AA/NOAA/NPCC RM&E Workgroup.  2010.  Recommendations for Implementing Research, Monitoring and Evaluation for the 2008 NOAA Fisheries FCRPS BiOp. Portland, OR.

Almodovar, A., G. G. Nicola, and B. Elvira.  2006.  Spatial variation in brown trout production: the role of environmental factors.  Transactions of the American Fisheries Society 135:1248-1360.

AREMP.  2007.  Field protocol manual.  Aquatic and Riparian Effectiveness Monitoring Program, Interagency Monitoring Program, Northwest Forest Plan, USDA Forest Service Pacific Northwest Regional Office and Bureau of Land Management, Corvallis, OR.

AREMP.  2010.  Field protocol manual.  Aquatic and Riparian Effectiveness Monitoring Program, Interagency Monitoring Program, Northwest Forest Plan, USDA Forest Service Pacific Northwest Regional Office and Bureau of Land Management, Corvallis, OR.

Becker, C.D., and D.A. Neitzel.  1982.  Assessment of inter-gravel conditions influencing egg and alevin survival during salmonid redd dewatering.  Environmental Biology of Fishes 12 (1): 33-46, DOI: 10.1007/BF00007708.

Beechie, T., E. Buhle1, M. Ruckelshaus, A. Fullerton and L. Holsinger.  2006.  Hydrologic regime and the conservation of salmon life history diversity.  Biological Conservation 130(4): 560-572.

Bisson, P. A., D. R. Montgomery, and J. M. Buffington.  2006.  Valley segments, stream reaches, and channel units.  Pages 23-49 in Methods in Stream Ecology, 2nd edition. Elsevier.

Bisson, P.A., K. Sullivan, and J.L. Nielsen.  1988.  Channel Hydraulics, Habitat Use, and Body Form of Juvenile Coho Salmon, Steelhead, and Cutthroat Trout in Streams.  Transactions of the American Fisheries Society 1988; 117: 262-273 doi: 10.1577/1548-8659(1988)117<0262:CHHUAB>2.3.CO;2.

Bisson, P. A., R. E. Bilby, M. D. Bryant, C. A. Dolloff, G. B. Grette, R. A. House, M. L. Murphy, K. V. Koski, and J. R. Sedell.  1987.  Large woody debris in forested streams in the Pacific Northwest: past, present, and future.  Pages 143-190 in E.O. Salo and T.W. Cundy (eds.) Streamside management: forestry and fishery interactions.  Contribution No. 57.  Institute of Forest Resources, University of Washington, Seattle.

Bjornn, T.C., and Reiser, D.W.  1991.  Habitat requirements of salmonids in streams. In “Influence of forest and rangeland management on salmonid fishes and their habitats” Edited by W.R. Meehan. Am. Fish. Soc. Spec. Publ. 19. Bethesda, Md. pp. 83–138.

Boss, S.M., and J.S. Richardson.  2002.  Effects of food and cover on the growth, survival, and movement of cutthroat trout (Oncorhynchus clarki) in coastal streams.  Can. J. Fish. Aquat. Sci. 59(6): 1044–1053.  DOI:10.1139/f02-079.

Bouwes, N., N. Weber, S. Bennett, J. Moberg, B. Bouwes, and C.E. Jordan.  2010.  Tributary Habitat Monitoring at the Watershed or Population Scale: Preliminary Recommendations for Standardized Fish Habitat Monitoring in the Columbia River Basin.  Prepared for NOAA-Fisheries and Bonneville Power Administration.  June 1, 2010.

Brasington J, B.T. Rumsby, and R.A. McVey.  2000.  Monitoring and modeling morphological change in a braided gravel-bed river using high resolution GPS-based survey.  Earth Surface Processes and Landforms. 25(9): 973-990. DOI: 10.1002/1096-9837(200008)25:9<973::AID-ESP111>3.0.CO;2-Y

Brewer P.A., and D.G. Passmore.  2002.  Sediment budgeting techniques in gravel bed rivers. Jones S and Frostick L (Eds), In Sediment Flux to Basins: Causes, Controls and Consequences, Special Publication 191.  Geological Society: London, pp. 97-113.

Brierley, G. J. and K. A. Fryirs.  2005.  Geomorphology and River Management.  First edition. Blackwell Publishing, Malden, MA, USA.

