@techreport{obrien_geomorphic_2019,
	address = {Logan, UT},
	title = {Geomorphic {Assessment} of the {Lower} {White} {River}: {Valley} {Landform} {Delineation}, {Reach} {Typing}, and {Geomorphic} {Condition} {Assessment}.},
	institution = {Prepared for Bureau of Land Management by the Utah State University Ecogeomorphology and Topographic Analysis Lab},
	author = {O'Brien, Gary R. and Stevens, Geoff and Macfalrane, W. W. and Wheaton, Joseph M.},
	year = {2019},
	pages = {99},
}

@article{obrien_mapping_2019,
	title = {Mapping valley bottom confinement at the network scale},
	issn = {0197-9337, 1096-9837},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/esp.4615},
	doi = {10.1002/esp.4615},
	abstract = {In this article, we demonstrate the application of a continuous confinement metric across entire river networks. Confinement is a useful metric for characterizing and discriminating valley setting. At the reach scale, valley bottom confinement is measured and quantified as the ratio of the length of channel confined on either bank by a confining margin divided by the reach length. The valley bottom is occupied by the contemporary floodplain and/or its channel(s); confining margins can be any landform or feature that makes up the valley bottom margin, such as bedrock hillslopes, terraces, fans, or anthropogenic features such as stopbanks or constructed levees. To test the reliability of calculating confinement across entire networks, we applied our geoprocessing scripts across four physiographically distinct watersheds of the Pacific Northwest, USA using freely available national datasets. Comparison of manually digitized and mapped with modeled calculations of confinement revealed that roughly one-third of reaches were equivalent and about two-thirds of the sites differ by less than ±15\%. A sensitivity analysis found that a 500 m reach segmentation length produced reasonable agreement with manual, categorical, expert-derived analysis of confinement. Confinement accuracy can be improved (c. 4\% to 17\% gains) using a more accurately mapped valley bottom and channel position (i.e. with higher-resolution model inputs). This is particularly important when differentiating rivers in the partly confined valley setting. However, at the watershed scale, patterns derived from mapping confinement are not fundamentally different, making this a reasonably accurate and rapid technique for analysis and measurement of confinement across broad spatial extents. © 2019 John Wiley \& Sons, Ltd.},
	language = {en},
	urldate = {2020-04-01},
	journal = {Earth Surface Processes and Landforms},
	author = {O'Brien, Gary R. and Wheaton, Joseph M. and Fryirs, Kirstie and Macfarlane, William W. and Brierley, Gary and Whitehead, Kelly and Gilbert, Jordan and Volk, Carol},
	month = may,
	year = {2019},
	pages = {esp.4615},
}

In this article, we demonstrate the application of a continuous confinement metric across entire river networks. Confinement is a useful metric for characterizing and discriminating valley setting. At the reach scale, valley bottom confinement is measured and quantified as the ratio of the length of channel confined on either bank by a confining margin divided by the reach length. The valley bottom is occupied by the contemporary floodplain and/or its channel(s); confining margins can be any landform or feature that makes up the valley bottom margin, such as bedrock hillslopes, terraces, fans, or anthropogenic features such as stopbanks or constructed levees. To test the reliability of calculating confinement across entire networks, we applied our geoprocessing scripts across four physiographically distinct watersheds of the Pacific Northwest, USA using freely available national datasets. Comparison of manually digitized and mapped with modeled calculations of confinement revealed that roughly one-third of reaches were equivalent and about two-thirds of the sites differ by less than ±15%. A sensitivity analysis found that a 500 m reach segmentation length produced reasonable agreement with manual, categorical, expert-derived analysis of confinement. Confinement accuracy can be improved (c. 4% to 17% gains) using a more accurately mapped valley bottom and channel position (i.e. with higher-resolution model inputs). This is particularly important when differentiating rivers in the partly confined valley setting. However, at the watershed scale, patterns derived from mapping confinement are not fundamentally different, making this a reasonably accurate and rapid technique for analysis and measurement of confinement across broad spatial extents. © 2019 John Wiley & Sons, Ltd.

@article{nahorniak_how_2018,
	title = {How do we efficiently generate high-resolution hydraulic models at large numbers of riverine reaches?},
	volume = {119},
	issn = {00983004},
	doi = {10.1016/j.cageo.2018.07.001},
	journal = {Computers \& Geosciences},
	author = {Nahorniak, Matthew and Wheaton, Joe and Volk, Carol and Bailey, Phillip and Reimer, Matt and Wall, Eric and Whitehead, Kelly and Jordan, Chris},
	year = {2018},
	pages = {80--91},
}

@article{wall_design_2017,
	title = {Design and monitoring of woody structures and their benefits to juvenile steelhead ( \textit{{Oncorhynchus} mykiss} ) using a net rate of energy intake model},
	volume = {74},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfas-2016-0131},
	doi = {10.1139/cjfas-2016-0131},
	abstract = {Despite substantial effort and resources being invested in habitat rehabilitation for stream fishes, mechanistic approaches to designing and evaluating how habitat actions influence the fish populations they are intended to benefit remain rare. We used a net rate of energy intake (NREI) model to examine expected and observed changes in energetic habitat quality and capacity from woody debris additions in a 40 m long study reach being treated as part of a restoration experiment in Asotin Creek, Washington. We simulated depths, velocities, and NREI values for pre-treatment, expected, and post-treatment habitat conditions, and we compared pre-treatment versus expected and pre-treatment versus post-treatment simulation results. The pre-treatment versus expected topography simulations suggested treatment would increase energetically favorable area, mean NREI, and capacity in the study reach. Pre-treatment versus post-treatment comparisons yielded similar predictions, though to smaller magnitudes, likely due to the short time span and single high-flow event between pre- and post-treatment data collection. We feel the NREI modelling approach is an important tool for improving the efficacy of habitat rehabilitation actions for stream fishes.},
	language = {en},
	number = {5},
	urldate = {2022-01-09},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Wall, C. Eric and Bouwes, Nicolaas and Wheaton, Joseph M. and Bennett, Stephen N. and Saunders, W. Carl and McHugh, Pete A. and Jordan, Chris E.},
	month = may,
	year = {2017},
	keywords = {NREI, ecohydraulics},
	pages = {727--738},
}

Despite substantial effort and resources being invested in habitat rehabilitation for stream fishes, mechanistic approaches to designing and evaluating how habitat actions influence the fish populations they are intended to benefit remain rare. We used a net rate of energy intake (NREI) model to examine expected and observed changes in energetic habitat quality and capacity from woody debris additions in a 40 m long study reach being treated as part of a restoration experiment in Asotin Creek, Washington. We simulated depths, velocities, and NREI values for pre-treatment, expected, and post-treatment habitat conditions, and we compared pre-treatment versus expected and pre-treatment versus post-treatment simulation results. The pre-treatment versus expected topography simulations suggested treatment would increase energetically favorable area, mean NREI, and capacity in the study reach. Pre-treatment versus post-treatment comparisons yielded similar predictions, though to smaller magnitudes, likely due to the short time span and single high-flow event between pre- and post-treatment data collection. We feel the NREI modelling approach is an important tool for improving the efficacy of habitat rehabilitation actions for stream fishes.

