, and incorporates original data and + parameter sets as built-in objects that serve as default values for + arguments of the primary user-facing functions. However, it also + allows exploration of uncertainty associated with life-history + parameters and investigation of future restoration scenarios through a + variety of user-facing options.

+

The two primary user-facing functions within the + dia package are + run_dia() and + run_dia_shiny(), which provide redundant + interfaces for using Dam Impact Analysis (DIA) models in different + ways. The run_dia() function provides an + extensible interface to DIA. It can be used for long-run simulation or + decision-optimization studies. It allows incorporation of + user-specified data sets such as flow-correlated survival + probabilities at dams and in free-flowing river reaches, marine + survival and other life-history inputs, or fish-stocking data. The + run_dia_shiny() function deploys a graphical + user interface using the shiny package + (Chang + et al., 2024) that is less extensible but more easily used by + fishery managers and practitioners who may be less familiar with + programming and it also includes exportable results from simulation + models including .csv or other flat-file + formats and default plots through the ggplot2 R + package [Wickham + (2016); + Wickham et al. + (2019); + Figure 1]. Both can be deployed on networked servers as other R or + shiny applications to improve accessibility or + facilitate use on high performance computers for large simulations. + The GitHub repository + (Stich et + al., 2021) includes additional instructions for installation + and a variety of potential uses of run_dia() + and run_dia_shiny(), with shorter examples + included in the package help files. While implementation is currently + limited to the Penobscot River as a priority conservation water in the + USA, the package serves as one example to help generalize these + modeling approaches to Atlantic salmon and other sea-run fish in + watersheds globally. Specifically, while many of the built-in datasets + and helper functions in dia are generalized or + could be used to simulate life-history information for other systems + and species, generalizing the geographic component (i.e., structural + river system) represents an important priority for future + development.

+ +

Example graphical outputs using the default argument + values + (Nieland + & Sheehan, 2020) for run_dia() to + run 10,000 simulations, showing (a) the number of two-sea-winter + adult females of hatchery or wild origin returning to the watershed + during each generation to spawn, and (b) the number of those fish + returning to each production unit within the watershed after 15 + generations.

+ + + + + Acknowledgements +

We acknowledge contributions from Rory Saunders, Tara Trinko-Lake, + Jeffrey Murphy, and Justin Stevens in the original development of the + NOAA Dam Impact Analysis model. This work was funded by the NOAA + National Marine Fisheries Service Northeast Fisheries Science Center + (award number NMFS-NEFSC-199 MOU), with additional support from the + SUNY Oneonta Biological Field Station. We thank the reviewers for + helpful guidance and comments that greatly improved the quality of + this paper and the open-source software package. Any use of trade, + firm, or product names is for descriptive purposes only and does not + imply endorsement by the U.S. Government.

