refs_ets_update.bib

@article{Adams2009,
abstract = {Maintaining proper freshwater and marine inputs is essential for estuarine function. Alteration of freshwater flows into small tributaries that traverse the upland- estuarine margin may be especially problematic, e.g., by impacting the nursery areas for juvenile finfish and shellfish. We used stomach contents and stable isotope analysis ($\delta$13C, $\delta$15N) to examine effects of freshwater flow alterations on the trophic ecology of juvenile common snook (Centropomus undecimalis) in four mangrove creeks with different freshwater flow regimes. Diet diversity in less degraded creeks was greater than in more degraded creeks, and the importance (by {\%} mass) of the top three preys was disproportionately higher in the more degraded creeks. Stable isotope measures of trophic diversity corroborate these trends, suggesting higher intraspecific trophic diversity in less degraded creeks. The difference in diet diversity of juvenile snook may be an indicator of an overall change in ecosystem function and these shifts in food web structure may affect the rate that juveniles of this and other species with similar habitat requirements successfully join the adult population.},
author = {Adams, Aaron J and Wolfe, R Kirby and Layman, Craig A},
doi = {10.1007/s12237-009-9156-x},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2009{\_}Adams{\_}Preliminary{\_}Examination.pdf:pdf},
issn = {1559-2723},
journal = {Estuaries and Coasts},
keywords = {Food web,Freshwater flow alteration,Intraspecific niche variation,Juvenile fish,Lavage,Trophic ecology},
number = {4},
pages = {819--828},
title = {{Preliminary examination of how human-driven freshwater flow alteration affects trophic ecology of juvenile snook (Centropomus undecimalis) in estuarine creeks}},
volume = {32},
year = {2009}
}
@article{Aguiar09,
author = {Aguiar, F C and Ferreira, M T and Albuquerque, A and Rodriguez-Gonzalez, P and Segurado, P},
journal = {Fundamental and Applied Limnology},
number = {3},
pages = {249--267},
title = {{Structural and functional responses of riparian vegetation to human disturbance: Performance and spatial scale-dependence}},
volume = {175},
year = {2009}
}
@incollection{Akaike73,
address = {Akademiai Kiado, Budapest},
author = {Akaike, H},
booktitle = {Second International Symposium on Information Theory},
editor = {Petrov, B N and Csaki, F},
pages = {267--281},
title = {{Information theory and an extension of the maximum likelihood principle}},
year = {1973}
}
@article{Alexander08,
author = {Alexander, M L and Woodford, M P and Hotchkiss, S C},
journal = {Aquatic Botany},
number = {1},
pages = {77--86},
title = {{Freshwater macrophyte communities in lakes of variable landscape position and development in northern {\{}W{\}}isconsin, {\{}U.S.A.{\}}}},
volume = {88},
year = {2008}
}
@article{Alpine92,
author = {Alpine, A E and Cloern, J E},
journal = {Limnology and Oceanography},
number = {5},
pages = {946--955},
title = {{Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary}},
volume = {37},
year = {1992}
}
@article{Alpine88,
author = {Alpine, A E and Cloern, J E},
journal = {Marine Ecology Progress Series},
number = {2},
pages = {167--173},
title = {{Phytoplankton growth rates in a light-limited environment, {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {44},
year = {1988}
}
@techreport{Anderson01,
address = {St. Paul, Minnesota},
author = {Anderson, J L and Bell, J C and Cooper, T H and Grigal, D F},
institution = {University of Minnesota Extension},
title = {{Soils and landscapes of {\{}M{\}}innesota}},
url = {http://www.extension.umn.edu/distribution/cropsystems/dc2331.html},
year = {2001}
}
@techreport{Anderson99,
address = {Duluth, Minnesota},
author = {Anderson, K A and Kelly, T J and Sushak, R M and Hagley, C A and Jensen, D A and Kreag, G M},
institution = {University of Minnesota Sea Grant Program, Minnesota Department of Natural Resources, Office of Management and Budget Services},
title = {{Summary report on public perceptions of the impacts, use, and future of {\{}M{\}}innesota lakes: Results of the 1998 {\{}M{\}}innesota lake survey}},
year = {1999}
}
@techreport{Anon93,
address = {St. Paul, Minnesota},
author = {Anonymous},
institution = {Division of Fish and Wildlife, Section of Fisheries, Minnesota Department of Natural Resources},
number = {No. 147},
title = {{Manual of Instructions for Lake Survey}},
url = {http://files.dnr.state.mn.us/publications/fisheries/special{\_}reports/147.pdf},
year = {1993}
}
@article{Ansola95,
author = {Ansola, G and Fernandez, C and Deluis, E},
journal = {Ecological Engineering},
number = {1},
pages = {13--19},
title = {{Removal of organic-matter and nutrients from urban waste-water by using an experimental emergent aquatic macrophyte system}},
volume = {5},
year = {1995}
}
@misc{APHA05,
annote = {Washington, DC},
author = {{APHA (American Public Health Association)}},
title = {{Standard methods for the examination of water and wastewater}},
year = {2005}
}
@article{Arhonditsis08,
author = {Arhonditsis, G B and Perhar, G and Zhang, W and Massos, E and Shi, M and Das, A},
journal = {Water Resources Research},
number = {1},
pages = {W01420},
title = {{Addressing equifinality and uncertainty in eutrophication models}},
volume = {44},
year = {2008}
}
@article{Arlot10,
author = {Arlot, S and Celisse, A},
journal = {Statistics Surveys},
pages = {40--79},
title = {{A survey of cross-validation procedures for model selection}},
volume = {4},
year = {2010}
}
@misc{ASC17,
annote = {Report v1.2},
author = {ASC},
title = {{Assessment of nutrient status and trends in the Delta in 2001-2016: Effects of drought on ambient concentrations and trends. Prepared by the Aquatic Science Center (ASC), T. Jabusch, P. Trowbridge, A. Wong, and M. Heberger for the Delta Regional Monitorin}},
year = {2017}
}
@article{Asif2014,
author = {Asif, Muhammad and Saqib, Muhammad and Yousaf, Balal and Adnan, Muhammad and Yousaf, Amina and Ali, Athar},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2014{\_}Asif{\_}Growth{\_}and.pdf:pdf},
keywords = {buttonwood,conocarpus erectus l,growth,potassium status,soil salinity,water stress},
pages = {42--52},
title = {{Growth and Ionic Composition of Buttonwood ( Conocarpus erectus L .) in Response to Soil Salinity and Water Stress}},
volume = {19},
year = {2014}
}
@article{Aulenbach06,
author = {Aulenbach, B T and Hooper, R P},
journal = {Hydrological Processes},
number = {14},
pages = {3029--3047},
title = {{The composite-method: An improved method for stream-water solute load estimation}},
volume = {20},
year = {2006}
}
@incollection{Baatz00,
address = {Berlin},
author = {Baatz, M and Sch{\"{a}}pe, A},
booktitle = {Angewandte Geographische Informationsverarbeitung XII. Beitr{\"{a}}ge zum AGIT-Symposium Salzburg 2000},
editor = {Strobl, J and Blaschke, T and Griesebner, G},
pages = {12--23},
publisher = {Herbert Wichmann Verlag},
title = {{Multiresolution segmentation: An optimization approach for high quality multi-scale image segmentation}},
year = {2000}
}
@article{Bajer16,
author = {Bajer, P G and Beck, M W and Cross, T K and Koch, J and Bartodziej, B and Sorensen, P W},
doi = {10.1111/gcb.13377},
journal = {Global Change Biology},
number = {12},
pages = {3937--3947},
title = {{Biological invasion by a benthivorous fish reduced the cover and species richness of aquatic plants in most lakes of a large {\{}N{\}}orth {\{}A{\}}merican region}},