@article{mchugh_linking_2017,
	title = {Linking models across scales to assess the viability and restoration potential of a threatened population of steelhead ( {Oncorhynchus} mykiss ) in the {Middle} {Fork} {John} {Day} {River}, {Oregon}, {USA}},
	volume = {355},
	issn = {03043800},
	doi = {10.1016/j.ecolmodel.2017.03.022},
	journal = {Ecological Modelling},
	author = {McHugh, Peter A. and Saunders, W. Carl and Bouwes, Nicolaas and Wall, C. Eric and Bangen, Sara and Wheaton, Joseph M. and Nahorniak, Matthew and Ruzycki, James R. and Tattam, Ian A. and Jordan, Chris E.},
	year = {2017},
	pages = {24--38},
}

@article{macfarlane_modeling_2017,
	series = {Connectivity in {Geomorphology} from {Binghamton} 2016},
	title = {Modeling the capacity of riverscapes to support beaver dams},
	volume = {277},
	issn = {0169-555X},
	url = {http://www.sciencedirect.com/science/article/pii/S0169555X15302166},
	doi = {10.1016/j.geomorph.2015.11.019},
	abstract = {The construction of beaver dams facilitates a suite of hydrologic, hydraulic, geomorphic, and ecological feedbacks that increase stream complexity and channel–floodplain connectivity that benefit aquatic and terrestrial biota. Depending on where beaver build dams within a drainage network, they impact lateral and longitudinal connectivity by introducing roughness elements that fundamentally change the timing, delivery, and storage of water, sediment, nutrients, and organic matter. While the local effects of beaver dams on streams are well understood, broader coverage network models that predict where beaver dams can be built and highlight their impacts on connectivity across diverse drainage networks are lacking. Here we present a capacity model to assess the limits of riverscapes to support dam-building activities by beaver across physiographically diverse landscapes. We estimated dam capacity with freely and nationally-available inputs to evaluate seven lines of evidence: (1) reliable water source, (2) riparian vegetation conducive to foraging and dam building, (3) vegetation within 100m of edge of stream to support expansion of dam complexes and maintain large colonies, (4) likelihood that channel-spanning dams could be built during low flows, (5) the likelihood that a beaver dam is likely to withstand typical floods, (6) a suitable stream gradient that is neither too low to limit dam density nor too high to preclude the building or persistence of dams, and (7) a suitable river that is not too large to restrict dam building or persistence. Fuzzy inference systems were used to combine these controlling factors in a framework that explicitly also accounts for model uncertainty. The model was run for 40,561km of streams in Utah, USA, and portions of surrounding states, predicting an overall network capacity of 356,294 dams at an average capacity of 8.8dams/km. We validated model performance using 2852 observed dams across 1947km of streams. The model showed excellent agreement with observed dam densities where beaver dams were present. Model performance was spatially coherent and logical, with electivity indices that effectively segregated capacity categories. That is, beaver dams were not found where the model predicted no dams could be supported, beaver avoided segments that were predicted to support rare or occasional densities, and beaver preferentially occupied and built dams in areas predicted to have pervasive dam densities. The resulting spatially explicit reach-scale (250m long reaches) data identifies where dam-building activity is sustainable, and at what densities dams can occur across a landscape. As such, model outputs can be used to determine where channel–floodplain and wetland connectivity are likely to persist or expand by promoting increases in beaver dam densities.},
	language = {en},
	urldate = {2020-01-30},
	journal = {Geomorphology},
	author = {Macfarlane, William W. and Wheaton, Joseph M. and Bouwes, Nicolaas and Jensen, Martha L. and Gilbert, Jordan T. and Hough-Snee, Nate and Shivik, John A.},
	month = jan,
	year = {2017},
	keywords = {Connectivity, Fuzzy inference systems, Habitat modeling, North American beaver, Riparian restoration, Stream restoration},
	pages = {72--99},
}

The construction of beaver dams facilitates a suite of hydrologic, hydraulic, geomorphic, and ecological feedbacks that increase stream complexity and channel–floodplain connectivity that benefit aquatic and terrestrial biota. Depending on where beaver build dams within a drainage network, they impact lateral and longitudinal connectivity by introducing roughness elements that fundamentally change the timing, delivery, and storage of water, sediment, nutrients, and organic matter. While the local effects of beaver dams on streams are well understood, broader coverage network models that predict where beaver dams can be built and highlight their impacts on connectivity across diverse drainage networks are lacking. Here we present a capacity model to assess the limits of riverscapes to support dam-building activities by beaver across physiographically diverse landscapes. We estimated dam capacity with freely and nationally-available inputs to evaluate seven lines of evidence: (1) reliable water source, (2) riparian vegetation conducive to foraging and dam building, (3) vegetation within 100m of edge of stream to support expansion of dam complexes and maintain large colonies, (4) likelihood that channel-spanning dams could be built during low flows, (5) the likelihood that a beaver dam is likely to withstand typical floods, (6) a suitable stream gradient that is neither too low to limit dam density nor too high to preclude the building or persistence of dams, and (7) a suitable river that is not too large to restrict dam building or persistence. Fuzzy inference systems were used to combine these controlling factors in a framework that explicitly also accounts for model uncertainty. The model was run for 40,561km of streams in Utah, USA, and portions of surrounding states, predicting an overall network capacity of 356,294 dams at an average capacity of 8.8dams/km. We validated model performance using 2852 observed dams across 1947km of streams. The model showed excellent agreement with observed dam densities where beaver dams were present. Model performance was spatially coherent and logical, with electivity indices that effectively segregated capacity categories. That is, beaver dams were not found where the model predicted no dams could be supported, beaver avoided segments that were predicted to support rare or occasional densities, and beaver preferentially occupied and built dams in areas predicted to have pervasive dam densities. The resulting spatially explicit reach-scale (250m long reaches) data identifies where dam-building activity is sustainable, and at what densities dams can occur across a landscape. As such, model outputs can be used to determine where channel–floodplain and wetland connectivity are likely to persist or expand by promoting increases in beaver dam densities.

@article{justice_can_2017,
	title = {Can stream and riparian restoration offset climate change impacts to salmon populations?},
	volume = {188},
	issn = {03014797},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0301479716309793},
	doi = {10.1016/j.jenvman.2016.12.005},
	abstract = {Understanding how stream temperature responds to restoration of riparian vegetation and channel morphology in context of future climate change is critical for prioritizing restoration actions and recovering imperiled salmon populations. We used a deterministic water temperature model to investigate potential thermal benefits of riparian reforestation and channel narrowing to Chinook Salmon populations in the Upper Grande Ronde River and Catherine Creek basins in Northeast Oregon, USA. A legacy of intensive land use practices in these basins has significantly reduced streamside vegetation and increased channel width across most of the stream network, resulting in water temperatures that far exceed the optimal range for salmon growth and survival. By combining restoration scenarios with climate change projections, we were able to evaluate whether future climate impacts could be offset by restoration actions. A combination of riparian restoration and channel narrowing was predicted to reduce peak summer water temperatures by 6.5  C on average in the Upper Grande Ronde River and 3.0  C in Catherine Creek in the absence of other perturbations. These results translated to increases in Chinook Salmon parr abundance of 590\% and 67\% respectively. Although projected climate change impacts on water temperature for the 2080s time period were substantial (i.e., median increase of 2.7  C in the Upper Grande Ronde and 1.5  C in Catherine Creek), we predicted that basin-wide restoration of riparian vegetation and channel width could offset these impacts, reducing peak summer water temperatures by about 3.5  C in the Upper Grande Ronde and 1.8  C in Catherine Creek. These results underscore the potential for riparian and stream channel restoration to mitigate climate change impacts to threatened salmon populations in the Pacific Northwest.},
	language = {en},
	urldate = {2020-04-20},
	journal = {Journal of Environmental Management},
	author = {Justice, Casey and White, Seth M. and McCullough, Dale A. and Graves, David S. and Blanchard, Monica R.},
	month = mar,
	year = {2017},
	pages = {212--227},
}

Understanding how stream temperature responds to restoration of riparian vegetation and channel morphology in context of future climate change is critical for prioritizing restoration actions and recovering imperiled salmon populations. We used a deterministic water temperature model to investigate potential thermal benefits of riparian reforestation and channel narrowing to Chinook Salmon populations in the Upper Grande Ronde River and Catherine Creek basins in Northeast Oregon, USA. A legacy of intensive land use practices in these basins has significantly reduced streamside vegetation and increased channel width across most of the stream network, resulting in water temperatures that far exceed the optimal range for salmon growth and survival. By combining restoration scenarios with climate change projections, we were able to evaluate whether future climate impacts could be offset by restoration actions. A combination of riparian restoration and channel narrowing was predicted to reduce peak summer water temperatures by 6.5 C on average in the Upper Grande Ronde River and 3.0 C in Catherine Creek in the absence of other perturbations. These results translated to increases in Chinook Salmon parr abundance of 590% and 67% respectively. Although projected climate change impacts on water temperature for the 2080s time period were substantial (i.e., median increase of 2.7 C in the Upper Grande Ronde and 1.5 C in Catherine Creek), we predicted that basin-wide restoration of riparian vegetation and channel width could offset these impacts, reducing peak summer water temperatures by about 3.5 C in the Upper Grande Ronde and 1.8 C in Catherine Creek. These results underscore the potential for riparian and stream channel restoration to mitigate climate change impacts to threatened salmon populations in the Pacific Northwest.