Bryce, S. A., G. A. Lomnicky, and P. R. Kaufmann.  2010.  Protecting sediment-sensitive aquatic species in mountain streams through the application of biologically based streambed sediment criteria.  Journal of North American Benthological Society 29:657-672.

Bryce, S. A., G. A. Lomnicky, P. R. Kaufmann, L. S. McAllister, and T. L. Ernst.  2008.  Development of Biologically Based Sediment Criteria in Mountain Streams of the Western United States. North American Journal of Fisheries Management 28:1714-1724.

Buffington, J. M., T. E. Lisle, R. D. Woodsmith, and S. Hilton.  2002.  Controls on the size and occurrence of pools in coarse-grained forest rivers.  River Research and Applications, 18: 507–531. doi: 10.1002/rra.693

Bunte, K., S.R., Abt, J.P., Potyondy, and K.W. Swingle.  2009.  Comparison of Three Pebble Count Protocols (EMAP, PIBO, and SFT) in Two Mountain Gravel-Bed Streams.  J. Am. Water Resource Association. 45(5): 1209-1227.

Bunte, K., and S. R. Abt.  2001.  Sampling surface and subsurface particle-size distributions in wadeable gravel- and cobble-bed streams for analyses in sediment transport, hydraulics, and streambed monitoring.  General Technical Report. RMRS-GTR-74. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 428 p.

Cada, G. F., J. M. Loar, and D. K. Cox.  1987.  Food and feeding preferences of rainbow and brown trout in southern Appalachian streams.  American Midland Naturalist 117(2):374-385.

Chen, X. Y., X. H. Wei, R. Scherer, and D. Hogan.  2008.  Effects of large woody debris on surface structure and aquatic habitat in forested streams, southern interior British Columbia, Canada. River Research and Applications 24:862-875.

Coles-Ritchie M., R.C. Henderson, E.K. Archer, C. Kennedy, and J. L. Kershner.  2004.  Repeatability of Riparian Vegetation Sampling Methods: How Useful Are These Techniques for Broad-Scale, Long-Term Monitoring?  United States Department of Agriculture Forest Service Rocky Mountain Research Station General Technical Report RMRS-GTR-138.

Crowder D.W., and P. Diplas.  2000.  Using two-dimensional hydrodynamic models at scales of ecological importance.  Journal of Hydrology. 230(3-4): 172-191

Cunjack, R. A.  1996.  Winter habitat of selected stream fishes and potential impacts from land-use activity.  Canadian Journal of Fisheries and Aquatic Sciences 53:267–282.

Dauwalter, D.C., F.J. Rahel, and K.G. Gerow.  2009.  Temporal variation in trout populations: Implications for monitoring and trend detection.  Transactions of the American Fisheries Society 138:38–51.

Downie, S.T.  2004.  Stream channel measurement methods for core attributes.  Coastal Watershed Planning and Assessment Program, California Department of Fish and Game, Fortuna, CA.

Ebersole, J.L., W.J. Liss, and C.A. Frissell.  2003.  Thermal heterogeneity, stream channel morphology, and salmonid abundance in northeastern Oregon streams.  Canadian Journal of Fisheries and Aquatic Sciences 60:1266-1280.

EPA, U. S.  2004.  Wadeable Stream Assessment: Field Operations Manual.  U.S. Environmental Protection Agency, Office of Water and Office of Research and Development, Washington, DC.

Fausch, K. D., C. E. Torgersen, C. V. Baxter, and H. W. Li.  2002.  Landscapes to Riverscapes: Bridging the Gap between Research and Conservation of Stream Fishes.  Bioscience 52(6): 483-498.

Fausch, K. D., Y. Taniguchi, S. Nakano, G. D. Grossman, and C. R. Townsend.  2001.  Flood disturbance regimes influence rainbow trout invasion success among five holarctic regions.  Ecological Applications 11:1438-1455.

Filbert, R. B., and C. P. Hawkins.  1995.  Variation in condition of rainbow trout in relation to food, temperature, and individual length in the Green River, Utah.  Transactions of the American Fisheries Society 124:824-835.

Fuller, I. C., A. R. G. Large, M. E. Charlton, G. L. Heritage, and D. J. Milan.  2003.  Reach-scale sediment transfers: An evaluation of two morphological budgeting approaches.  Earth Surface Processes and Landforms 28:889-903.