volume = {22},
year = {2016}
}
@article{Bajer18,
author = {Bajer, P G and Beck, M W and Hundt, P J},
doi = {10.1007/s10750-018-3592-1},
journal = {Hydrobiologia},
title = {{Effect of non-native versus native invaders on macrophyte richness: are carp and bullheads ecological proxies?}},
year = {2018}
}
@incollection{Ball00,
address = {Berlin, Germany},
author = {Ball, G R and Palmer-Brown, D and Mills, G E},
booktitle = {Artificial Neuronal Networks: Application to Ecology and Evolution},
editor = {Lek, S and Gu{\'{e}}gan, J F},
pages = {165--183},
publisher = {Springer-Verlag},
title = {{A comparison of artificial neuronal network and conventional statistical techniques for analysing environmental data}},
year = {2000}
}
@article{Barbour96,
author = {Barbour, M T and Gerritsen, J and Griffith, G E and Frydenborg, R and McCarron, E and White, J S and Bastian, M L},
journal = {Journal of the North American Benthological Society},
number = {2},
pages = {185--211},
title = {{A framework for biological criteria for {\{}F{\}}lorida streams using benthic macroinvertebrates}},
volume = {15},
year = {1996}
}
@article{Barbour00,
author = {Barbour, M T and Swietlik, W F and Jackson, S K and Courtemanch, D L and Davies, S P and Yoder, C O},
journal = {Hydrobiologia},
number = {0},
pages = {453--464},
title = {{Measuring the attainment of biological integrity in the {\{}USA{\}}: A critical element of ecological integrity}},
volume = {422-423},
year = {2000}
}
@incollection{Barendregt2016,
author = {Barendregt, Aat},
booktitle = {The Wetland Book},
doi = {10.1007/978-94-007-6173-5_103-2},
editor = {Finlayson, C M and Everard, M and Irvine, K and McInnes, R J and Middleton, B A and van Dam, A A and Davidson, N C},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Barendregt{\_}Tidal{\_}Freshwater.pdf:pdf},
isbn = {978-94-007-6173-5},
month = {jan},
pages = {1--14},
publisher = {Springer Nertherlands},
title = {{Tidal Freshwater Wetlands, the Fresh Dimension of the Estuary}},
year = {2016}
}
@article{Barko91,
author = {Barko, J W and Gunnison, D and Carpenter, S R},
journal = {Aquatic Botany},
pages = {41--65},
title = {{Sediment interactions with submersed macrophyte growth and community dynamics}},
volume = {41},
year = {1991}
}
@article{Barko82,
author = {Barko, J W and Hardin, D G and Matthews, M S},
journal = {Canadian Journal of Botany},
number = {6},
pages = {877--887},
title = {{Growth and morphology of submersed freshwater macrophytes in relation to light and temperature}},
volume = {60},
year = {1982}
}
@incollection{Bates92,
address = {Pacific Grove, California},
author = {Bates, D M and Chambers, J M},
booktitle = {Statistical Models in S},
editor = {Chambers, J M and Hastie, T J},
pages = {421--454},
publisher = {Wadsworth and Brooks/Cole},
title = {{Nonlinear models}},
year = {1992}
}
@article{Batt12,
author = {Batt, R D and Carpenter, S R},
journal = {Limnology and Oceanography: Methods},
pages = {20--30},
title = {{Free-water lake metabolism: Addressing noisy time series with a {\{}K{\}}alman filter}},
volume = {10},
year = {2012}
}
@inproceedings{Batten2003,
author = {Batten, Jeffrey and Delahoya, Nancy and Holmstr{\"{o}}m, Kimberly and Kissler, Aaron and Qi, Xiaodong and Sanford, Reginald and Sorenson, Bernard and Truncale, Thomas and Poor, Noreen and Health, Occupational and Boulevard, Bruce B Downs and Shell, Patrick and Foster, James},
booktitle = {Proceedings of the AWMA 96th Annual Meeting {\&} Exhibition},
file = {:G$\backslash$:/TECHNICAL and SCIENCE ISSUES/Atmospheric deposition/200x{\_}Batten{\_}Has{\_}the{\_}AWMA{\_}69689.pdf:pdf},
pages = {1--19},
title = {{Has the installation of a FGD unit on a coal-fired utility plant reduced SO2 ambient air concentrations near Tampa , Florida?}},
year = {2003}
}
@article{Bay2006,
author = {Bay, Tampa and Program, Estuary and Florida, South and Management, Water and Beach, West Palm and Harbor, Charlotte and Estuary, National and Myers, Fort},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}Greening{\_}Hurricane{\_}Impacts.pdf:pdf},
journal = {Estuaries and coasts},
number = {6},
pages = {877--879},
title = {{Hurricane Impacts on Coastal Ecosystems}},
volume = {29},
year = {2006}
}
@article{Bayraktarov2016,
abstract = {Land-use change in the coastal zone has led to worldwide degradation of marine coastal ecosystems and a loss of the goods and services they provide. Restoration is the process of assisting the recovery of an ecosystem that has been degraded, damaged, or destroyed and is critical for habitats where natural recovery is hindered. Uncertainties about restoration cost and feasibility can impede decisions on whether, what, how, where, and how much to restore. Here, we perform a synthesis of 235 studies with 954 observations from restoration or rehabilitation projects of coral reefs, seagrass, mangroves, saltmarshes and oyster reefs worldwide, and evaluate cost, survival of restored organisms, project duration, area, and techniques applied. Findings showed that while the median and average reported costs for restoration of one hectare of marine coastal habitat were around 80,000 US{\$} (2010) and 1,600,000 US{\$} (2010) respectively, the real total costs (median) are likely to be 2-4 times higher. Coral reefs and seag...},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Bayraktarov, Elisa and Saunders, Megan I. and Abdullah, Sabah and Mills, Morena and Beher, Jutta and Possingham, Hugh P. and Mumby, Peter J. and Lovelock, Catherine E.},
doi = {10.1890/15-1077},
eprint = {arXiv:1011.1669v3},
isbn = {9780874216561},
issn = {10510761},
journal = {Ecological Applications},
month = {jun},
number = {4},
pages = {1055--1074},
pmid = {25246403},
title = {{The cost and feasibility of marine coastal restoration}},
url = {http://doi.wiley.com/10.1890/15-1077},
volume = {26},
year = {2016}
}
@article{Beck87,
author = {Beck, M B},
journal = {Water Resources Research},
number = {8},
pages = {1393--1442},
title = {{Water quality modeling: A review of the analysis of uncertainty}},
volume = {23},
year = {1987}
}
@article{BeckIP,
author = {Beck, M W},
journal = {Journal of Statistical Software},
title = {{{\{}NeuralNetTools{\}}: Visualization and analysis tools for neural networks}}
}
@manual{Beck17b,
annote = {R package version 1.1.0},
author = {Beck, M W},
title = {{WRTDStidal: Weighted Regression for Water Quality Evaluation in Tidal Waters}},
year = {2017}
}
@article{Beck16,
author = {Beck, M W},
journal = {The R Journal},
number = {1},
pages = {219--232},
title = {{{\{}SWMPr{\}}: An {\{}R{\}} package for retrieving, organizing, and analyzing environmental data for estuaries}},
volume = {8},
year = {2016}
}
@phdthesis{Beckdiss,
address = {St. Paul, Minnesota},
author = {Beck, M W},
school = {University of Minnesota},
title = {{{\{}M{\}}innesota macrophytes: Linking aquatic plants, lake health, and human activities}},
year = {2013}
}
@article{Beck16c,
author = {Beck, M W and Alahuhta, J},
doi = {10.1007/s00027-016-0508-x},
journal = {Aquatic Sciences},
pages = {1--15},
title = {{Ecological determinants of {\{}P{\}}otamogetontaxa in glacial lakes: assemblage composition, species richness, and species-level approach}},
year = {2016}
}
@article{Beck12,
author = {Beck, M W and Claassen, A H and Hundt, P},
doi = {10.1080/15715124.2012.656133},
journal = {International Journal of River Basin Management},
number = {1},
pages = {73--92},
title = {{Environmental and livelihood impacts of dams: Common lessons across development gradients that challenge sustainability}},