@article{obrien_geomorphic_2017,
	title = {A geomorphic assessment to inform strategic stream restoration planning in the {Middle} {Fork} {John} {Day} {Watershed}, {Oregon}, {USA}},
	volume = {13},
	issn = {1744-5647},
	doi = {10.1080/17445647.2017.1313787},
	number = {2},
	journal = {Journal of Maps},
	author = {O’Brien, Gary R. and Wheaton, Joseph and Fryirs, Kirstie and McHugh, Peter and Bouwes, Nicolaas and Brierley, Gary and Jordan, Chris},
	year = {2017},
	pages = {369--381},
}

@article{wheaton_upscaling_2017,
	title = {Upscaling {Site}-{Scale} {Ecohydraulic} {Models} to {Inform} {Salmonid} {Population}-{Level} {Life} {Cycle} {Modelling} and {Restoration} {Actions} – {Lessons} from the {Columbia} {River} {Basin}},
	doi = {10.1002/esp.4137},
	journal = {Earth Surface Processes and Landforms},
	author = {Wheaton, J. and Bouwes, N. and McHugh, P. and Saunders, W. Carl and Bangen, S. G. and Bailey, P. E. and Nahorniak, M. and Wall, C. Eric and Jordan, C.},
	year = {2017},
}

@article{kemp_introducing_2016,
	title = {Introducing the {Journal} of {Ecohydraulics}: fundamental and applied research on the road to transdisciplinarity},
	volume = {1},
	issn = {2470-5357},
	shorttitle = {Introducing the {Journal} of {Ecohydraulics}},
	url = {https://doi.org/10.1080/24705357.2016.1259139},
	doi = {10.1080/24705357.2016.1259139},
	number = {1-2},
	urldate = {2020-03-28},
	journal = {Journal of Ecohydraulics},
	author = {Kemp, Paul S. and Katopodis, Christos},
	month = jul,
	year = {2016},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/24705357.2016.1259139},
	keywords = {ecohydraulics},
	pages = {1--4},
}

@article{gilbert_valley_2016,
	title = {The {Valley} {Bottom} {Extraction} {Tool} ({V}-{BET}): {A} {GIS} tool for delineating valley bottoms across entire drainage networks},
	volume = {97},
	issn = {00983004},
	doi = {10.1016/j.cageo.2016.07.014},
	journal = {Computers \& Geosciences},
	author = {Gilbert, Jordan T. and Macfarlane, William W. and Wheaton, Joseph M.},
	year = {2016},
	pages = {1--14},
}

@article{william_w_macfarlane_riparian_2016,
	title = {Riparian vegetation as an indicator of riparian condition: detecting departures from historic condition across the {North} {American} {West}},
	doi = {10.1016/j.jenvman.2016.10.054},
	journal = {Journal of Environmental Management},
	author = {William W. Macfarlane and Jordan T. Gilbert and Martha L. Jensen and Joshua D. Gilbert and Peter A. McHugh and Nate Hough-Snee and Joseph M. Wheaton and Stephen N. Bennett},
	year = {2016},
}

@article{kasprak_blurred_2016,
	title = {The {Blurred} {Line} between {Form} and {Process}: {A} {Comparison} of {Stream} {Channel} {Classification} {Frameworks}},
	volume = {11},
	issn = {1932-6203},
	shorttitle = {The {Blurred} {Line} between {Form} and {Process}},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150293},
	doi = {10.1371/journal.pone.0150293},
	abstract = {Stream classification provides a means to understand the diversity and distribution of channels and floodplains that occur across a landscape while identifying links between geomorphic form and process. Accordingly, stream classification is frequently employed as a watershed planning, management, and restoration tool. At the same time, there has been intense debate and criticism of particular frameworks, on the grounds that these frameworks classify stream reaches based largely on their physical form, rather than direct measurements of their component hydrogeomorphic processes. Despite this debate surrounding stream classifications, and their ongoing use in watershed management, direct comparisons of channel classification frameworks are rare. Here we implement four stream classification frameworks and explore the degree to which each make inferences about hydrogeomorphic process from channel form within the Middle Fork John Day Basin, a watershed of high conservation interest within the Columbia River Basin, U.S.A. We compare the results of the River Styles Framework, Natural Channel Classification, Rosgen Classification System, and a channel form-based statistical classification at 33 field-monitored sites. We found that the four frameworks consistently classified reach types into similar groups based on each reach or segment’s dominant hydrogeomorphic elements. Where classified channel types diverged, differences could be attributed to the (a) spatial scale of input data used, (b) the requisite metrics and their order in completing a framework’s decision tree and/or, (c) whether the framework attempts to classify current or historic channel form. Divergence in framework agreement was also observed at reaches where channel planform was decoupled from valley setting. Overall, the relative agreement between frameworks indicates that criticism of individual classifications for their use of form in grouping stream channels may be overstated. These form-based criticisms may also ignore the geomorphic tenet that channel form reflects formative hydrogeomorphic processes across a given landscape.},
	language = {en},
	number = {3},
	urldate = {2020-03-29},
	journal = {PLOS ONE},
	author = {Kasprak, Alan and Hough-Snee, Nate and Beechie, Tim and Bouwes, Nicolaas and Brierley, Gary and Camp, Reid and Fryirs, Kirstie and Imaki, Hiroo and Jensen, Martha and O’Brien, Gary and Rosgen, David and Wheaton, Joseph},
	month = mar,
	year = {2016},
	note = {Publisher: Public Library of Science},
	keywords = {Decision trees, Flooding, Geomorphology, Principal component analysis, Rivers, Sediment, Statistical data, Watersheds},
	pages = {e0150293},
}

Stream classification provides a means to understand the diversity and distribution of channels and floodplains that occur across a landscape while identifying links between geomorphic form and process. Accordingly, stream classification is frequently employed as a watershed planning, management, and restoration tool. At the same time, there has been intense debate and criticism of particular frameworks, on the grounds that these frameworks classify stream reaches based largely on their physical form, rather than direct measurements of their component hydrogeomorphic processes. Despite this debate surrounding stream classifications, and their ongoing use in watershed management, direct comparisons of channel classification frameworks are rare. Here we implement four stream classification frameworks and explore the degree to which each make inferences about hydrogeomorphic process from channel form within the Middle Fork John Day Basin, a watershed of high conservation interest within the Columbia River Basin, U.S.A. We compare the results of the River Styles Framework, Natural Channel Classification, Rosgen Classification System, and a channel form-based statistical classification at 33 field-monitored sites. We found that the four frameworks consistently classified reach types into similar groups based on each reach or segment’s dominant hydrogeomorphic elements. Where classified channel types diverged, differences could be attributed to the (a) spatial scale of input data used, (b) the requisite metrics and their order in completing a framework’s decision tree and/or, (c) whether the framework attempts to classify current or historic channel form. Divergence in framework agreement was also observed at reaches where channel planform was decoupled from valley setting. Overall, the relative agreement between frameworks indicates that criticism of individual classifications for their use of form in grouping stream channels may be overstated. These form-based criticisms may also ignore the geomorphic tenet that channel form reflects formative hydrogeomorphic processes across a given landscape.