Gallo, K, C. Moyer, and S. Lanigan.  2001.  Aquatic and Riparian Effectiveness-Monitoring Program: 2001 Pilot Summary Report.  U.S. Forest Service, Corvallis, OR. 82 pp.

Gregory, S. V., F. J. Swanson, W. A. McKee, and K. W. Cummins.  1991.  An Ecosystem Perspective of Riparian Zones: Focus on links between land and water.  Bioscience 41:540-551.

Guensch, G. R., T. B. Hardy, and R. C. Addley.  2001.  Examining feeding strategies and position choice of drift-feeding salmonids using an individual-based, mechanistic foraging model.  Can. J. Fish. Aquat. Sci. 58(3): 446–457 (2001). doi:10.1139/cjfas-58-3-446.

Hanson, P., T. Johnson, J. Kitchell, and D. E. Schindler.  1997.  Fish bioenergetics 3.0.  University of Wisconsin Sea Grant Institute, Madison, Wisconsin.

Harrelson, C. C., C. L. Rawlins, and J. P. Potyondy.  1994.  Stream channel reference sites: an illustrated guide to field technique.  USDA Forest Service, Rocky Mountain Forest and Range Experiment Station, General Technical Report RM-245, Fort Collins, CO.

Harvey, B. C.  1998.  Influence of large woody debris on retention, immigration, and growth of coastal cutthroat trout (Oncorhynchus clarki clarki) in stream pools.  Canadian Journal of Fisheries and Aquatic Sciences 55:1902-1908.

Harvey, B. C., R. J. Nakamoto, and J. L. White.  1999.  Influence of large woody debris and a bankfull flood on movement of adult resident coastal cutthroat trout (Oncorhynchus clarki) during fall and winter.  Canadian Journal of Fisheries and Aquatic Sciences 56:2161-2166.

Hawkins, C.P., J.L. Kershner, P.A. Bisson, M.D. Bryant, L.M. Decker, S.V. Gregory, D.A. McCullough, C.K. Overton, G.H. Reeves, , R.J. Steedman and M.K. Young.  1993.  A hierarchical approach to classifying stream habitat features.  Fisheries 18: 3-12.

Hayes, J. W., N. F. Hughes, and L. H. Kelly.  2007.  Process-based modeling of invertebrate drift transport, net energy intake and reach carrying capacity for drift-feeding salmonids.  Ecological Modeling 207:171-188.

Heitke, J.D., E.J. Archer, D.D. Dugaw, B.A. Bouwes, E.A. Archer, R.C. Henderson, and J.L. Kershner.   2008.  Effectiveness monitoring for streams and riparian areas: sampling protocol for stream channel attributes.  PACFISH/INFISH Biological Opinion (PIBO) Effectiveness Monitoring Program, Logan, UT.

Herlihy, A. T., D. P. Larsen, S. G. Paulsen, N. S. Urquhart, and B. J. Rosenbaum.  2000.  Designing a spatially balanced, randomized site selection process for regional stream surveys: The EMAP Mid-Atlantic Pilot Study. Environmental Monitoring and Assessment 63(1):95-113.

Holden,Z.A., M. A. Crimmins, S. A. Cushman, and J. S. Littell.  2010.  Empirical modeling of spatial and temporal variation in warm season nocturnal air temperatures in two North Idaho mountain ranges, USA, Agricultural and Forest Meteorology, Vol 151 (3): 261-269, ISSN 0168-1923, DOI: 10.1016/j.agrformet.2010.10.006.

(http://www.sciencedirect.com/science/article/pii/S0168192310002819)

Hughes, N. F.  1998.  A model of habitat selection by drift-feeding stream salmonids at different scales.  Ecology 79:281-294.

Hughes, N. F., J. W. Hayes, K. A. Shearer, and R. G. Young.  2003.  Testing a model of drift-feeding using three-dimensional videography of wild Brown Trout, Salmo trutta, in a New Zealand river.  Canadian Journal of Fisheries and Aquatic Sciences 60:1462-1476.

Hughes, N. F., and L. M. Dill.  1990.  Position choice by drift-feeding salmonids: model and test for Arctic grayling (Thymallusarcticus) in subarctic mountain streams.  Canadian Journal of Fisheries and Aquatic Sciences 47:2039-2048.