volume = {10},
year = {2012}
}
@article{Beck18,
author = {Beck, M W and Cressman, K and Griffin, C and Caffrey, J},
doi = {10.18785/gcr.2901.02},
journal = {Gulf and Caribbean Research},
number = {1},
pages = {1--14},
title = {{Water quality trends following anomalous phosphorus inputs to Grand Bay}},
volume = {29},
year = {2018}
}
@article{Beck15,
author = {Beck, M W and {Hagy III}, J D},
doi = {10.1007/s10666-015-9452-8},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2015{\_}Beck{\_}Weighted-regression-for-tidal-waters.pdf:pdf},
journal = {Environmental Modelling and Assessment},
number = {6},
pages = {637--655},
title = {{Adaptation of a weighted regression approach to evaluate water quality trends in an estuary}},
volume = {20},
year = {2015}
}
@article{Beck09,
author = {Beck, M W and Hatch, L K},
doi = {10.1139/A09-001},
journal = {Environmental Reviews},
pages = {21--44},
title = {{A review of research on the development of lake indices of biotic integrity}},
volume = {17},
year = {2009}
}
@article{Beck10,
author = {Beck, M W and Hatch, L K and Vondracek, B and Valley, R D},
doi = {10.1016/j.ecolind.2010.02.006},
journal = {Ecological Indicators},
number = {5},
pages = {968--979},
title = {{Development of a macrophyte-based index of biotic integrity for {\{}M{\}}innesota lakes}},
volume = {10},
year = {2010}
}
@article{BeckIR,
author = {Beck, M W and Jabusch, T W and Trowbridge, P R and Senn, D B},
journal = {Environmental Science {\&} Technology},
title = {{Four decades of water quality change in the upper {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary}}
}
@article{Beck17,
author = {Beck, M W and Murphy, R R},
doi = {10.1111/1752-1688.12489},
journal = {Journal of the American Water Resources Association},
number = {1},
pages = {197--219},
title = {{Numerical and qualitative contrasts of two statistical models for water quality change in tidal waters}},
volume = {53},
year = {2017}
}
@article{Beck14b,
author = {Beck, M W and Tomcko, C M and Valley, R D and Staples, D F},
doi = {10.1016/j.ecolind.2014.07.002},
journal = {Ecological Indicators},
pages = {323--335},
title = {{Analysis of macrophyte indicator variation as a function of sampling, temporal, and stressor effects}},
volume = {46},
year = {2014}
}
@article{Beck13c,
author = {Beck, M W and Voncracek, B and Hatch, L K},
doi = {10.1080/10402381.2013.828806},
journal = {Lake and Reservoir Managmenet},
number = {3},
pages = {179--193},
title = {{Between- and within-lake responses of macrophyte richness metrics to shoreline development}},
volume = {29},
year = {2013}
}
@article{Beck13,
author = {Beck, M W and Vondracek, B and Hatch, L K},
doi = {10.1016/j.aquabot.2013.02.003},
journal = {Aquatic Botany},
pages = {16--25},
title = {{Environmental clustering of lakes to evaluate performance of a macrophyte index of biotic integrity}},
volume = {108},
year = {2013}
}
@article{Beck13b,
author = {Beck, M W and Vondracek, B and Hatch, L K and Vinje, J},
doi = {10.1016/j.isprsjprs.2013.04.006},
journal = {ISPRS Journal of Photogrammetry and Remote Sensing},
pages = {60--69},
title = {{Semi-automated analysis of high-resolution aerial images to quantify docks in glacial lakes}},
volume = {81},
year = {2013}
}
@article{Beck14a,
author = {Beck, M W and Wilson, B N and Vondracek, B and Hatch, L K},
doi = {10.1016/j.ecolind.2014.04.002},
journal = {Ecological Indicators},
pages = {195--208},
title = {{Application of neural networks to quantify the utility of indices of biotic integrity for biological monitoring}},
volume = {45},
year = {2014}
}
@article{Beck17c,
author = {Beck, Marcus W and Hagy, James D. and Le, Chengfeng},
doi = {10.1007/s12237-017-0287-1},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Beck{\_}QuantifyingSeagrassDepthofColonization.pdf:pdf},
issn = {1559-2723},
journal = {Estuaries and Coasts},
month = {mar},
number = {2},
pages = {592--610},
title = {{Quantifying Seagrass Light Requirements Using an Algorithm to Spatially Resolve Depth of Colonization}},
url = {http://link.springer.com/10.1007/s12237-017-0287-1},
volume = {41},
year = {2018}
}
@article{Beck15b,
author = {Beck, Marcus W and Hagy, James D. and Murrell, Michael C},
doi = {10.1002/lom3.10062},
issn = {15415856},
journal = {Limnology and Oceanography: Methods},
month = {dec},
number = {12},
pages = {731--745},
title = {{Improving estimates of ecosystem metabolism by reducing effects of tidal advection on dissolved oxygen time series}},
url = {http://doi.wiley.com/10.1002/lom3.10062},
volume = {13},
year = {2015}
}
@article{Bedoya11,
author = {Bedoya, D and Manolakos, E S and Novotny, V},
journal = {Water Research},
number = {7},
pages = {2359--2374},
title = {{Prediction of biological integrity based on environmental similarity - Revealing the scale-dependent link between study area and top environmental predictors}},
volume = {45},
year = {2011}
}
@techreport{Beever2016,
author = {Beever, L and Beever, J and Lewis, R R and Flynn, L and Tattar, T and Donley, E and Neafsey, E},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Beever{\_}identifying{\_}and.pdf:pdf},
title = {{Identifying and Diagnosing Locations of Ongoing and Future Saltwater Wetland Loss : Mangrove Heart Attack Charlotte Harbor National Estuary Program Technical Report 16-3}},
year = {2016}
}
@article{Beisner06,
author = {Beisner, B E and Peres-Neto, P R and Lindstrom, E S and Barnett, A and Longhi, M L},
journal = {Ecology},
number = {12},
pages = {2985--2991},
title = {{The role of environmental and spatial processes in structuring lake communities from bacteria to fish}},
volume = {87},
year = {2006}
}
@article{Bell09,
author = {Bell, G and Hey, T and Szalay, A},
journal = {Science},
number = {5919},
pages = {1297--1298},
title = {{Beyond the data deluge}},
volume = {323},
year = {2009}
}
@article{Benitez97,
author = {Benitez, J M and Castro, J L and Requena, I},
journal = {IEEE Transactions on Neuronal Networks},
number = {5},
pages = {1156--1164},
title = {{Are artificial neuronal networks black boxes?}},
volume = {8},
year = {1997}
}
@article{Bergmeir12,
author = {Bergmeir, Christoph and Ben{\'{i}}tez, Jos{\'{e}} M},
journal = {Journal of Statistical Software},
number = {7},
pages = {1--26},
title = {{Neural Networks in {\{}R{\}} Using the Stuttgart Neural Network Simulator: {\{}RSNNS{\}}}},
url = {http://www.jstatsoft.org/v46/i07/},
volume = {46},
year = {2012}
}
@article{Beyer2016,
abstract = {The Deepwater Horizon oil spill constituted an ecosystem-level injury in the northern Gulf of Mexico. Much oil spread at 1100–1300 m depth, contaminating and affecting deepwater habitats. Factors such as oil-biodegradation, ocean currents and response measures (dispersants, burning) reduced coastal oiling. Still, {\textgreater} 2100 km of shoreline and many coastal habitats were affected. Research demonstrates that oiling caused a wide range of biological effects, although worst-case impact scenarios did not materialize. Biomarkers in individual organisms were more informative about oiling stress than population and community indices. Salt marshes and seabird populations were hard hit, but were also quite resilient to oiling effects. Monitoring demonstrated little contamination of seafood. Certain impacts are still understudied, such as effects on seagrass communities. Concerns of long-term impacts remain for large fish species, deep-sea corals, sea turtles and cetaceans. These species and their habitats should continue to receive attention (monitoring and research) for years to come.},