@techreport{gary_obrien_river_2015,
	address = {Logan, UT},
	title = {River {Styles} {Report} for the {Middle} {Fork} {John} {Day} {Watershed}, {Oregon} - {Example} {Report} for {Exploring} {Leveraging} the {River} {Styles} {Framework} in {Tributary} {Habitat} {Management} for the {Columbia} {River} {Basin}},
	institution = {Ecogeomorphology and Topographic Analysis Lab, Utah State University, Prepared for Eco Logical Research and the Bonneville Power Administration},
	author = {Gary O'Brien and Wheaton, J. M.},
	year = {2015},
	pages = {207},
}

@techreport{gary_obrien_synthesis_2015,
	address = {Logan, UT},
	title = {Synthesis \& {Recommendations} from {Middle} {Fork} {John} {Day} {River} {Styles} - {Leveraging} the {River} {Styles} {Framework} in {Tributary} {Habitat} {Management} for the {Columbia} {River} {Basin}},
	institution = {Fluvial Habitats Center, Utah State University, Prepared for Eco Logical Research and Bonneville Power Administration},
	author = {Gary O'Brien and Joseph M. Wheaton},
	year = {2015},
	pages = {20},
}

@article{fryirs_approach_2015,
	title = {An approach for measuring confinement and assessing the influence of valley setting on river forms and processes},
	doi = {10.1002/esp.3893},
	journal = {Earth Surface Processes and Landfroms},
	author = {Fryirs, K. and Wheaton, J. and Brierley, G. J.},
	year = {2015},
}

@article{fryirs_developing_2015,
	title = {Developing and using geomorphic condition assessments for river rehabilitation planning, implementation and monitoring},
	volume = {2},
	issn = {2049-1948},
	doi = {10.1002/wat2.1100},
	number = {6},
	journal = {Wiley Interdisciplinary Reviews: Water},
	author = {Fryirs, Kirstie A.},
	year = {2015},
	pages = {649--667},
}

@article{wheaton_geomorphic_2015,
	title = {Geomorphic {Mapping} and {Taxonomy} of {Fluvial} {Landforms}},
	volume = {248},
	doi = {10.1016/j.geomorph.2015.07.010},
	journal = {Geomorphology},
	author = {Wheaton, J. and Fryirs, K. and Brierley, G. J. and Bangen, S. G. and Bouwes, N. and O'Brien, Gary},
	year = {2015},
	pages = {273--295},
}

@article{weber_estimation_2014,
	title = {Estimation of salmonid habitat growth potential through measurements of invertebrate food abundance and temperature},
	volume = {71},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfas-2013-0390},
	doi = {10.1139/cjfas-2013-0390},
	abstract = {Criteria used to characterize lotic salmonid habitat suitability are often based on correlations between physical habitat characteristics and salmonid abundance. Focusing on physical habitat features ignores other habitat components, such as an adequate food supply, that limit the amount of energy available for growth and survival. We tested the degree that food availability and temperature influence lotic salmonid consumption and growth rates and outline an approach for assessing habitat quality based on measurements of these features. We collected benthic and drifting invertebrate abundances, stream temperatures, and juvenile steelhead – rainbow trout (Onchorhynchus mykiss gairdneri) summer growth rates among nine stream segments in central Oregon. Stream temperatures and growth rates were used in bioenergetics model simulations to estimate O. mykiss consumption rates. The variation in O. mykiss consumption rates was explained by measurements of total drift biomass along a type II predator response curve (R2 = 0.71). This simplified foraging relationship between food abundance and consumption is then used to estimate the consumption component of the bioenergetics model to allow estimation of salmonid growth potential. Validation of the growth potential model produced reasonably accurate estimates of fish growth rates at reaches within the study area and precise but biased estimates in novel systems. While additional reach-level habitat information may be required to make the model more generalizable, the assessment of invertebrate food availability offers a simple yet powerful approach for describing the growth potential of stream habitat.},
	language = {en},
	number = {8},
	urldate = {2022-01-09},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Weber, Nicholas and Bouwes, Nicolaas and Jordan, Chris E.},
	editor = {Jonsson, Bror},
	month = aug,
	year = {2014},
	keywords = {NREI, drift, ecohydraulics},
	pages = {1158--1170},
}

Criteria used to characterize lotic salmonid habitat suitability are often based on correlations between physical habitat characteristics and salmonid abundance. Focusing on physical habitat features ignores other habitat components, such as an adequate food supply, that limit the amount of energy available for growth and survival. We tested the degree that food availability and temperature influence lotic salmonid consumption and growth rates and outline an approach for assessing habitat quality based on measurements of these features. We collected benthic and drifting invertebrate abundances, stream temperatures, and juvenile steelhead – rainbow trout (Onchorhynchus mykiss gairdneri) summer growth rates among nine stream segments in central Oregon. Stream temperatures and growth rates were used in bioenergetics model simulations to estimate O. mykiss consumption rates. The variation in O. mykiss consumption rates was explained by measurements of total drift biomass along a type II predator response curve (R2 = 0.71). This simplified foraging relationship between food abundance and consumption is then used to estimate the consumption component of the bioenergetics model to allow estimation of salmonid growth potential. Validation of the growth potential model produced reasonably accurate estimates of fish growth rates at reaches within the study area and precise but biased estimates in novel systems. While additional reach-level habitat information may be required to make the model more generalizable, the assessment of invertebrate food availability offers a simple yet powerful approach for describing the growth potential of stream habitat.

@article{rosenfeld_successes_2014,
	title = {Successes, failures, and opportunities in the practical application of drift-foraging models},
	volume = {97},
	issn = {0378-1909, 1573-5133},
	url = {http://link.springer.com/10.1007/s10641-013-0195-6},
	doi = {10.1007/s10641-013-0195-6},
	language = {en},
	number = {5},
	urldate = {2022-01-09},
	journal = {Environmental Biology of Fishes},
	author = {Rosenfeld, Jordan S. and Bouwes, Nicolaas and Wall, C. Eric and Naman, Sean M.},
	month = may,
	year = {2014},
	pages = {551--574},
}

@book{fryirs_geomorphic_2013,
	address = {Chichester, U.K.},
	title = {Geomorphic {Analysis} of {River} {Systems}: {An} {Approach} to {Reading} the {Landscape}, {First} {Edition}.},
	publisher = {Blackwell Publishing Ltd.},
	author = {Fryirs, Kirstie A. and Brierley, Gary A.},
	year = {2013},
}

@book{maddock_ecohydraulics_2013,
	address = {Chichester, U.K.},
	title = {Ecohydraulics: {An} {Integrated} {Approach} {\textbar} {Wiley}},
	isbn = {978-0-470-97600-5},
	shorttitle = {Ecohydraulics},
	url = {https://www.wiley.com/en-us/Ecohydraulics%3A+An+Integrated+Approach-p-9780470976005},
	abstract = {Ecohydraulics: An Integrated Approachprovides a research level text which highlights recent developments of this emerging and expanding field. With a focus on interdisciplinary research the text examines:- the evolution and scope of ecohydraulics interactions between hydraulics, hydrology, fluvial geomorphology and aquatic ecology the application of habitat modelling in ecohydraulic studies state of the art methodological developments and approaches detailed case studies including fish passage design and the management of environmental flow regimes research needs and the future of ecohydraulics research The contributions offer broad geographic coverage to encapsulate the wide range of approaches, case studies and methods used to conduct ecohydraulics research. The book considers a range of spatial and temporal scales of relevance and aquatic organisms ranging from algae and macrophytes to macroinvertebrates and fish. River management and restoration are also considered in detail, making this volume of direct relevance to those concerned with cutting edge research and its application for water resource management. Aimed at academics and postgraduate researchers in departments of physical geography, earth sciences, environmental science, environmental management, civil engineering, biology, zoology, botany and ecology; Ecohydraulics: An Integrated Approach will be of direct relevance to academics, researchers and professionals working in environmental research organisations, national agencies and consultancies.},
	language = {en-us},
	urldate = {2020-03-28},
	publisher = {Wiley},
	author = {Maddock, Ian and Harby, Atle and Kemp, Paul S. and Wood, Paul J.},
	year = {2013},
}