Isaak, D., D. Horan, and S. Wolrab.  2010.  A Simple Method Using Underwater Epoxy to Permanently Install Temperature Sensors in Mountain Streams.  U.S. Forest Service, Rocky Mountain Research Station Air, Water, and Aquatics Program- Boise Aquatic Sciences Lab, Boise, ID

ISRPa.  2010.  Final Review of 2010 Proposals for the Research, Monitoring, and Evaluation and Artificial Production Category.  Part 1: Programmatic Comments.  ISRP 2010-44A.  December 16, 2010.

ISRPb.  2010.  Final Review of 2010 Proposals for the Research, Monitoring, and Evaluation and Artificial Production Category.  Part 2: Recommendations and Comments on Individual Proposals.  ISRP 2010-44B.  December 16, 2010.

Jacobs, S.E., W. Gaeuman, M.A. Weeber, S.L. Gunckel, and S.J. Starcevich.  2009.  Utility of a probabilistic sampling design to determine bull trout population status using redd counts in basins of the Columbia River Plateau.  North American Journal of Fish Management 29:1590-1604

Jensen, D.W., E. A. Steel, A.H. Fullerton, and G.R. Pess.  2009.  Impact of Fine Sediment on Egg-To-Fry Survival of Pacific Salmon: A Meta-Analysis of Published Studies.  Reviews in Fisheries Science, 17: 3, 348 -359.  DOI: 10.1080/10641260902716954URL: http://dx.doi.org/10.1080/10641260902716954

Johnson, D. H., and coauthors.  2001.  Inventory and monitoring of salmon habitat in the Pacific Northwest: Directory and synthesis of protocols for management/research and volunteers in Washington, Oregon, Idaho, Montana, and British Columbia.  Washington Department of Fish and Wildlife, Olympia, WA.

Kaufmann, P. R., P. Levine, E. G. Robison, C. Seeliger, and D.V. Peck.  1999.  Quantifying Physical Habitat in Wadeable Streams.  EPA/620/R-99/003, U.S. Environmental Protection Agency, Washington D.C.

Keim, R.F., and A.E. Skaugset.  2002.  Physical aquatic habitat I. Errors associated with measurement and estimation of residual pool volumes.  N. Am. J. Fish. Manag. 22(2): 145-150.

Kondolf, G.M., E.W. Larsen, and J.G. Williams.  2000.  Measuring and Modeling the Hydraulic Environment for Assessing Instream Flows.  North American Journal of Fisheries Management 20: 1016-1028.

Kondolf, G. M.  1997.  Application of the pebble count: Notes on purpose, methods and variants.  Journal of the American Water Resources Association 38:79-87.

Leary, R.J., and P. Ebertowski.  2010.  Effectiveness monitoring for streams and riparian areas: sampling protocol for vegetation parameters.  Unpublished paper on file at: http://www.fs.fed.us/biology/fishecology/emp.

Leclerc M., A. Boudreault, J.A. Bechara, and G. Corfa.  1995.  Two-dimensional hydrodynamic modeling: a neglected tool in the instream flow incremental methodology.  Transactions of the American Fisheries Society. 124(5): 645-662

Lohr, S. L.  1999.  Sampling: Design and Analysis.  Duxbury Press, Pacific Grove, CA.

McKean, J., D. Nagel, D. Tonina, P. Bailey, C.W. Wright, C. Bohn, and A. Nayegandhi.  2009.  Remote sensing of channels and riparian zones with a narrow-beam aquatic-terrestrial LiDAR. Remote Sensing, 1, 1065-1096; DOI:10.3390/rs1041065.

Merritt, G.  2009.  Status and Trends Monitoring for Watershed Health & Salmon Recovery: Field Data Collection Protocol, Washington State Department of Ecology, Olympia, WA.

Moberg, J.  2009.  A Scientific Protocol for the Collection of Habitat Data within the Upper Columbia Monitoring Strategy, Terraqua, Inc.  Prepared for and funded by: Bonneville Power Administration's Integrated Status and Effectiveness Monitoring Program, Wauconda, WA.

Moberg, J. M., and M. B. Ward.  2009.  A Field Manual of Scientific Protocols for Selecting Sampling Sites used in the Integrated Status and Effectiveness Monitoring Program.  2010 Working Version. Terraqua Inc., Wauconda, WA. for Bonneville Power Administration’s Integrated Status and Effectiveness Monitoring Program.