author = {Beyer, Jonny and Trannum, Hilde C. and Bakke, Torgeir and Hodson, Peter V. and Collier, Tracy K.},
doi = {10.1016/j.marpolbul.2016.06.027},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Beyer{\_}Environmental{\_}effects.pdf:pdf},
isbn = {0025-326X},
issn = {0025326X},
journal = {Marine Pollution Bulletin},
keywords = {Deepwater Horizon oil spill,Environmental effects,Review},
month = {sep},
number = {1},
pages = {28--51},
pmid = {27301686},
title = {{Environmental effects of the Deepwater Horizon oil spill: A review}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0025326X16304313},
volume = {110},
year = {2016}
}
@article{Bhangu97,
author = {Bhangu, I and Whitfield, P H},
journal = {Water Research},
number = {9},
pages = {2187--2194},
title = {{Seasonal and long-term variations in water quality of the {\{}S{\}}keena {\{}R{\}}iver at {\{}U{\}}sk, {\{}B{\}}ritish {\{}C{\}}olumbia}},
volume = {31},
year = {1997}
}
@article{Bianchi10,
author = {Bianchi, T S and DiMarco, S F and Jr, J H Cowan and Hetland, R D and Chapman, P and Day, J W and Allison, M A},
journal = {Science of the Total Environment},
number = {7},
pages = {1471--1484},
title = {{The science of hypoxia in the {\{}N{\}}orthern {\{}G{\}}ulf of {\{}M{\}}exico: a review}},
volume = {408},
year = {2010}
}
@article{Bierman94,
author = {Bierman, V J and Hinz, S C and Zhu, D W and Wiseman, W J and Rabalais, N N and Turner, R E},
journal = {Estuaries},
number = {4},
pages = {886--899},
title = {{A preliminary mass-balance model of primary productivity and dissolved oxygen in the {\{}M{\}}ississippi {\{}R{\}}iver plume/ inner {\{}G{\}}ulf shelf region}},
volume = {17},
year = {1994}
}
@book{Bishop95,
address = {Oxford, United Kingdom},
author = {Bishop, C M},
pages = {482},
publisher = {Carendon Press},
title = {{Neuronal Networks for Pattern Recognition}},
year = {1995}
}
@book{Bivand08,
address = {New York, New York},
author = {Bivand, R S and Pebesma, E J and G{\'{o}}mez-Rubio, V},
pages = {376},
publisher = {Springer-Verlag},
title = {{Applied Spatial Data Analysis with {\{}R{\}}}},
year = {2008}
}
@manual{Bivand14,
annote = {R package version 0.3-8},
author = {Bivand, Roger and Rundel, Colin},
title = {{rgeos: Interface to Geometry Engine - Open Source (GEOS)}},
url = {http://cran.r-project.org/package=rgeos},
year = {2014}
}
@article{Blake14,
author = {Blake, R E and Duffy, J E and Richardson, J P},
journal = {Estuaries and Coasts},
number = {6},
pages = {1549--1561},
title = {{Patterns of seagrass community response to local shoreline development}},
volume = {37},
year = {2014}
}
@techreport{Blann08,
address = {Minneapolis, Minnesota},
author = {Blann, K and Cornett, M},
institution = {The Nature Conservancy},
title = {{Identifying lake conservation priorities for The Nature Conservancy in Minnesota, North Dakota, and South Dakota}},
year = {2008}
}
@article{Blaschke10,
author = {Blaschke, T},
journal = {ISPRS Journal of Photogrammetry and Remote Sensing},
number = {1},
pages = {2--16},
title = {{Object based image analysis for remote sensing}},
volume = {65},
year = {2010}
}
@article{Blaschke01,
author = {Blaschke, T and Strobl, J},
journal = {Interfacing Remote Sensing and GIS},
number = {6},
pages = {12--17},
title = {{What's wrong with pixels? {\{}S{\}}ome recent development interfacing remote sensing and {\{}GIS{\}}}},
volume = {14},
year = {2001}
}
@article{Blindow93,
author = {Blindow, I and Andersson, G and Hargeby, A and Johansson, S},
journal = {Freshwater Biology},
number = {1},
pages = {159--167},
title = {{Long-term pattern of alternative stable states in two shallow eutrophic lakes}},
volume = {30},
year = {1993}
}
@incollection{Boet00,
address = {Berlin, Germany},
author = {Bo{\"{e}}t, P and Fuhs, T},
booktitle = {Artificial Neuronal Networks: Application to Ecology and Evolution},
editor = {Lek, S and Gu{\'{e}}gan, J F},
pages = {131--142},
publisher = {Springer-Verlag},
title = {{Predicting presence of fish species in the {\{}S{\}}eine river basin using artifical neuronal networks}},
year = {2000}
}
@techreport{Boicourt98,
address = {Baltimore, Maryland},
author = {Boicourt, W C and Sanford, L P},
institution = {Maryland Department of the Environment},
title = {{A hydrodynamic study of the {\{}P{\}}atuxent {\{}R{\}}iver estuary}},
year = {1998}
}
@article{Bokde16,
author = {Bokde, N and Kulat, K and Beck, M W and Gualberto, A C},
journal = {arXiv},
title = {{R package imputeTestbench to compare imputation methods for univariate time series}},
volume = {arXiv prep},
year = {2016}
}
@techreport{Boler01,
address = {Tampa, Florida, USA},
author = {Boler, R},
institution = {Environmental Protection Commission of Hillsborough County},
title = {{Surface water quality 1999-2000 {\{}H{\}}illsborough {\{}C{\}}ounty, {\{}F{\}}lorida}},
year = {2001}
}
@article{Borja2008,
abstract = {Increasingly on a worldwide scale, legislation has been adopted to determine the ecological integrity of surface waters including streams, rivers, lakes, estuaries and coastal waters. An integral part of determining ecological integrity is the measurement of biological integrity, typically emphasizing analyses of plankton, benthos, macroalgae and fish. In the development of protocols for evaluating biological integrity, benthic macroinvertebrate communities are the most consistently emphasized biotic component of aquatic ecosystems. A plethora of methodologies with hundreds of indices, metrics and evaluation tools are presently available. An ecologically parsimonious approach dictates that investigators should place greater emphasis on evaluating the suitability of indices that already exist prior to developing new ones. Hence, the authors organized within the American Society of Limnology and Oceanography 2006 Summer Meeting, 4-9 June 2006, in Victoria, BC, Canada, a special session with the objective to compare methodologies, applications and interpretations existing in various countries and attempting to contribute to an improved understanding of the suitability of such approaches when using benthic communities. From the 25 contributions presented in this session, eight manuscripts were selected to be included in this special issue of Ecological Indicators including new index development, novel validation approaches, assessment of spatio-temporal applications, interpretations relative to management needs and potential adaptive management modifications to maximize the robustness, sensitivity, and representativeness of environmental information conveyed to management. {\textcopyright} 2007 Elsevier Ltd. All rights reserved.},
author = {Borja, A. and Dauer, D. M.},
doi = {10.1016/j.ecolind.2007.05.004},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2008{\_}Borja{\_}Assessing{\_}the.pdf:pdf},
isbn = {1470160X},
issn = {1470160X},
journal = {Ecological Indicators},
keywords = {Aquatic systems,Benthic communities,Biotic indices,Comparison of methods,Ecological integrity,Indicator application,Indicator development,Indicator interpretation},
number = {4},
pages = {331--337},
title = {{Assessing the environmental quality status in estuarine and coastal systems: Comparing methodologies and indices}},
volume = {8},
year = {2008}
}
@article{Borja09,
author = {Borja, A and Ranasinghe, A and Weisberg, S B},
journal = {Marine Pollution Bulletin},
number = {1-3},
pages = {1--4},