Ecohydraulics: An Integrated Approachprovides a research level text which highlights recent developments of this emerging and expanding field. With a focus on interdisciplinary research the text examines:- the evolution and scope of ecohydraulics interactions between hydraulics, hydrology, fluvial geomorphology and aquatic ecology the application of habitat modelling in ecohydraulic studies state of the art methodological developments and approaches detailed case studies including fish passage design and the management of environmental flow regimes research needs and the future of ecohydraulics research The contributions offer broad geographic coverage to encapsulate the wide range of approaches, case studies and methods used to conduct ecohydraulics research. The book considers a range of spatial and temporal scales of relevance and aquatic organisms ranging from algae and macrophytes to macroinvertebrates and fish. River management and restoration are also considered in detail, making this volume of direct relevance to those concerned with cutting edge research and its application for water resource management. Aimed at academics and postgraduate researchers in departments of physical geography, earth sciences, environmental science, environmental management, civil engineering, biology, zoology, botany and ecology; Ecohydraulics: An Integrated Approach will be of direct relevance to academics, researchers and professionals working in environmental research organisations, national agencies and consultancies.

@book{noauthor_ecohydraulics_2013,
	edition = {1},
	title = {Ecohydraulics},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781118526576#page=46},
	urldate = {2020-02-03},
	publisher = {John Wiley \& Sons, Ltd},
	year = {2013},
	doi = {10.1002/9781118526576},
}

@article{tonina_hydraulic_2013,
	title = {Hydraulic modeling approaches for ecohydraulic studies: {3D}, {2D}, {1D} and non-numerical models},
	shorttitle = {Hydraulic modeling approaches for ecohydraulic studies},
	journal = {Ecohydraulics: An integrated approach},
	author = {Tonina, Daniele and Jorde, Klaus},
	year = {2013},
	pages = {31--66},
}

@article{tonina_hydraulic_2013-1,
	title = {Hydraulic modeling approaches for ecohydraulic studies: {3D}, {2D}, {1D} and non-numerical models},
	shorttitle = {Hydraulic modeling approaches for ecohydraulic studies},
	journal = {Ecohydraulics: An integrated approach},
	author = {Tonina, Daniele and Jorde, Klaus},
	year = {2013},
	pages = {31--66},
}

@book{maddock_ecohydraulics_2013-1,
	title = {Ecohydraulics: {An} {Integrated} {Approach}},
	isbn = {978-1-118-52674-3},
	shorttitle = {Ecohydraulics},
	abstract = {Ecohydraulics: An Integrated Approachprovides a research level text which highlights recent developments of this emerging and expanding field. With a focus on interdisciplinary research the text examines:-  the evolution and scope of ecohydraulics interactions between hydraulics, hydrology, fluvial geomorphology and aquatic ecology the application of habitat modelling in ecohydraulic studies state of the art methodological developments and approaches detailed case studies including fish passage design and the management of environmental flow regimes research needs and the future of ecohydraulics research  The contributions offer broad geographic coverage to encapsulate the wide range of approaches, case studies and methods used to conduct ecohydraulics research. The book considers a range of spatial and temporal scales of relevance and aquatic organisms ranging from algae and macrophytes to macroinvertebrates and fish. River management and restoration are also considered in detail, making this volume of direct relevance to those concerned with cutting edge research and its application for water resource management. Aimed at academics and postgraduate researchers in departments of physical geography, earth sciences, environmental science, environmental management, civil engineering, biology, zoology, botany and ecology; Ecohydraulics: An Integrated Approach will be of direct relevance to academics, researchers and professionals working in environmental research organisations, national agencies and consultancies.},
	language = {en},
	publisher = {John Wiley \& Sons},
	author = {Maddock, Ian and Harby, Atle and Kemp, Paul and Wood, Paul J.},
	month = jul,
	year = {2013},
	note = {Google-Books-ID: Bl73vwEZFaMC},
	keywords = {Science / Earth Sciences / General, Technology \& Engineering / Hydraulics},
}

Ecohydraulics: An Integrated Approachprovides a research level text which highlights recent developments of this emerging and expanding field. With a focus on interdisciplinary research the text examines:- the evolution and scope of ecohydraulics interactions between hydraulics, hydrology, fluvial geomorphology and aquatic ecology the application of habitat modelling in ecohydraulic studies state of the art methodological developments and approaches detailed case studies including fish passage design and the management of environmental flow regimes research needs and the future of ecohydraulics research The contributions offer broad geographic coverage to encapsulate the wide range of approaches, case studies and methods used to conduct ecohydraulics research. The book considers a range of spatial and temporal scales of relevance and aquatic organisms ranging from algae and macrophytes to macroinvertebrates and fish. River management and restoration are also considered in detail, making this volume of direct relevance to those concerned with cutting edge research and its application for water resource management. Aimed at academics and postgraduate researchers in departments of physical geography, earth sciences, environmental science, environmental management, civil engineering, biology, zoology, botany and ecology; Ecohydraulics: An Integrated Approach will be of direct relevance to academics, researchers and professionals working in environmental research organisations, national agencies and consultancies.

@incollection{noack_habitat_2013,
	title = {The {Habitat} {Modelling} {System} {CASiMiR}: {A} {Multivariate} {Fuzzy} {Approach} and its {Applications}},
	copyright = {This edition first published 2013 © 2013 John Wiley \& Sons, Ltd},
	isbn = {978-1-118-52657-6},
	shorttitle = {The {Habitat} {Modelling} {System} {CASiMiR}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781118526576.ch4},
	abstract = {This chapter focuses on the application of the habitat simulation model computer aided simulation model for instream flow riparia (CASiMiR), with its fuzzy approach to the interface of biological responses to flow changes and physical habitat variables. After a brief introduction to the fuzzy approach, a comparison with the classical preference functions approach is presented together with two state-of-the-art model concepts and applications beyond classical physical habitat modelling applications, implying the adaptability of the fuzzy approach to present issues in ecohydraulic modeling. The chapter also presents case studies on simulation of spawning habitats for grayling},
	language = {en},
	urldate = {2020-02-03},
	booktitle = {Ecohydraulics},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Noack, Markus and Schneider, Matthias and Wieprecht, Silke},
	year = {2013},
	doi = {10.1002/9781118526576.ch4},
	keywords = {classical preference functions, habitat simulation model CASiMiR, morphodynamic processes, multivariate fuzzy approach, spawning habitats},
	pages = {75--91},
}

This chapter focuses on the application of the habitat simulation model computer aided simulation model for instream flow riparia (CASiMiR), with its fuzzy approach to the interface of biological responses to flow changes and physical habitat variables. After a brief introduction to the fuzzy approach, a comparison with the classical preference functions approach is presented together with two state-of-the-art model concepts and applications beyond classical physical habitat modelling applications, implying the adaptability of the fuzzy approach to present issues in ecohydraulic modeling. The chapter also presents case studies on simulation of spawning habitats for grayling

@article{diez-hernandez_hydrodynamic_2008,
	title = {Hydrodynamic ecohydraulic habitat assessment aimed at conserving and restoring fluvial hydrosystems},
	volume = {28},
	number = {2},
	journal = {Ingeniería e Investigación},
	author = {Diez-Hernández, Juan Manuel},
	year = {2008},
	pages = {97--107},
}

@article{diez-hernandez_hydrodynamic_2008-1,
	title = {Hydrodynamic ecohydraulic habitat assessment aimed at conserving and restoring fluvial hydrosystems},
	volume = {28},
	number = {2},
	journal = {Ingeniería e Investigación},
	author = {Diez-Hernández, Juan Manuel},
	year = {2008},
	pages = {97--107},
}

