references.bib

@article{alexander2019bridging,
  title={Bridging Indigenous and science-based knowledge in coastal and marine research, monitoring, and management in Canada},
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  journal={Environmental Evidence},
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  number={1},
  pages={1--24},
  year={2019}
}

@article{bear2007comparative,
  title={Comparative thermal requirements for westslope cutthroat trout and rainbow trout: Implications for species interactions and development of thermal protection standards},
  author={Bear, E. A. and McMahon, T. T. and Zale, A. V.},
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  volume={136},
  pages={1113--1121},
  year={2007},
  doi={10.1577/T06-072.1}
}

@techreport{beechie2021chum,
  title={Chum Salmon Life-Cycle Model Description and Results for the Chehalis River Basin},
  author={Beechie, T. J. and Nicol, C. and Fogel, C. and Jorgensen, J. and Timpane-Padgham, B.},
  year={2021},
  institution={U.S. Department of Commerce, NOAA},
  number={NMFS-NWFSC-CR-2021-02}
}

@techreport{beechie2021modeling,
  title={Modeling Effects of Habitat Change and Restoration Alternatives on Salmon in the Chehalis River Basin Using a Salmonid Life-Cycle Model},
  author={Beechie, T. J. and Nicol, C. and Fogel, C. and Jorgensen, J. and Thompson, J. and Seixas, G. and Chamberlin, J. and Hall, J. and Timpane-Padgham, B. and Kiffney, P. and Kubo, S. and Keaton, J.},
  year={2021},
  institution={U.S. Department of Commerce, NOAA},
  number={NMFS-NWFSC-CR-2021-01}
}

@phdthesis{Chen2024ChinookCV,
  author       = {Chen, Emily Katherine},
  year         = {2024},
  title        = {Life History and Population Dynamics of Chinook Salmon in the Central Valley},
  school       = {University of California, Berkeley},
  type         = {Ph.D. dissertation},
  address      = {Berkeley, CA},
  month        = summer,
  note         = {Department of Environmental Science, Policy, and Management. Committee: Stephanie M. Carlson (Chair), Theodore E. Grantham, Carl Boettiger, William H. Satterthwaite.}
}

@techreport{CoxRogersEtAl2010SkeenaSockeye,
  author       = {Cox-Rogers, S. and Hume, J. M. B. and Shortreed, K. S. and Spilsted, B.},
  year         = {2010},
  title        = {A Risk Assessment Model for Skeena River Sockeye Salmon},
  institution  = {Fisheries and Oceans Canada},
  series       = {Canadian Manuscript Report of Fisheries and Aquatic Sciences},
  number       = {2920},
  address      = {Prince Rupert, BC, Canada},
  note         = {Science Branch, Pacific Region, North Coast Stock Assessment Unit}
}

@inproceedings{cramer2009linking,
  title={Linking stream carrying capacity for salmonids to habitat features},
  author={Cramer, S. P. and Ackerman, N. K.},
  booktitle={American Fisheries Society Symposium},
  volume={71},
  pages={225--254},
  year={2009}
}

@article{halpern2013assumptions,
  title={Assumptions, challenges, and future directions in cumulative impact analysis},
  author={Halpern, B. S. and Fujita, R.},
  journal={Ecosphere},
  volume={4},
  pages={1--11},
  year={2013}
}

@article{houde2007six,
  title={The six faces of traditional ecological knowledge: challenges and opportunities for Canadian co-management arrangements},
  author={Houde, N.},
  journal={Ecology and Society},
  volume={12},
  number={2},
  year={2007}
}

@article{jarvis2023process,
  title={A process framework for integrating stressor-response functions into cumulative effects models},
  author={Jarvis, L. and Rosenfeld, J. and Gonzalez-Espinosa, P. and Enders, E.},
  journal={Science of the Total Environment},
  volume={XXX},
  pages={167456},
  year={2023}
}

@article{jensen2009impact,
  title={Impact of fine sediment on incubation survival of Pacific salmon: a meta-analysis of published studies},
  author={Jensen, D. W. and Steel, E. A. and Fullerton, A. H. and Pess, G. R.},
  journal={Reviews in Fisheries Science},
  volume={17},
  number={3},
  pages={348--359},
  year={2009},
  doi={10.1080/10641260902716954}
}