title = {{Assessing ecological integrity in marine waters, using multiple indices and ecosystem components: Challenges for the future}},
volume = {59},
year = {2009}
}
@article{Borja2016,
abstract = {Using a long-term (1995–2014) monitoring network, from 51 sampling stations in estuaries and coasts of the Basque Country (Bay of Biscay), the objective of this investigation was to assess the responsiveness of 83 variables in water (18), sediments (27), biota (26), phytoplankton (2), macroinvertebrates (5) and fishes (5) to different human pressures and management actions. We used a total of 3247 series of data to analyse trends of improvement and worsening in quality. In a high percentage of the cases, the management actions taken have resulted in positive effects in the environment, as shown by the trend analysis in this investigation. Overall, much more trends of improvement than of worsening have been observed; this is true for almost all the media and biological components studied, with the exception of phytoplankton; and it applies as well to almost all the stations and water bodies, with the exception of those corresponding to areas with water treatment pending of accomplishment. In estuaries with decreasing human pressures during the period, the percentage of series showing quality improvement was higher (approx. 30{\%}) than those showing worsening of quality (12{\%}). Moreover, in those water bodies showing an increase of pressure, variables which can be considered indicators of anthropogenic effects showed negative trends (quality worsening). On the other hand, some of the variables analysed were more affected by natural variability than by changes in pressures. That was the case of silicate, nitrate and suspended solids, which followed trends correlated to salinity, which, in turn, was related to the rainfall regime during the study period.},
author = {Borja, {\'{A}}ngel and Chust, Guillem and Rodr{\'{i}}guez, Jos{\'{e}} G. and Bald, Juan and Belzunce-Segarra, M{\textordfeminine} Jes{\'{u}}s and Franco, Javier and Garmendia, Joxe Mikel and Larreta, Joana and Menchaca, Iratxe and Muxika, I{\~{n}}igo and Solaun, Oihana and Revilla, Marta and Uriarte, Ainhize and Valencia, Victoriano and Zorita, Izaskun},
doi = {10.1016/j.scitotenv.2016.05.111},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Borja{\_}The{\_}past.pdf:pdf},
isbn = {0048-9697},
issn = {18791026},
journal = {Science of the Total Environment},
keywords = {,Basque Country,Biological monitoring,Human pressures,Management actions,Phyisico-chemical monitoring},
pages = {698--711},
pmid = {27239713},
publisher = {Elsevier B.V.},
title = {{‘The past is the future of the present': Learning from long-time series of marine monitoring}},
url = {http://dx.doi.org/10.1016/j.scitotenv.2016.05.111},
volume = {566-567},
year = {2016}
}
@article{Borman09,
author = {Borman, S C and Galatowitsch, S M and Newman, R M},
journal = {Aquatic Botany},
number = {3},
pages = {143--150},
title = {{The effects of species immigrations and changing conditions on isoetid communities}},
volume = {91},
year = {2009}
}
@book{Borman01,
address = {Stevens Point, Wisconsin},
author = {Borman, S and Korth, R and Temte, J},
pages = {248},
publisher = {Wisconsin Lakes Partnership, Reindl Printing, Inc.},
title = {{Through the Looking Glass: A Field Guide to Aquatic Plants}},
year = {2001}
}
@article{Borsuk01,
author = {Borsuk, M E and Stow, C A and {Leuttich Jr.}, R A and Pearl, H W and Pinckney, J L},
journal = {Estuarine, Coastal and Shelf Science},
number = {1},
pages = {33--49},
title = {{Modelling oxygen dynamics in an intermittently stratified estuary: Estimation of process rates using field data}},
volume = {52},
year = {2001}
}
@article{Borsuk04,
author = {Borsuk, M E and Stow, C A and Reckhow, K H},
journal = {Ecological Modelling},
number = {2-3},
pages = {219--239},
title = {{A {\{}B{\}}ayesian network of eutrophication models for synthesis, prediction, and uncertainty analysis}},
volume = {173},
year = {2004}
}
@article{Borsuk04b,
author = {Borsuk, M E and Stow, C A and Reckhow, K H},
journal = {Journal of Environmental Engineering-ASCE},
number = {6},
pages = {605--614},
title = {{Confounding effect of flow on estuarine response to nitrogen loading}},
volume = {130},
year = {2004}
}
@misc{Boto1984,
author = {Boto, K G},
booktitle = {The mangrove ecosystem: research methods},
editor = {Snedaker, S C and Snedaker, J G},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1984{\_}Boto{\_}waterlogged{\_}saline.pdf:pdf},
pages = {114--130},
publisher = {Unesco},
title = {{Waterlogged saline soils}},
year = {1984}
}
@incollection{Bowden06,
address = {Berlin, Germany},
author = {Bowden, G J and Dandy, G C and Maier, H R},
booktitle = {Ecological Informatics: Scope, Techniques and Applications},
edition = {2nd},
editor = {Recknagel, F},
pages = {275--292},
publisher = {Springer-Verlag},
title = {{An evaluation of methods for the selection of inputs for an artificial neural network based river model}},
year = {2006}
}
@article{Bowes09,
author = {Bowes, M J and Smith, J T and Neal, C},
journal = {Journal of Hydrology},
pages = {82--96},
title = {{The value of high resolution nutrient monitoring: a case study of the {\{}R{\}}iver {\{}F{\}}rome, {\{}D{\}}orset, {\{}UK{\}}}},
volume = {378},
year = {2009}
}
@article{Boyer02,
author = {Boyer, E W and Goodale, C L and Jaworski, N A and Howarth, R W},
journal = {Biogeochemistry},
number = {1},
pages = {137--169},
title = {{Anthropogenic nitrogen sources and relationships to riverine nitrogen export in the northeastern {\{}U.S.A.{\}}}},
volume = {57},
year = {2002}
}
@article{Brabec02,
author = {Brabec, E and Schulte, S and Richards, P L},
journal = {Journal of Planning Literature},
number = {4},
pages = {499--514},
title = {{Impervious surfaces and water quality: {\{}A{\}} review of current literature and its implications for watershed planning}},
volume = {16},
year = {2002}
}
@article{Brauns11,
author = {Brauns, M and G{\"{u}}cker, B and Wagner, C and Garcia, X F and Walz, N and Pusch, M T},
journal = {Journal of Applied Ecology},
number = {4},
pages = {916--925},
title = {{Human lakeshore development alters the structure and trophic basis of littoral food webs}},
volume = {48},
year = {2011}
}
@article{Breiman01,
author = {Breiman, L},
journal = {Machine Learning},
pages = {5--32},
title = {{Random forests}},
volume = {45},
year = {2001}
}
@book{Breiman84,
address = {Belmont, California},
author = {Breiman, L and Friedman, J H and Olshen, R A and Stone, C J},
pages = {358},
publisher = {Wadsworth International Group},
title = {{Classification and Regression Trees}},
year = {1984}
}
@article{Breine04,
author = {Breine, J and Simoens, I and Goethals, P and Quataert, P and Ercken, D and Liefferinghe, C Van and Belpaire, C},
journal = {Hydrobiologia},
number = {1-3},
pages = {133--148},
title = {{A fish-based index of biotic integrity for upstream brooks in {\{}F{\}}landers ({\{}B{\}}elgium)}},
volume = {522},
year = {2004}
}
@article{Brosse01,
author = {Brosse, S and Lek, S and Townsend, C R},
journal = {New Zealand Journal of Marine and Freshwater Research},
number = {1},
pages = {135--145},
title = {{Abundance, diversity, and structure of freshwater invertebrates and fish communities: An artificial neural network approach}},
volume = {35},
year = {2001}
}
@unpublished{Brown2005,