@article{moir_relationships_2008,
	title = {Relationships between mesoscale morphological units, stream hydraulics and {Chinook} salmon ({Oncorhynchus} tshawytscha) spawning habitat on the {Lower} {Yuba} {River}, {California}},
	volume = {100},
	issn = {0169-555X},
	doi = {10.1016/j.geomorph.2008.02.001},
	abstract = {An expert-based approach was used to identify 10 morphological unit types within a reach of the gravel bed, regulated Yuba River, California, that is heavily utilized by spawning Chinook salmon (Oncorhynchus tshawytscha). Analysis of these units was carried out using two-dimensional hydrodynamic modeling, field-based geomorphic assessment, and detailed spawning Surveying. Differently classified morphological units tended to exhibit discrete hydraulic signatures. In most cases, the Froude number adequately differentiated morphological units, but joint depth-velocity distributions proved the most effective hydraulic classification approach. Spawning activity was statistically differentiated at the mesoscale of the morphological unit. Salmon preferred lateral bar, riffle, and riffle entrance units. These units had moderately high velocity (unit median {\textgreater}0.45 m s(-1)) and low depth (unit median {\textless}0.6 m), but each exhibited a unique joint depth-velocity distribution. A large proportion of redds (79\%) were associated with conditions of convective flow acceleration at riffle and riffle entrance locations. In addition to reflecting microhabitat requirements of fish, it was proposed that the hydraulic segregation of preferred from avoided or tolerated morphological units was linked to the Mutual association of specific hydraulic conditions with suitable caliber sediment that promotes the provision and maintenance of spawning habitat. (C) 2008 Elsevier B.V. All rights reserved.},
	number = {3-4},
	journal = {Geomorphology},
	author = {Moir, H. J. and Pasternack, G. B.},
	month = aug,
	year = {2008},
	keywords = {ATLANTIC SALMON, BASIN, CHANNEL, Chinook salmon, ELECTIVITY, FLOODPLAIN ENVIRONMENTS, FLOW STRUCTURE, GRAVEL-BED RIVER, HIGH-RESOLUTION, INDEXES, MODELS, SEDIMENT, fluvial geomorphology, hydraulics, morphological units, spawning, two-dimensional modeling},
	pages = {527--548},
}

An expert-based approach was used to identify 10 morphological unit types within a reach of the gravel bed, regulated Yuba River, California, that is heavily utilized by spawning Chinook salmon (Oncorhynchus tshawytscha). Analysis of these units was carried out using two-dimensional hydrodynamic modeling, field-based geomorphic assessment, and detailed spawning Surveying. Differently classified morphological units tended to exhibit discrete hydraulic signatures. In most cases, the Froude number adequately differentiated morphological units, but joint depth-velocity distributions proved the most effective hydraulic classification approach. Spawning activity was statistically differentiated at the mesoscale of the morphological unit. Salmon preferred lateral bar, riffle, and riffle entrance units. These units had moderately high velocity (unit median \textgreater0.45 m s(-1)) and low depth (unit median \textless0.6 m), but each exhibited a unique joint depth-velocity distribution. A large proportion of redds (79%) were associated with conditions of convective flow acceleration at riffle and riffle entrance locations. In addition to reflecting microhabitat requirements of fish, it was proposed that the hydraulic segregation of preferred from avoided or tolerated morphological units was linked to the Mutual association of specific hydraulic conditions with suitable caliber sediment that promotes the provision and maintenance of spawning habitat. (C) 2008 Elsevier B.V. All rights reserved.

@article{hayes_process-based_2007,
	title = {Process-based modelling of invertebrate drift transport, net energy intake and reach carrying capacity for drift-feeding salmonids},
	volume = {207},
	issn = {03043800},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S030438000700258X},
	doi = {10.1016/j.ecolmodel.2007.04.032},
	abstract = {We present an overview of a process-based modelling approach for predicting how change in flow affects drift density, net rate of energy intake (NREI) and numbers of drift-feeding salmonids. It involves linking an existing two-dimensional flow model (River2D) with models of invertebrate drift transport and drift-foraging which we have developed. We describe, demonstrate and partially test our models in an application on a 80 m × 20 m pool on a New Zealand river. We show how these models realistically capture hydraulic, drift dispersion and bioenergetics drift-foraging processes to predict the relationship between stream flow, habitat quality and quantity (in terms of NREI), and carrying capacity for drift-feeding salmonids. Overall, the 2D hydraulic model made good predictions of water levels, depths and water velocity at the calibration flow and a lower (validation) flow. The drift transport model made good predictions of the spatial distribution of invertebrate drift density throughout the pool at low flow after it was calibrated against observed drift density at the higher flow. The model correctly predicted that drift density would decline downstream and into the margins due to the process of settling dominating over entry from the stream bed, and that drift would be carried further downstream and laterally as flow increased. The foraging model made a reasonable prediction (6–7) of the numbers of 0.5 m adult brown trout observed (5) in the pool. It accurately predicted that trout should be distributed down the thalweg where net rate of energy intake (NREI) was highest, but when NREI was adjusted for depletion by feeding fish the predicted drift-feeding locations were more closely spaced (bunched) than observed fish locations. Our processbased modelling approach has important implications for improving biological realism in predictions of the response of drift-feeding fishes to flow change within the context of the IFIM.},
	language = {en},
	number = {2-4},
	urldate = {2022-01-09},
	journal = {Ecological Modelling},
	author = {Hayes, John W. and Hughes, Nicholas F. and Kelly, Lon H.},
	month = oct,
	year = {2007},
	pages = {171--188},
}

We present an overview of a process-based modelling approach for predicting how change in flow affects drift density, net rate of energy intake (NREI) and numbers of drift-feeding salmonids. It involves linking an existing two-dimensional flow model (River2D) with models of invertebrate drift transport and drift-foraging which we have developed. We describe, demonstrate and partially test our models in an application on a 80 m × 20 m pool on a New Zealand river. We show how these models realistically capture hydraulic, drift dispersion and bioenergetics drift-foraging processes to predict the relationship between stream flow, habitat quality and quantity (in terms of NREI), and carrying capacity for drift-feeding salmonids. Overall, the 2D hydraulic model made good predictions of water levels, depths and water velocity at the calibration flow and a lower (validation) flow. The drift transport model made good predictions of the spatial distribution of invertebrate drift density throughout the pool at low flow after it was calibrated against observed drift density at the higher flow. The model correctly predicted that drift density would decline downstream and into the margins due to the process of settling dominating over entry from the stream bed, and that drift would be carried further downstream and laterally as flow increased. The foraging model made a reasonable prediction (6–7) of the numbers of 0.5 m adult brown trout observed (5) in the pool. It accurately predicted that trout should be distributed down the thalweg where net rate of energy intake (NREI) was highest, but when NREI was adjusted for depletion by feeding fish the predicted drift-feeding locations were more closely spaced (bunched) than observed fish locations. Our processbased modelling approach has important implications for improving biological realism in predictions of the response of drift-feeding fishes to flow change within the context of the IFIM.