@article{jorgensen2021identifying,
  title={Identifying the potential of anadromous salmonid habitat restoration with life cycle models},
  author={Jorgensen, J. C. and Nicol, C. and Fogel, C. and Beechie, T. J.},
  journal={Plos one},
  volume={16},
  number={9},
  pages={e0256792},
  year={2021}
}

@article{kendall2023life,
  title={Life Cycle Model Reveals Sensitive Life Stages and Evaluates Recovery Options for a Dwindling Pacific Salmon Population},
  author={Kendall, N. W. and Unrein, J. and Volk, C. and Beauchamp, D. A. and Fresh, K. L. and Quinn, T. P.},
  journal={North American Journal of Fisheries Management},
  volume={43},
  number={1},
  pages={203--230},
  year={2023}
}

@article{larned2019stressor,
  title={Stressor-response relationships and the prospective management of aquatic ecosystems},
  author={Larned, S. T. and Schallenberg, M.},
  journal={New Zealand Journal of Marine and Freshwater Research},
  volume={53},
  pages={489--512},
  year={2019}
}

@techreport{macpherson2020alberta,
  title={Alberta's Fisheries Sustainability Assessment: A Guide to Assessing Population Status, and Quantifying Cumulative Effects Using the Joe Modelling Technique},
  author={MacPherson, L. and Sullivan, M. and Reilly, J. and Paul, A.},
  year={2020},
  institution={Canadian Science Advisory Secretariat (CSAS)}
}

@article{macpherson2023prioritizing,
  title={Prioritizing bull trout recovery actions using a novel cumulative effects modelling framework},
  author={MacPherson, L. M. and Reilly, J. R. and Neufeld, K. R. and Sullivan, M. G. and Paul, A. J. and Johnston, F. D.},
  journal={Fisheries Management and Ecology},
  pages={1--17},
  year={2023}
}

@article{murray2012tribute,
  title={A tribute to Joseph Schieser Nelson, 1937--2011},
  author={Murray, A. M. and Sullivan, M. G. and Acorn, J.},
  journal={Can. Field-Nat.},
  volume={125},
  pages={373--380},
  year={2012}
}

@techreport{pearsall2022nicola,
  title={Nicola Watershed RAMS Final Report 2022: Nicola Basin Chinook Risk Assessment Final Report},
  author={Pearsall, et al.},
  year={2022},
  institution={A Process Developed with the Nicola Collaborative Research and Technical Committee}
}

@article{piet2021roadmap,
  title={A roadmap towards quantitative cumulative impact assessments: every step of the way},
  author={Piet, G. J. and Tamis, J. E. and Volwater, J. and de Vries, P. and van der Wal, J. T. and Jongbloed, R. H.},
  journal={Science of The Total Environment},
  volume={784},
  pages={146847},
  year={2021}
}

@article{pirotta2022understanding,
  title={Understanding the combined effects of multiple stressors: A new perspective on a longstanding challenge},
  author={Pirotta, E. and Thomas, L. and Costa, D. P. and Hall, A. J. and Harris, C. M. and Harwood, J. and others},
  journal={Science of the Total Environment},
  volume={821},
  pages={153322},
  year={2022}
}

@article{roni2018review,
  title={Review of tools for identifying, planning, and implementing habitat restoration for Pacific salmon and steelhead},
  author={Roni, P. and Anders, P. J. and Beechie, T. J. and Kaplowe, D. J.},
  journal={North American Journal of Fisheries Management},
  volume={38},
  number={2},
  pages={355--376},
  year={2018},
  publisher={Chicago}
}

@article{rosenfeld2017developing,
  title={Developing flow--ecology relationships: Implications of nonlinear biological responses for water management},
  author={Rosenfeld, J. S.},
  journal={Freshwater Biology},
  volume={62},
  pages={1305--1324},
  year={2017}
}

@article{rosenfeld2022stressor,
  title={Stressor-response functions as a generalizable model for context dependence},
  author={Rosenfeld, Jordan and Gonzalez-Espinosa, Pedro and Jarvis, Lauren and Enders, Eva and Bayly, Matthew and Paul, Andrew and MacPherson, Laura and Moore, Jonathan and Sullivan, Michael and Ulaski, Marta and others},
  journal={Trends in Ecology \& Evolution},
  year={2022},
  publisher={Elsevier}
}