abstract = {Restoration and rehabilitation* of existing or former mangrove forest areas is extremely important today. In fact, given the importance of mangrove forest ecosystems, and the current threat to these coastal forests, this is an imperative. But actual planting of mangroves is rarely needed as mangroves annually produce hundreds or thousands of seeds or seedlings per tree, which under the proper hydrologic conditions can recolonize former mangrove areas (returned to normal hydrology) very rapidly. There are many different techniques and methods utilized in restoring mangroves. Because some of these have resulted in identifiable successes or failures, we wish to present herein a summary description of several preferred methods for planning and implementing mangrove rehabilitation. In summary, five critical steps are necessary to achieve successful mangrove restoration: 1. Understand the autecology (individual species ecology) of the mangrove species at the site; in particular the patterns of reproduction, propagule distribution, and successful seedling establishment. 2. Understand the normal hydrologic patterns that control the distribution and successful establishment and growth of targeted mangrove species. 3. Assess modifications of the original mangrove environment that currently prevent natural secondary succession (recovery after damage). 4. Design the restoration program to restore appropriate hydrology and, if possible, utilize natural volunteer mangrove propagule recruitment for plant establishment. 5. Only utilize actual planting of propagules, collected seedlings, or cultivated seedlings after determining (through steps a-d) that natural recruitment will not provide the quantity of successfully established seedlings, rate of stabilization, or rate of growth of saplings established as objectives for the restoration project (Lewis and Marshall 1997).},
author = {Brown, B},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2005{\_}Brown{\_}5{\_}Steps.pdf:pdf},
pages = {64},
title = {{Five Steps to..Successful Ecological Restoration of Mangroves}},
year = {2005}
}
@article{Brun01,
author = {Brun, R and Reichert, P and K{\"{u}}nsch, H R},
journal = {Water Resources Research},
number = {4},
pages = {1015--1030},
title = {{Practical identifiability analysis of large environmental simulation models}},
volume = {37},
year = {2001}
}
@article{Brunner2016,
abstract = {Ecosystem services (ES) modeling studies typically use a forecasting approach to predict scenarios of future ES provision. Usually, these forecasts do not inform on how specific policy alternatives will influence future ES supply and whether this supply can match ES demand - important information for policy-makers in practice. Addressing these gaps, we present a multi-method backcasting approach that links normative visions with explorative land-use and ES modeling to infer land-use policy strategies for matching regional ES supply and demand. Applied to a case study, the approach develops and evaluates a variety of ES transition pathways and identifies types, combinations and timings of policy interventions that increase ES benefits. By making explicit ES sensitivity towards regional policy strategies and global boundary conditions over time, the approach allows to address key uncertainties involved in ES modeling studies.},
author = {Brunner, Sibyl Hanna and Huber, Robert and Gr{\^{e}}t-Regamey, Adrienne},
doi = {10.1016/j.envsoft.2015.10.018},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Brunner{\_}A{\_}backcasting.pdf:pdf},
isbn = {13648152},
issn = {13648152},
journal = {Environmental Modelling and Software},
keywords = {Backcasting,Ecosystem services,Normative vision,Policy strategies,Social-ecological modeling,Transition pathways},
pages = {439--458},
title = {{A backcasting approach for matching regional ecosystem services supply and demand}},
volume = {75},
year = {2016}
}
@article{Brush2017,
abstract = {With changing climate and increased human populations, oyster reefs have$\backslash$nbeen negatively affected by excessive wave action; contamination;$\backslash$noverharvesting; decreased freshwater inputs; and shifts in oxygen,$\backslash$nsalinity, and turbidity regimes. In Florida's Big Bend, intertidal reefs$\backslash$ndominated by the eastern oyster (Crassostrea virginica) have experienced$\backslash$na net decline in area of 66 {\%} since the 1980s, a loss likely to have$\backslash$nsubstantial impacts on reef-dependent wildlife. Our study examined the$\backslash$nuse of intertidal oyster reefs by wintering American oystercatchers$\backslash$n(Haematopus palliatus) in this area. The minimum foraging time required$\backslash$nto meet daily caloric needs was conservatively estimated at 37 min per$\backslash$nadult oystercatcher, indicating that at present, foraging habitat is not$\backslash$na limiting factor within our study area. We found high-tide roosts to be$\backslash$naway from all vegetation and limited in number. They were located in$\backslash$noffshore oyster reef habitat, which has experienced an 88 {\%} decline in$\backslash$narea over the past 30 years. We suggest that offshore, high-tide roost$\backslash$nhabitat is a limiting factor and worthy of further attention.},
author = {Brush, Janell M and Schwarzer, Amy C and Frederick, Peter C},
doi = {10.1007/s12237-016-0137-6},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Brush{\_}Importance{\_}and.pdf:pdf},
journal = {Estuaries and Coasts},
keywords = {American oystercatcher,Crassostrea virginica,Eastern oyster,Estuary,Haematopus palliatus,Oyster reef},
number = {1},
pages = {286--295},
publisher = {Estuaries and Coasts},
title = {{Importance and Function of Foraging and Roost Habitat for Wintering American Oystercatchers}},
url = {http://dx.doi.org/10.1007/s12237-016-0137-6},
volume = {40},
year = {2017}
}
@article{Bryan92,
author = {Bryan, M D and Scarnecchia, D L},
journal = {Environmental Biology of Fishes},
number = {4},
pages = {329--341},
title = {{Species richness, composition, and abundance of fish larvae and juveniles inhabiting natural and developed shorelines of a glacial {\{}I{\}}owa lake}},
volume = {35},
year = {1992}
}
@article{Bulthius95,
author = {Bulthius, D A},
journal = {Aquatic Botany},
number = {1},
pages = {99--105},
title = {{Distribution of seagrasses in a north {\{}P{\}}uget {\{}S{\}}ound estuary - {\{}P{\}}adilla {\{}B{\}}ay, {\{}W{\}}ashington, {\{}USA{\}}}},
volume = {50},
year = {1995}
}
@article{Burdick99,
author = {Burdick, D M and Short, F T},
journal = {Environmental Management},
number = {2},
pages = {231--240},
title = {{The effects of boat docks on eelgrass beds in coastal waters of {\{}M{\}}assachusetts}},
volume = {23},
year = {1999}
}
@article{Burke97,
author = {Burke, L and Ignizio, J P},
journal = {Journal of Intelligent Manufacturing},
number = {3},
pages = {157--165},
title = {{A practical overview of neural networks}},
volume = {8},
year = {1997}
}
@book{Burrough98,
address = {New York, New York},
author = {Burrough, P A and McDonnell, R A},
edition = {second},
pages = {356},
publisher = {Oxford University Press},
title = {{Principles of Geographical Information Systems}},
year = {1998}
}
@article{Butler2006,
author = {Butler, J A and Heinrich, G L and Seigel, R A},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}butler{\_}third{\_}workshop.pdf:pdf},
journal = {Chelonian Conservation and Biology},
number = {2},
pages = {331--334},
title = {{Third workshop on the ecology, status, and conservation of diamondback terrapins (Malaclemys terrapin): results and recommendations}},