@book{brierley_geomorphology_2005,
	address = {Victoria, Australia},
	title = {Geomorphology and {River} {Management}: {Applications} of the {River} {Styles} {Framework}},
	isbn = {1 74138 153 3},
	publisher = {Blackwell Publishing},
	author = {Brierley, G. and Fryirs, K.},
	year = {2005},
}

@article{leclerc_ecohydraulics_2005,
	title = {Ecohydraulics: a new interdisciplinary frontier for {CDF}},
	shorttitle = {Ecohydraulics},
	journal = {Computational Fluid Dynamics: Applications in Environmental Hydraulics, Bates P, Lane S, Ferguson R (eds). John Wiley \& Sons Ltd: Chichester, UK},
	author = {Leclerc, M.},
	year = {2005},
}

@article{leclerc_ecohydraulics_2005-1,
	title = {Ecohydraulics: a new interdisciplinary frontier for {CDF}},
	shorttitle = {Ecohydraulics},
	journal = {Computational Fluid Dynamics: Applications in Environmental Hydraulics, Bates P, Lane S, Ferguson R (eds). John Wiley \& Sons Ltd: Chichester, UK},
	author = {Leclerc, M.},
	year = {2005},
}

@article{doyle_effective_2005,
	title = {Effective discharge analysis of ecological processes in streams},
	volume = {41},
	copyright = {Copyright 2005 by the American Geophysical Union.},
	issn = {1944-7973},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2005WR004222},
	doi = {10.1029/2005WR004222},
	abstract = {Discharge is a master variable that controls many processes in stream ecosystems. However, there is uncertainty of which discharges are most important for driving particular ecological processes and thus how flow regime may influence entire stream ecosystems. Here the analytical method of effective discharge from fluvial geomorphology is used to analyze the interaction between frequency and magnitude of discharge events that drive organic matter transport, algal growth, nutrient retention, macroinvertebrate disturbance, and habitat availability. We quantify the ecological effective discharge using a synthesis of previously published studies and modeling from a range of study sites. An analytical expression is then developed for a particular case of ecological effective discharge and is used to explore how effective discharge varies within variable hydrologic regimes. Our results suggest that a range of discharges is important for different ecological processes in an individual stream. Discharges are not equally important; instead, effective discharge values exist that correspond to near modal flows and moderate floods for the variable sets examined. We suggest four types of ecological response to discharge variability: discharge as a transport mechanism, regulator of habitat, process modulator, and disturbance. Effective discharge analysis will perform well when there is a unique, essentially instantaneous relationship between discharge and an ecological process and poorly when effects of discharge are delayed or confounded by legacy effects. Despite some limitations the conceptual and analytical utility of the effective discharge analysis allows exploring general questions about how hydrologic variability influences various ecological processes in streams.},
	language = {en},
	number = {11},
	urldate = {2020-02-03},
	journal = {Water Resources Research},
	author = {Doyle, Martin W. and Stanley, Emily H. and Strayer, David L. and Jacobson, Robert B. and Schmidt, John C.},
	year = {2005},
	keywords = {dominant discharge, ecohydrology, flow regime, flow regulation, fluvial geomorphology, magnitude-frequency analysis},
}

Discharge is a master variable that controls many processes in stream ecosystems. However, there is uncertainty of which discharges are most important for driving particular ecological processes and thus how flow regime may influence entire stream ecosystems. Here the analytical method of effective discharge from fluvial geomorphology is used to analyze the interaction between frequency and magnitude of discharge events that drive organic matter transport, algal growth, nutrient retention, macroinvertebrate disturbance, and habitat availability. We quantify the ecological effective discharge using a synthesis of previously published studies and modeling from a range of study sites. An analytical expression is then developed for a particular case of ecological effective discharge and is used to explore how effective discharge varies within variable hydrologic regimes. Our results suggest that a range of discharges is important for different ecological processes in an individual stream. Discharges are not equally important; instead, effective discharge values exist that correspond to near modal flows and moderate floods for the variable sets examined. We suggest four types of ecological response to discharge variability: discharge as a transport mechanism, regulator of habitat, process modulator, and disturbance. Effective discharge analysis will perform well when there is a unique, essentially instantaneous relationship between discharge and an ecological process and poorly when effects of discharge are delayed or confounded by legacy effects. Despite some limitations the conceptual and analytical utility of the effective discharge analysis allows exploring general questions about how hydrologic variability influences various ecological processes in streams.

@article{payne_number_2004,
	title = {The {Number} of {Transects} {Required} to {Compute} a {Robust} {PHABSIM} {Habitat} {Index}},
	volume = {14},
	copyright = {© EDF, 2004},
	issn = {1147-9213, 1958-556X},
	url = {https://www.hydroecologie.org/articles/hydro/abs/2004/01/hydro04103/hydro04103.html},
	doi = {10.1051/hydro:2004003},
	abstract = {The value of the number of transects within a segment of an instream flow study that will generate a stable relationship between the PHABSIM habitat index and discharge is examined. Over 600 instream flow studies were reviewed to determine the common practice standard, showing a median number of eight transects per four mile reach. Since the number of study transects varies by length of reach and purpose of study, transects per mile were computed as a more standardized value, with a median result of 2.32 transects per mile for 552 reaches. Studies conducted for water rights claims (255) had a median of 1.30 transects per mile and those conducted for project evaluations (259) had a median of 4.17 transects per mile. Several high transect number data sets were also systematically subsampled to determine how many transects are required to produce a robust habitat index function. This analysis showed that approximately 18-20 transects will in most cases yield a result nearly identical to one obtained using 40-70 transects per segment. When used for time series analysis and comparison of flow alternatives, remaining small differences in the functions would be inconsequential.If used for standard setting purposes, however, the differences could affect flow recommendations and more transects are likely to be necessary.},
	language = {en},
	urldate = {2020-02-03},
	journal = {Hydroécologie Appliquée},
	author = {Payne, Thomas R. and Eggers, Steven D. and Parkinson, Douglas B.},
	year = {2004},
	pages = {27--53},
}

The value of the number of transects within a segment of an instream flow study that will generate a stable relationship between the PHABSIM habitat index and discharge is examined. Over 600 instream flow studies were reviewed to determine the common practice standard, showing a median number of eight transects per four mile reach. Since the number of study transects varies by length of reach and purpose of study, transects per mile were computed as a more standardized value, with a median result of 2.32 transects per mile for 552 reaches. Studies conducted for water rights claims (255) had a median of 1.30 transects per mile and those conducted for project evaluations (259) had a median of 4.17 transects per mile. Several high transect number data sets were also systematically subsampled to determine how many transects are required to produce a robust habitat index function. This analysis showed that approximately 18-20 transects will in most cases yield a result nearly identical to one obtained using 40-70 transects per segment. When used for time series analysis and comparison of flow alternatives, remaining small differences in the functions would be inconsequential.If used for standard setting purposes, however, the differences could affect flow recommendations and more transects are likely to be necessary.

@inproceedings{leclerc_ecohydraulics_2002,
	title = {Ecohydraulics, last frontier for fluvial hydraulics: research challenges and multidisciplinary perspectives},
	shorttitle = {Ecohydraulics, last frontier for fluvial hydraulics},
	booktitle = {Proceedings of {RiverFlow} 2002 {Conference}, {Louvain}-la-{Neuve}, {Belgium}},
	author = {Leclerc, Michel},
	year = {2002},
}

@inproceedings{leclerc_ecohydraulics_2002-1,
	title = {Ecohydraulics, last frontier for fluvial hydraulics: research challenges and multidisciplinary perspectives},
	shorttitle = {Ecohydraulics, last frontier for fluvial hydraulics},
	booktitle = {Proceedings of {RiverFlow} 2002 {Conference}, {Louvain}-la-{Neuve}, {Belgium}},
	author = {Leclerc, Michel},
	year = {2002},
}

@article{poole_ecological_2001,
	title = {An {Ecological} {Perspective} on {In}-{Stream} {Temperature}: {Natural} {Heat} {Dynamics} and {Mechanisms} of {Human}-{CausedThermal} {Degradation}},
	volume = {27},
	issn = {0364-152X, 1432-1009},
	shorttitle = {An {Ecological} {Perspective} on {In}-{Stream} {Temperature}},
	url = {http://link.springer.com/10.1007/s002670010188},
	doi = {10.1007/s002670010188},
	language = {en},
	number = {6},
	urldate = {2020-04-20},
	journal = {Environmental Management},
	author = {Poole, Geoffrey C. and Berman, Cara H.},
	month = jun,
	year = {2001},
	pages = {787--802},
}