Mohseni, O, and H. G. Stefan.  1999.  Stream temperature/air temperature relationship: a physical interpretation.  Journal of Hydrology 218 (3-4): 128-141.

Montgomery, D. R., and J. M. Buffington.  1998.  Channel processes, classification, and response.  Pages 13-42 in R. J. Naiman and R. E. Bilby, editors. River Ecology and Management: Lessons from the Pacific Coastal Ecoregion.  Springer, New York, NY.

Montgomery, D. R., and J. M. Buffington.  1997.  Channel reach morphology in mountain drainage basins.  Geological Society of America Bulletin 109:596-611.

Montgomery, D. R. and J.M. Buffington.  1993.  Channel Classification, Prediction of Channel Response, and Assessment of Channel Condition.  Washington State Department of Natural Resources Report TFW-SH10-93-002, Olympia, WA.

Moore, K.M.S., K.K. Jones, and J.M. Dambacher.  2002.  Methods for Stream Habitat Surveys: Aquatic Inventories Project.  Oregon Department of Fish and Wildlife, Aquatic Inventories Project, Natural Production Program, Corvallis, OR, 97333.

Mulholland, P.J., J.N. Housera, and K.O. Maloney.  2005.  Stream diurnal dissolved oxygen profiles as indicators of in-stream metabolism and disturbance effects: Fort Benning as a case study.  Ecological Indicators: 5 (3): 243-252.

Naiman, R. J., H. Decamps, and M. McClain.  2005.  Riparian ecology, conservation, and management of streamside communities.  Elsevier Academic Press, New York.

Naiman, R.J., and H. Decamps.  1997.  The Ecology of Interfaces: Riparian Zones.  Annu. Rev. Ecol. Syst. 28:621-58.

Naiman, R. J., T. J. Beechie, L. E. Benda, D. R. Berg, P. A. Bisson, L. H. MacDonald, M. D. O’Connor, P. L. Olson, and E. A. Steel.  1992.  Fundamental elements of ecologically healthy watersheds in the Pacific Northwest coastal ecoregion.  Pages 127-188 in R. J. Naiman, editor.  Watershed management: balancing sustainability and environmental change. Springer-Verlag, New York.

NCEAS.  2010.  The Salmon Monitoring Advisor Website. https://salmonmonitoringadvisor.org/

Oakley, K. L., L. P. Thomas, S. G. Fancy.  2003.  Guidelines for long-term monitoring protocols.  Wildlife Society Bulletin 2003, 31(4):1000-1003.

Olsen, D. S., B. B. Roper, J. L. Kershner, R. Henderson, and E. Archer.  2005.  Sources of variability in conducting pebble counts: their potential influence on the results of stream monitoring programs.  Journal of the American Water Resources Association 41(5):1225-1236.

Overton, K.C., S.P. Wollrab, B.C. Roberts, and M.A. Radko.  1997.  R1/R4 (Northern/Intermountain Regions) Fish and Fish Habitat Standard Inventory Procedures Handbook, U.S. Department of Agriculture, General Technical Report INT-GTR-346, Ogden, UT.

OWEB.  1999.  http://www.oregon.gov/OWEB/docs/pubs/wq_mon_guide.pdf?ga=t

Peck, D.V., A.T. Herlihy, B.H. Hill, R.M. Hughes, P.R. Kaufmann, D.J. Klemm, J.M. Lazorchak, F.H. McCormick, S.A. Peterson, P.L. Ringold, T. Magee, and M.R. Cappaert.  2001.  Environmental Monitoring and Assessment Program-Surface Waters Western Pilot Study: Field Operations Manual for Wadeable Streams. EPA/620/R-06/003, U.S. Environmental Protection Agency, Office of Research and Development, Washington, DC.

Peitz, D.G., S.G. Fancy, L.P. Thomas, and B. Witcher.  2002.  Bird monitoring protocol for Agate Fossil Beds National Monument, Nebraska and Tallgrass Prairie National Preserve, Kansas.  Prairie Cluster Prototype Monitoring Program, National Park Service, U.S. Department of the Interior.

Platts, W.S., C. Armour, G.D. Booth, M. Bryant, J.L. Bufford, P. Cuplin, S. Jensen, G.W. Lienkaemper, G.W. Minshall, S.B. Monson, R.L. Nelson, J.R. Sedell, J.S. Tuhy.  1987.  Methods for evaluating riparian habitats with applications to management.  Gen. Tech. Rpt. INT-221. USDA Forest Service, Ogden UT.