volume = {5},
year = {2006}
}
@article{Butler08,
author = {Butler, R G and DeMaynadier, P G},
journal = {Journal of Insect Conservation},
number = {1},
pages = {23--36},
title = {{The significance of littoral and shoreline habitat integrity to the conservation of lacustrine damselflies ({\{}O{\}}donata)}},
volume = {12},
year = {2008}
}
@article{Byrd95,
author = {Byrd, R H and Lu, P and Nocedal, J and Zhu, C},
journal = {SIAM Journal on Scientific Computing},
number = {5},
pages = {1190--1208},
title = {{A limited memory algorithm for bound constrained optimization}},
volume = {16},
year = {1995}
}
@article{Cade03,
author = {Cade, B S and Noon, B R},
journal = {Frontiers in Ecology and the Environment},
number = {8},
pages = {412--420},
title = {{A gentle introduction to quantile regression for ecologists}},
volume = {1},
year = {2003}
}
@article{Caffrey04,
author = {Caffrey, J M},
journal = {Estuaries},
number = {1},
pages = {90--101},
title = {{Factors controlling net ecosystem metabolism in {\{}U.S.{\}} estuaries}},
volume = {27},
year = {2004}
}
@article{Caffrey03,
author = {Caffrey, J M},
journal = {Environmental Monitoring and Assessment},
number = {1-3},
pages = {207--219},
title = {{Production, respiration and net ecosystem metabolism in {\{}U.S.{\}} estuaries}},
volume = {81},
year = {2003}
}
@incollection{Caffrey16,
address = {Switzerland},
author = {Caffrey, J M and Murrell, M C},
booktitle = {Aquatic Microbial Ecology and Biogeochemistry: A Dual Perspective},
editor = {Glibert, P M and Kana, T M},
pages = {199--213},
publisher = {Springer International Publishing},
title = {{A historical perspective on eutrophication in the {\{}P{\}}ensacola {\{}B{\}}ay {\{}E{\}}stuary, {\{}FL{\}}, {\{}USA{\}}}},
year = {2016}
}
@article{Caffrey14,
author = {Caffrey, J M and Murrell, M C and Amacker, K S and Harper, J and Phipps, S and Woodrey, M},
journal = {Estuaries and Coasts},
number = {1},
pages = {222--241},
title = {{Seasonal and inter-annual patterns in primary production, respiration and net ecosystem metabolism in 3 estuaries in the northeast {\{}G{\}}ulf of {\{}M{\}}exico}},
volume = {37},
year = {2013}
}
@article{Cairns01,
author = {Cairns, D M},
journal = {Plant Ecology},
number = {1},
pages = {3--18},
title = {{A comparison of methods for predicting vegetation type}},
volume = {156},
year = {2001}
}
@article{Calderon2006,
abstract = {The research objective was to adapt the ultraviolet (UV)photolysis method to determine dissolved organic nitrogen (DON) in aqueous extracts of aerosol samples. DON was assumed to be the difference in total concentration of inorganic nitrogen forms before and after sample irradiation. Using a 2 2 factorial design the authors found that the optimal conversion of urea, amino acids (alanine, aspartic acid, glycine, and serine), and methylamine for a reactor temperature of 44 °C occurred at pH 2.0 with a 24-hr irradiance period at concentrations {\textless} µM of organic nitrogen. Different decomposition mechanisms were evident: the photolysis of amino acids and methylamine released mainly ammonium (NH 4 + ), but urea released a near equimolar ratio of NH 4 + and nitrate (NO 3 − ). The method was applied to measure DON in the extracts of aerosol samples from Tampa, FL, over a 32-day sampling period. Average dissolved inorganic (DIN) and DON concentrations in the particulate matter fraction PM 10 were 78.1 ± 29.2 nmol-Nm −3 and 8.3 ± 4.9 nmol-Nm −3 , respectively. The ratio between DON and total dissolved nitrogen ([TDN] = DIN + DON) was 10.1 ± 5.7{\%}, and the majority of the DON (79.1 ± 18.2{\%}) was found in the fine particulate matter (PM 2.5 ) fraction. The average concentrations of DIN and DON in the PM 2.5 fraction were 54.4 ± 25.6 nmol-Nm −3 and 6.5 ± 4.4 nmol-Nm −3 , respectively. {\textcopyright} 2006 Air and Waste Management Association.},
author = {Calder{\'{o}}n, S M and Poor, N D and Campbell, S W},
doi = {10.1080/10473289.2006.10464584},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}Calderon{\_}Investigation{\_}of.pdf:pdf},
journal = {Journal of the Air and Waste Management Association},
number = {September},
pages = {1278--1286},
title = {{Investigation of the ultraviolet photolysis method for the determination of organic nitrogen in aerosol samples}},
volume = {56},
year = {2006}
}
@article{Camacho14b,
author = {Camacho, R A and Martin, J L and Diaz-Ramirez, J and McAnally, W and Rodriguez, H and Suscy, P and Zhang, S},
journal = {Applied Ocean Research},
pages = {138--153},
title = {{Uncertainty analysis of estuarine hydrodynamic models: an evaluation of input data uncertainty in the {\{}W{\}}eeks {\{}B{\}}ay estuary, {\{}A{\}}labama}},
volume = {47},
year = {2014}
}
@article{Camacho14a,
author = {Camacho, R A and Martin, J L and Watson, B and Paul, M J and Zheng, L and Stribling, J B},
journal = {Journal of Environmental Engineering},
number = {3},
pages = {4014067},
title = {{Modeling the factors controlling phytoplankton in the {\{}S{\}}t. {\{}L{\}}ouis {\{}B{\}}ay estuary, {\{}M{\}}ississippi and evaluating estuarine responses to nutrient load modifications}},
volume = {141},
year = {2014}
}
@article{Campbell13,
author = {Campbell, J L and Rustad, L E and Porter, J H and Taylor, J R and Dereszynski, E W and Shanley, J B and Gries, C and Henshaw, D L and Martin, M E and Sheldon, W M and Boose, E R},
journal = {BioScience},
number = {7},
pages = {574--585},
title = {{Quantity is nothing without quality: Automated {\{}QA/QC{\}} for streaming environmental sensor data}},
volume = {63},
year = {2013}
}
@article{Campbell09,
author = {Campbell, K R and Baird, R},
journal = {Lake and Reservoir Management},
number = {1},
pages = {87--101},
title = {{The effects of residential docks on light availability and distribution of submerged aquatic vegetation in two {\{}F{\}}lorida lakes}},
volume = {25},
year = {2009}
}
@incollection{Campbell07,
address = {New York, New York},
author = {Campbell, N and MacKenzie, K and Zuur, A F and Ieno, E N and Smith, G M},
booktitle = {Analysing Ecological Data},
editor = {Zuur, A F and Ieno, E N and Smith, G M},
pages = {449--462},
publisher = {Springer-Verlag},
title = {{Fish stock identification through neural network analysis of parasite fauna}},
year = {2007}
}
@manual{Cannon15,
annote = {R package version 1.1.3},
author = {Cannon, Alex J},
title = {{monmlp: Monotone Multi-Layer Perceptron Neural Network}},
url = {http://cran.r-project.org/package=monmlp},
year = {2015}
}
@article{Cannon11,
author = {Cannon, Alex J},
journal = {Computers {\&} Geosciences},
pages = {1277--1284. doi:10.1016/j.cageo.2010.07.005},
title = {{Quantile regression neural networks: implementation in R and application to precipitation downscaling}},
volume = {37},
year = {2011}
}
@article{Canuel09,
author = {Canuel, E A and Lerberg, E J and Dickhut, R M and Kuehl, S A and Bianchi, T S and Wakeham, S G},
journal = {Marine Pollution Bulletin},
number = {4-7},
pages = {154--163},
title = {{Changes in sediment and organic carbon accumulation in a highly-disturbed ecosystem: The {\{}S{\}}acramento-{\{}S{\}}an {\{}J{\}}oaquin {\{}R{\}}iver {\{}D{\}}elta ({\{}C{\}}alifornia, {\{}USA{\}})}},
volume = {59},
year = {2009}
}
@article{Carlisle09,
author = {Carlisle, D M and Falcone, J and Meador, M R},
doi = {10.1007/s10661-008-0256-z},
journal = {Environmental Monitoring and Assessment},
number = {1-4},
pages = {143--160},