@techreport{waddle_phabsim_2001,
	type = {{USGS} {Numbered} {Series}},
	title = {{PHABSIM} for {Windows} {User}'s {Manual} and {Exercises}},
	url = {http://pubs.er.usgs.gov/publication/ofr2001340},
	abstract = {This document is a combined self-study textbook and reference manual. The material is presented in the general order of a PHABSIM study placed within the context of an IFIM application. The document may also be used as reading material for a lecture-based course. This manual provides documentation of the various PHABSIM programs so every option of each program is treated.This text is not a guidebook for organization and implementation of a PHABSIM study. Use of PHABSIM should take place in the context of an IFIM application. See Bovee et al. (1998) for guidance in designing and performing a PHABSIM study as part of a larger IFIM application.The document concludes with a set of 12 laboratory exercises. Users are strongly encouraged to work through the laboratory exercises prior to applying the software to a study. Working through the exercises will enhance familiarity with the programs and answer many questions that may arise during a PHABSIM analysis.},
	number = {2001-340},
	urldate = {2020-02-03},
	author = {Waddle, Terry},
	year = {2001},
}

This document is a combined self-study textbook and reference manual. The material is presented in the general order of a PHABSIM study placed within the context of an IFIM application. The document may also be used as reading material for a lecture-based course. This manual provides documentation of the various PHABSIM programs so every option of each program is treated.This text is not a guidebook for organization and implementation of a PHABSIM study. Use of PHABSIM should take place in the context of an IFIM application. See Bovee et al. (1998) for guidance in designing and performing a PHABSIM study as part of a larger IFIM application.The document concludes with a set of 12 laboratory exercises. Users are strongly encouraged to work through the laboratory exercises prior to applying the software to a study. Working through the exercises will enhance familiarity with the programs and answer many questions that may arise during a PHABSIM analysis.

@article{hughes_physiological_2000,
	title = {Physiological {Ecology} {Meets} the {Ideal}-free {Distribution}: {Predicting} the {Distribution} of {Size}-structured {Fish} {Populations} {Across} {Temperature} {Gradients}},
	volume = {59},
	issn = {0378-1909, 1573-5133},
	shorttitle = {Physiological {Ecology} {Meets} the {Ideal}-free {Distribution}},
	url = {http://link.springer.com/10.1023/A:1007608720672},
	doi = {10.1023/A:1007608720672},
	language = {en},
	number = {3},
	urldate = {2022-01-09},
	journal = {Environmental Biology of Fishes},
	author = {Hughes, Nicholas F. and Grand, Tamara C.},
	month = nov,
	year = {2000},
	keywords = {NREI, drift, ecohydraulics},
	pages = {285--298},
}

@techreport{bovee_stream_1998,
	address = {Fort Collins, CO},
	type = {Federal {Government} {Series}},
	title = {Stream habitat analysis using the instream flow incremental methodology},
	url = {http://pubs.er.usgs.gov/publication/itr19980004},
	abstract = {This document describes the Instream Flow Methodology in its entirety. This also is to serve as a comprehensive introductory textbook on IFIM for training courses as it contains the most complete and comprehensive description of IFIM in existence today. This should also serve as an official guide to IFIM in publication to counteract the misconceptions about the methodology that have pervaded the professional literature since the mid-1980's as this describes IFIM as it is envisioned by its developers. The document is aimed at the decisionmakers of management and allocation of natural resources in providing them an overview; and to those who design and implement studies to inform the decisionmakers. There should be enough background on model concepts, data requirements, calibration techniques, and quality assurance to help the technical user design and implement a cost-effective application of IFIM that will provide policy-relevant information. Some of the chapters deal with basic organization of IFIM, procedural sequence of applying IFIM starting with problem identification, study planning and implementation, and problem resolution.},
	number = {1998-0004},
	urldate = {2020-02-03},
	institution = {U.S. Geological Survey},
	author = {Bovee, Ken D. and Lamb, Berton L. and Bartholow, John M. and Stalnaker, Clair B. and Taylor, Jonathan and Henriksen, Jim},
	year = {1998},
	pages = {138},
}

This document describes the Instream Flow Methodology in its entirety. This also is to serve as a comprehensive introductory textbook on IFIM for training courses as it contains the most complete and comprehensive description of IFIM in existence today. This should also serve as an official guide to IFIM in publication to counteract the misconceptions about the methodology that have pervaded the professional literature since the mid-1980's as this describes IFIM as it is envisioned by its developers. The document is aimed at the decisionmakers of management and allocation of natural resources in providing them an overview; and to those who design and implement studies to inform the decisionmakers. There should be enough background on model concepts, data requirements, calibration techniques, and quality assurance to help the technical user design and implement a cost-effective application of IFIM that will provide policy-relevant information. Some of the chapters deal with basic organization of IFIM, procedural sequence of applying IFIM starting with problem identification, study planning and implementation, and problem resolution.

@inproceedings{bovee_perspectives_1996,
	title = {Perspectives on two-dimensional river habitat models: the {PHABSIM} experience},
	volume = {B},
	author = {Bovee, K.},
	editor = {Leclerc, M. and Capra, H. and Valentin, S. and Boudreault, A. and Cote, I.},
	year = {1996},
}

@article{cavendish_use_1986,
	title = {Use of the instream flow incremental methodology: {A} tool for negotiation},
	volume = {6},
	issn = {0195-9255},
	shorttitle = {Use of the instream flow incremental methodology},
	url = {http://www.sciencedirect.com/science/article/pii/0195925586900272},
	doi = {10.1016/0195-9255(86)90027-2},
	abstract = {The resolution of conflicts arising from differing values and water uses requires technical information and negotiating skills. This article outlines the Instream Flow Incremental Methodology (IFIM), developed by the US Fish and Wildlife Service, and demonstrates that its use to quantify flows necessary to protect desired instream values aids negotiation by illustrating areas of agreement and possible compromises between conflicting water interests. Pursuant to a Section 404 permit application to the US Army Corps of Engineers made by City Utilities of Springfield, Missouri, in 1978, IFIM provided the means by which City Utilities, concerned with a secure water supply for a growing population, and those advocating instream values were satisfied that their requirements were met. In tracing the 15-month process, the authors conclude that the application of IFIM, as well as the cooperative stance adopted by the parties involved, were the key ingredients of the successful permit application.},
	language = {en},
	number = {4},
	urldate = {2020-02-03},
	journal = {Environmental Impact Assessment Review},
	author = {Cavendish, Mary G. and Duncan, Margaret I.},
	month = dec,
	year = {1986},
	pages = {347--363},
}

The resolution of conflicts arising from differing values and water uses requires technical information and negotiating skills. This article outlines the Instream Flow Incremental Methodology (IFIM), developed by the US Fish and Wildlife Service, and demonstrates that its use to quantify flows necessary to protect desired instream values aids negotiation by illustrating areas of agreement and possible compromises between conflicting water interests. Pursuant to a Section 404 permit application to the US Army Corps of Engineers made by City Utilities of Springfield, Missouri, in 1978, IFIM provided the means by which City Utilities, concerned with a secure water supply for a growing population, and those advocating instream values were satisfied that their requirements were met. In tracing the 15-month process, the authors conclude that the application of IFIM, as well as the cooperative stance adopted by the parties involved, were the key ingredients of the successful permit application.

@book{bovee_hydraulic_1978,
	title = {Hydraulic {Simulation} in {Instream} {Flow} {Studies}: {Theory} and {Techniques}},
	shorttitle = {Hydraulic {Simulation} in {Instream} {Flow} {Studies}},
	language = {en},
	publisher = {Department of the Interior, Fish and Wildlife Service, Office of Biological Services, Western Energy and Land Use Team, Cooperative Instream Flow Service Group},
	author = {Bovee, Ken D. and Milhous, Robert T. and Turow, Joseph},
	year = {1978},
	note = {Google-Books-ID: p4fzzOe3gagC},
}

@article{noauthor_fig_nodate,
	title = {Fig. 2 {\textbar} {Nature} {Communications}},
	copyright = {©2020 Macmillan Publishers Limited. All Rights Reserved.},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-019-12020-z/figures/2},
	language = {en},
	urldate = {2020-03-29},
}

@misc{noauthor_casimir_nodate,
	title = {{CASiMiR} - {Applications}},
	url = {http://www.casimir-software.de/ENG/veg_eng.html},
	urldate = {2020-02-03},
}