+ + + + + + + + + NielandJ. L. + SheehanT. F. + SaundersR. + MurphyJ. S. + Trinko LakeT. + StevensJ. R. + + Dam impact analysis model for Atlantic salmon in the Penobscot River, Maine + Northeast Fisheries Science Center Reference Document 13-09 + National Oceanic; Atmospheric Administration + 201306 + https://repository.library.noaa.gov/view/noaa/4559 + + + + + + National Marine Fisheries Service + + National Marine Fisheries Service Endangered Species Act Biological Opinion Amendment of License for the Mattaceunk Project f/NER/2013/9640 + National Oceanic and Atmospheric Administration + 2013 + https://repository.library.noaa.gov/view/noaa/55737 + + + + + + NielandJ. L. + SheehanT. F. + + Quantifying the effects of dams on Atlantic salmon in the Penobscot River watershed, with a focus on Weldon Dam + Northeast Fisheries Science Center Reference Document 19-16 + National Oceanic and Atmospheric Administration + 2020 + https://repository.library.noaa.gov/view/noaa/23714 + 10.25923/v67x-kk62 + + + + + + LimburgK. E. + WaldmanJ. R. + + Dramatic declines in North Atlantic diadromous fishes + BioScience + 200912 + 59 + 11 + 0006-3568 + https://doi.org/10.1525/bio.2009.59.11.7 + 10.1525/bio.2009.59.11.7 + 955 + 965 + + + + + + ZydlewskiJ. + StichD. S. + RoyS. + BaileyM. + SheehanT. + SprankleK. + + What have we lost? Modeling dam impacts on American shad populations through their native range + Frontiers in Marine Science + 2021 + 8 + 2296-7745 + https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2021.734213 + 10.3389/fmars.2021.734213 + + + + + + StichD. S. + NielandJ. L. + SheehanT. F. + + dia: Atlantic salmon dam impact analysis (DIA) for R + GitHub repository + GitHub + 2021 + https://github.com/danStich/dia + 10.5281/zenodo.13376045 + + + + + + NielandJ. L. + SheehanT. F. + SaundersR. + + Assessing demographic effects of dams on diadromous fish: a case study for Atlantic salmon in the Penobscot River, Maine + International Council for the Exploration of the Sea Journal of Marine Science + 201505 + 72 + 8 + 1054-3139 + 10.1093/icesjms/fsv083 + 10.1093/icesjms/fsv083 + 2423 + 2437 + + + + + + StichD. S. + SheehanT. F. + ZydlewskiJ. D. + + A dam passage performance standard model for American shad + Canadian Journal of Fisheries and Aquatic Sciences + 2019 + 76 + 5 + https://doi.org/10.1139/cjfas-2018-0008 + 10.1139/cjfas-2018-0008 + 762 + 779 + + + + + + BarberB. L. + GibsonA. J. + O’MalleyA. J. + ZydlewskiJ. + + Does what goes up also come down? Using a recruitment model to balance alewife nutrient import and export + Marine and Coastal Fisheries + 2018 + 10 + 2 + https://afspubs.onlinelibrary.wiley.com/doi/abs/10.1002/mcf2.10021 + 10.1002/mcf2.10021 + 236 + 254 + + + + + + ChangWinston + ChengJoe + AllaireJJ + SievertCarson + SchloerkeBarret + XieYihui + AllenJeff + McPhersonJonathan + DipertAlan + BorgesBarbara + + shiny: Web application framework for R + 2024 + https://CRAN.R-project.org/package=shiny + 10.32614/CRAN.package.shiny + + + + + + R Core Team + + R: A language and environment for statistical computing + R Foundation for Statistical Computing + Vienna, Austria + 2024 + https://www.R-project.org/ + + + + + + WickhamH. + + ggplot2: Elegant graphics for data analysis + Springer-Verlag New York + 2016 + 978-3-319-24277-4 + https://ggplot2.tidyverse.org + 10.32614/CRAN.package.ggplot2 + + + + + + WickhamH. + AverickM. + BryanJ. + ChangW. + D’Agostino McGowanL. + FrançoiR. + GrolemunG. + HayeA. + HenrL. + HesteJ. + KuhM. + Lin PederseT. + MilleE. + BachStephan Milton + MüllKirill + Jeroen Oo + D.Robins + SeidD. P. + V.Spi + TakahasK. + VaughD. + WilC. + KaraW + YutaniH. + + Welcome to the tidyverse + Journal of Open Source Software + 2019 + 4 + 43 + 10.21105/joss.01686 + 1686 + + + + + + + KellL. T. + MosqueiraI. + GrosjeanP. + FromentinJ-M. + GarciaD. + HillaryR. + JardimE. + MardleS. + PastoorsM. A. + PoosJ. J. + ScottF. + ScottR. D. + + FLR: An open-source framework for the evaluation and development of management strategies + ICES Journal of Marine Science + 2007 + 64 + 10.1093/icesjms/fsm012 + 640 + 646 + + + + + + OgleDerek H. + DollJason C. + WheelerPowell + DinnoAlexis + + FSA: Fisheries stock analysis + 2022 + https://github.com/fishR-Core-Team/FSA + 10.5281/zenodo.597719 + + + + + + EricksonRichard A. + StichDaniel S. + HebertJillian L. + + fishStan: Hierarchical Bayesian models for fisheries + Journal of Open Source Software + The Open Journal + 2022 + 7 + 71 + https://doi.org/10.21105/joss.03444 + 10.21105/joss.03444 + 3444 + + + + + +
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