Pleus, A.E., D. Schuett-Hames, and L. Bullchild.  1999.  TFW Monitoring Program Method Manual for the Habitat Unit Survey.  TFW-AM9-99-003, Northwest Indian Fisheries Commission.

Poff, L. N., and A. D. Huryn.  1998.  Multi-scale determinants of secondary production in Atlantic Salmon (Salmo salar) streams.  Canadian Journal of Fisheries and Aquatic Sciences 55: 201-217.

Poole, G. C. and C. H. Berman.  2001.  An ecological perspective on in-stream temperature: natural heat dynamics and mechanisms of human-caused thermal degradation.  Environmental Management 27:787-802.

Potyondy, J.P., and T.L. Sylte.  2008.  Discussion – "Assessment of Methods for Measuring Embeddedness: Application to Sedimentation in Flow Regulated Streams" by Kelly M. Sennatt, Nira L. Salant, Carl E. Renshaw, and Francis J. Magilligan.  J. Am. Water Resour. Assoc. 44(1): 259-261.

Quinn, T. P.  2005.  Behavior and ecology of Pacific salmon and trout.  University of Washington Press:378 p.

Railsback, S.F.  2006.  inSTREAM-2D: The Individual-based stream trout research and environmental assessment model with two-dimensional habitat simulation.  Prepared for the USDA Forest Service

Railsback, S. F., H. B. Stauffer, and B. C. Harvey.  2003.  What can habitat preferences models tell us?  Tests using a virtual trout population.  Ecological Applications 13:1580-1594.

Reiser, D.W., and R.G. White.  1988.  Effects of Two Sediment Size-Classes on Survival of Steelhead and Chinook Salmon Eggs.  North American Journal of Fisheries Management 1988; 8: 432-437.  doi: 10.1577/1548-8675(1988)008<0432:EOTSSC>2.3.CO;2

Reiser, D. W. and T. A. Wesche.  1986.  A survey of Instream flow issues in Noth America. Instream Flow Chronicle 3.

Romaniszyn, E. D., J. J. Hutchens, Jr, and B. J. Wallace.  2007.  Aquatic and terrestrial invertebrate drift in southern Appalachian Mountain streams: implications for trout food resources.  Freshwater Biology 52:1-11.

Roper, B.B., J.M. Buffington, S. Bennett, S.H. Lenigan, E. Archer, S. Downie, J. Faustini, T. Hillman, S. Hubler, K. Jones, C. Jordan, P. Kaufmann, G. Merritt, C. Moyer, and A. Pleus.  2010.  A comparison of the performance and compatibility of protocols used by seven monitoring programs to measure stream habitat in the Pacific Northwest.  North American Journal of Fisheries Management; 30: 565-587.

Roper, B. B., J.M. Buffington, E. Archer, C. Moyer, and M. Ward.  2008.  The Role of Observer Variation in Determining Rosgen Stream Types in Northeastern Oregon Mountain Streams.  Journal of the American Water Resources Association 44 (2): 417–427.

Roper, B. B., J.L. Kershner, E. Archer, R. Henderson, N. Bouwes.  2002.  An evaluation of physical stream habitat attributes used to monitor streams.  Journal of the American Water Resources Association 38 (6):1637–1646.

Rosenfeld, J. S. and S. Boss.  2001.  Fitness consequences of habitat use for juvenile cutthroat trout: energetic costs and benefits in pools and riffles.  Canadian Journal of Fisheries and Aquatic Sciences 58:585-593.

Rosgen, D. L.  1994.  A classification of natural rivers.  Catena 22:169-199.

Schlosser, I.J.  1991.  Stream fish ecology: A landscape perspective.  BioScience 41: 704–712.

Schumm, S.A, and H.R. Khan.  1972.  Experimental Study of Channel Patterns.  The Geological Society of America Bulletin 83 (6) p. 1755-1770.  doi: 10.1130/0016-7606(1972)?83[1755:ESOCP]?2.0.CO;2.

Sennatt, K.M., N.L. Salant, C.E. Renshaw, and F.J. Magilligan.  2006.  Assessment of methods for measuring embeddedness: Application to sedimentation in flow regulated streams.  J. Am. Water Resour. Assoc. 42(6): 1671-1682.