@inbook{rosenfeld2024determinants,
  title={Determinants of productive capacity for stream salmonids},
  author={Rosenfeld, J. S. and Ayll{\'o}n, D. and Grant, J. W. and Naman, S. M. and Post, J. R. and Matte, J.-M. and others},
  booktitle={Advances in the ecology of stream-dwelling salmonids},
  editor={Lobon-Cervia, J. and Budy, P. and Gresswell, R.},
  pages={1--12},
  year={2024},
  publisher={Springer Life Sciences}
}


@article{jensen2009impact,
  title={Impact of fine sediment on incubation survival of Pacific salmon: a meta-analysis of published studies},
  author={Jensen, D. W. and Steel, E. A. and Fullerton, A. H. and Pess, G. R.},
  journal={Reviews in Fisheries Science},
  volume={17},
  number={3},
  pages={348--359},
  year={2009},
  doi={10.1080/10641260902716954}
}

@article{jorgensen2021identifying,
  title={Identifying the potential of anadromous salmonid habitat restoration with life cycle models},
  author={Jorgensen, J. C. and Nicol, C. and Fogel, C. and Beechie, T. J.},
  journal={Plos one},
  volume={16},
  number={9},
  pages={e0256792},
  year={2021}
}

@article{kendall2023life,
  title={Life Cycle Model Reveals Sensitive Life Stages and Evaluates Recovery Options for a Dwindling Pacific Salmon Population},
  author={Kendall, N. W. and Unrein, J. and Volk, C. and Beauchamp, D. A. and Fresh, K. L. and Quinn, T. P.},
  journal={North American Journal of Fisheries Management},
  volume={43},
  number={1},
  pages={203--230},
  year={2023}
}

@article{larned2019stressor,
  title={Stressor-response relationships and the prospective management of aquatic ecosystems},
  author={Larned, S. T. and Schallenberg, M.},
  journal={New Zealand Journal of Marine and Freshwater Research},
  volume={53},
  pages={489--512},
  year={2019}
}

@techreport{macpherson2020alberta,
  title={Alberta's Fisheries Sustainability Assessment: A Guide to Assessing Population Status, and Quantifying Cumulative Effects Using the Joe Modelling Technique},
  author={MacPherson, L. and Sullivan, M. and Reilly, J. and Paul, A.},
  year={2020},
  institution={Canadian Science Advisory Secretariat (CSAS)}
}

@article{macpherson2023prioritizing,
  title={Prioritizing bull trout recovery actions using a novel cumulative effects modelling framework},
  author={MacPherson, L. M. and Reilly, J. R. and Neufeld, K. R. and Sullivan, M. G. and Paul, A. J. and Johnston, F. D.},
  journal={Fisheries Management and Ecology},
  pages={1--17},
  year={2023}
}

@article{murray2012tribute,
  title={A tribute to Joseph Schieser Nelson, 1937–2011},
  author={Murray, A. M. and Sullivan, M. G. and Acorn, J.},
  journal={Canadian Field-Naturalist},
  volume={125},
  pages={373--380},
  year={2012}
}

@techreport{pearsall2022nicola,
  title={Nicola Watershed RAMS Final Report 2022: Nicola Basin Chinook Risk Assessment Final Report. A Process Developed with the Nicola Collaborative Research and Technical Committee},
  author={Pearsall, et al.},
  year={2022}
}

@article{piet2021roadmap,
  title={A roadmap towards quantitative cumulative impact assessments: every step of the way},
  author={Piet, G. J. and Tamis, J. E. and Volwater, J. and de Vries, P. and van der Wal, J. T. and Jongbloed, R. H.},
  journal={Science of The Total Environment},
  volume={784},
  pages={146847},
  year={2021}
}

@article{pirotta2022understanding,
  title={Understanding the combined effects of multiple stressors: A new perspective on a longstanding challenge},
  author={Pirotta, E. and Thomas, L. and Costa, D. P. and Hall, A. J. and Harris, C. M. and Harwood, J. and others},
  journal={Science of the Total Environment},
  volume={821},
  pages={153322},
  year={2022}
}

@article{roni2018review,
  title={Review of tools for identifying, planning, and implementing habitat restoration for Pacific salmon and steelhead},
  author={Roni, P. and Anders, P. J. and Beechie, T. J. and Kaplowe, D. J.},
  journal={North American Journal of Fisheries Management},
  volume={38},
  number={2},
  pages={355--376},
  year={2018},
  publisher={Chicago}
}