Senter, A.E., and G.B. Pasternak.   2010.  Large wood aids spawning Chinook salmon (Oncorhynchus tshawytscha) in marginal habitat on a regulated river in California.  River Research and Applications n/a. doi: 10.1002/rra.1388.

Spence, B. C., G. A. Lomnicky, R. M. Hughes, and R. P. Novitzki.  1996.  An ecosystem approach to salmonid conservation. TR-4501-96-6057. ManTech Environmental Research Services Corp., Corvallis, OR.  Available from the National Marine Fisheries Service, Portland, Oregon.

Stevens, D. L., Jr., and A. R. Olsen.  2004.  Spatially-balanced sampling of natural resources.  Journal of American Statistical Association 99(465):262-278.

Stevens, D. L. Jr., and A. R. Olsen.  2003.  Variance estimation for spatially balanced samples of environmental resources.  Environmetrics 14:593-610.

Stevens, D. L., Jr., and N. S. Urquhart.  2000.  Response designs and support regions in sampling continuous domains.  Environmetrics 11(1):13-41.

Sutherland, A. B., J. M. Culp, and G. A. Benoy.  2010.  Characterizing deposited sediment for stream habitat assessment.  Limnology and Oceanography: Methods 8:30–44.

Sylte, T. and C. Fischenich.  2002.  Techniques for Measuring Substrate Embeddedness.  ERDC TN-EMRRP-SR-36

Tippets, W.E., and P. Moyle.  1978.  Epibenthic Feeding by Rainbow Trout (Salmo gairdneri) in the McCloud River, California.  Journal of Animal Ecology 47: 549-559.

Torgersen, C. E., R. N. Faux, B. A. McIntosh, N. J. Poage, and D. J. Norton.  2001.  Airborne thermal remote sensing for water temperature assessment in rivers and streams.  Remote Sensing of Environment 76:386-398.

Torgersen, C.E., D.M. Price, H.W. Li, and B.A. McIntosh.  1999.  Multiscale Thermal Refugia and Stream Habitat Associations of Chinook Salmon in Northeastern Oregon.  Ecological Applications 9:301–319. [doi:10.1890/1051-0761(1999)009[0301:MTRASH]2.0.CO;2]

USFS.  2009.  Stream Inventory Handbook: Level I & II, Pacific Northwest Region, Region 6.

Urquhart, N.S. and T.M. Kincaid.  1999.  Designs for detecting trend from repeated surveys of ecological resources.  Journal of Agricultural, Biological and Environmental Statistics 4, 404–414.

Vericat, D., J. Brasington, J. Wheaton, and M. Cowie.  2008.  Accuracy assessment of aerial photographs acquired using lighter-than-air blimps: low-cost tools for mapping river corridors.  River Research and Applications.

Wagner, T., J. R. Bence, M. T. Bremigan, D. B. Hayes, and M. J. Wilberg.  2007.  Regional trends in fish mean length at age: components of variance and the statistical power to detect trends.  Canadian Journal of Fisheries and Aquatic Sciences 64:968–978.

Warner, K.  1963.  Natural spawning success of landlocked salmon, Salmo salar.  Transactions of the American Fisheries Society 92:161-164.

Watershed Sciences, Inc.  2003.  Analytical Methods for Dynamic Open Channel Heat and Mass Transfer. Methodology for the Heat Source Model Version 7.0.  Portland, Oregon.

Wheaton J.M.  2008.  Uncertainty in Morphological Sediment Budgeting of Rivers.  Unpublished PhD, University of Southampton, Southampton, 412 pp.

Wheaton J.M, J. Brasington, S.E. Darby, and D. Sear.  2010.  Accounting for uncertainty in DEMs from repeat topographic surveys: Improved sediment budgets.  Earth Surface Processes and Landforms. 35(2): 136-156. DOI: 10.1002/esp.1886.  Also see: http://www.joewheaton.org/Home/research/software/GCD

Whitacre, H. W., B. B. Roper, and J. L. Kershner.  2007.  A comparison of protocols and observer precision for measuring physical stream attributes.  Journal of American Water Resources Association 43(4):923-937.

Williams, J. G.  2010.  Sampling for Environmental Flow Assessments.  Fisheries 35:434-443.