@article{rosenfeld2017developing,
  title={Developing flow–ecology relationships: Implications of nonlinear biological responses for water management},
  author={Rosenfeld, J. S.},
  journal={Freshwater Biology},
  volume={62},
  pages={1305--1324},
  year={2017}
}

@incollection{rosenfeld2024determinants,
  title={Determinants of productive capacity for stream salmonids},
  author={Rosenfeld, J. S. and Ayllón, D. and Grant, J. W. and Naman, S. M. and Post, J. R. and Matte, J.-M. and others},
  booktitle={Advances in the ecology of stream-dwelling salmonids},
  editor={Lobon-Cervia, J. and Budy, P. and Gresswell, R.},
  pages={1--12},
  year={2024},
  publisher={Springer Life Sciences}
}

@article{schafer2018advancing,
  title={Advancing understanding and prediction in multiple stressor research through a mechanistic basis for null models},
  author={Sch{\"a}fer, R. B. and Piggott, J. J.},
  journal={Global Change Biology},
  volume={24},
  pages={1817--1826},
  year={2018}
}

@book{schaub2021integrated,
  title={Integrated life cycle models: Theory and ecological applications with R and JAGS},
  author={Schaub, M. and K{\'e}ry, M.},
  year={2021},
  publisher={Academic Press}
}

@phdthesis{sorel2022informing,
  title={Informing salmon conservation with life cycle models that account for individual heterogeneity},
  author={Sorel, M.},
  year={2022},
  school={University of Washington}
}

@techreport{sullivan2017adaptive,
  title={Adaptive Management of Athabasca Rainbow Trout; cumulative effects modelling and potential management actions},
  author={Sullivan, M.},
  year={2017},
  institution={Alberta Environment and Parks; Fisheries Management Branch},
  month={January}
}

@techreport{vanderlee2020recovery,
  title={Recovery Potential Modelling of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi) in Designatable Unit 1: Saskatchewan-Nelson River populations},
  author={Van der Lee, A. S. and Koops, M. A.},
  year={2020},
  institution={Canadian Science Advisory Secretariat}
}

@article{walters1997challenges,
  title={Challenges in adaptive management of riparian and coastal ecosystems},
  author={Walters, C.},
  journal={Conservation Ecology [online]},
  volume={1},
  number={2},
  pages={1},
  year={1997}
}

@article{ward1993egg,
  title={Egg-to-smolt survival and fry-to-smolt density dependence of Keough River Steelhead Trout},
  author={Ward, B. R. and Slaney, P. A.},
  journal={Canadian Special Publication of Fisheries and Aquatic Sciences},
  pages={209--217},
  year={1993}
}


@article{davison2016,
  author    = {Davison, R. J. and Satterthwaite, W. H.},
  title     = {Use of age and stage structured matrix models to predict life history schedules for semelparous populations},
  journal   = {Natural Resource Modeling},
  year      = {2016},
  volume    = {29},
  number    = {4},
  pages     = {538--558},
  doi       = {10.1111/nrm.12109}
}

@book{schaub2021,
  author    = {Schaub, Michael and Kéry, Marc},
  title     = {Integrated Population Models: Theory and Ecological Applications with R and JAGS},
  year      = {2021},
  publisher = {Academic Press},
  address   = {Cambridge, MA},
  isbn      = {978-0128200215}
}

@techreport{vanderlee2020,
  author    = {Van der Lee, A. S. and Koops, M. A.},
  title     = {Recovery Potential Modelling of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi) in Designatable Unit 1: Saskatchewan-Nelson River populations},
  year      = {2020},
  institution = {Canadian Science Advisory Secretariat},
  type      = {Research Document},
  number    = {2020/020},
  address   = {Ottawa, ON},
  url       = {https://www.dfo-mpo.gc.ca/csas-sccs/publications/resdocs-docrech/2020/2020_020-eng.html}
}

@incollection{caswell1997,
  author    = {Caswell, Hal},
  title     = {Matrix methods for population analysis},
  booktitle = {Structured-Population Models in Marine, Terrestrial, and Freshwater Systems},
  editor    = {S. Tuljapurkar and H. Caswell},
  pages     = {19--58},
  year      = {1997},
  publisher = {Springer US},
  address   = {Boston, MA},
  doi       = {10.1007/978-1-4615-6005-0_2}
}