title = {{Predicting the biological condition of streams: use of geospatial indicators of natural and anthropogenic characteristics of watersheds}},
volume = {151},
year = {2009}
}
@article{Carlson77,
author = {Carlson, R E},
journal = {Limnology and Oceanography},
number = {2},
pages = {361--369},
title = {{A trophic state index for lakes}},
volume = {22},
year = {1977}
}
@article{Carlton90,
author = {Carlton, J T and Thompson, J K and Schemel, L E and Nichols, F H},
journal = {Marine Ecology Progress Series},
number = {1-2},
pages = {81--94},
title = {{Remarkable invasion of {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay ({\{}C{\}}alifornia, {\{}USA{\}}) by the {\{}A{\}}sian claim $\backslash$textit{\{}Potamocorbula amurensis{\}}. {\{}I.{\}} {\{}I{\}}ntroduction and dispersal}},
volume = {66},
year = {1990}
}
@article{Carollo2013,
abstract = {At the first Gulf of Mexico Ecosystem Services Workshop (2010), ecosystem services were linked to the Gulf of Mexico habitat types as defined in the Coastal and Marine Ecological Classification Standard (CMECS), recently endorsed as the first US standard for classifying coastal and marine ecosystems. Participants identified and classified the Gulf habitat types based on CMECS, linked ecosystem services to habitat types, and prioritized services using expert opinion. Only three categories of ecosystem services were considered: regulating, provisioning, and cultural. However, supporting services, such as biological interactions, were considered as part of reclassified services. Highly ranked services were distributed across all the three service categories for each Gulf habitat, except for mangroves and dune/beach (only regulating and cultural services). Predictably, the majority of the habitat types were linked to the service of food. The importance of this exercise lies in the utility of the results for r...},
author = {Carollo, Cristina and Allee, Rebecca J. and Yoskowitz, David W.},
doi = {10.1080/21513732.2013.811701},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Carollo{\_}CMECS{\_}ES{\_}Linkages.pdf:pdf},
isbn = {2151-3732},
issn = {2151-3732},
journal = {International Journal of Biodiversity Science, Ecosystem Services {\&} Management},
keywords = {classification standard,cmecs,ecosystem services,gulf of mexico,habitat},
number = {3},
pages = {249--256},
title = {{Linking the Coastal and Marine Ecological Classification Standard (CMECS) to ecosystem services: an application to the US Gulf of Mexico}},
url = {http://www.tandfonline.com/doi/abs/10.1080/21513732.2013.811701},
volume = {9},
year = {2013}
}
@article{Carpenter95,
author = {Carpenter, D O},
journal = {Environmental Health Perspectives},
number = {S6},
pages = {127--130},
title = {{Communicating with the public on issues of science and public health}},
volume = {103},
year = {1995}
}
@article{Carpenter00,
author = {Carpenter, J and Bithell, J},
journal = {Statistics in Medicine},
number = {9},
pages = {1141--1164},
title = {{Bootstrap confidence intervals: When, which, what? {\{}A{\}} guide for medical statisticians}},
volume = {19},
year = {2000}
}
@article{Carpenter98a,
author = {Carpenter, S R and Bolgrien, D and Lathrop, R C and Stow, C A and Reed, T and Wilson, M A},
journal = {Australian Journal of Ecology},
number = {1},
pages = {68--79},
title = {{Ecological and economic analysis of lake eutrophication by nonpoint pollution}},
volume = {23},
year = {1998}
}
@article{Carpenter06,
author = {Carpenter, S R and Brock, W A},
journal = {Ecology Letters},
number = {3},
pages = {308--315},
title = {{Rising variance: A leading indicator of ecological transition}},
volume = {9},
year = {2006}
}
@article{Carpenter98b,
author = {Carpenter, S R and Caraco, N F and Correll, D L and Howarth, R W and Sharpley, A N and Smith, V H},
journal = {Ecological Applications},
number = {3},
pages = {559--568},
title = {{Nonpoint pollution of surface waters with phosphorus and nitrogen}},
volume = {8},
year = {1998}
}
@article{Cashion2013,
abstract = {The uniquely adapted mangrove forests on the marine-terrestrial interface preserve coastline integrity by buffering wave energy from marine processes. The ecosystem services they provide and their support for coastal livelihoods worldwide are worth at least US {\$}1.6 billion a year. Despite their global importance, mangroves are being lost rapidly and action is urgently needed to protect them.},
author = {Cashion, B},
doi = {10.1016/j.envdev.2013.09.001},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Cashion{\_}Mangrove{\_}forest.pdf:pdf},
number = {August},
pages = {10},
title = {{Mangrove forest cover fading fast}},
url = {https://na.unep.net/geas/},
year = {2013}
}
@article{Casselman96,
author = {Casselman, J M and Lewis, C A},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {1},
pages = {161--174},
title = {{Habitat requirements of northern pike (Esox lucius)}},
volume = {53},
year = {1996}
}
@incollection{Castilla08,
address = {Heidelberg, Berlin, New York},
author = {Castilla, G and Hay, G J},
booktitle = {Object-Based Image Analysis: Spatial Concepts for Knowledge-Driven Remote Sensing Applications},
editor = {Blaschke, T and Lang, S and Hay, G J},
pages = {91--110},
publisher = {Springer-Verlag},
title = {{Image objects and geographic objects}},
year = {2008}
}
@article{Castro2014,
abstract = {Quantitative studies that assess and map the relationship between the supply and social demand of ecosystem services are scarce. Here we address both supply and social demand sides by spatially analyzing ecosystem service trade-offs from three value-dimensions - i.e., biophysical, socio-cultural and economic, and across different landscape units in southeast Spain. To accomplish this goal, within different landscape units, we quantify the supply side by mapping the biophysical values of five ecosystem services, and the social demand exploring their socio-cultural and economic values by analyzing social preferences and contingent valuation methods, respectively. Our results show that the assessments of ecosystem services using different value-dimensions are complementary and useful for (1) identifying ecosystem service trade-offs, both on the supply- and on the social demand-side, and (2) analyzing spatial mismatches among the three value-dimensions of ecosystem services. We also believe that our approach facilitates the exploration of ecosystem services trade-offs on a spatial landscape scale, and results can be used by managers to identify areas in which services are declining or priority areas for conservation based on maximizing ecosystem services, and will be useful in detecting potential conflicts associated with new management and planning practices.},
author = {Castro, Antonio J. and Verburg, Peter H. and Mart{\'{i}}n-L{\'{o}}pez, Berta and Garcia-Llorente, Marina and Cabello, Javier and Vaughn, Caryn C. and L{\'{o}}pez, Enrique},
doi = {10.1016/j.landurbplan.2014.08.009},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2014{\_}Castro{\_}Ecosystem{\_}service{\_}trade-offs.pdf:pdf},
isbn = {0169-2046},
issn = {01692046},
journal = {Landscape and Urban Planning},
keywords = {Biophysical indicator,Contingent valuation,Drylands,Landscape unit,Social preference,Spain,Stakeholder},
pages = {102--110},
publisher = {Elsevier B.V.},
title = {{Ecosystem service trade-offs from supply to social demand: A landscape-scale spatial analysis}},
url = {http://dx.doi.org/10.1016/j.landurbplan.2014.08.009},
volume = {132},
year = {2014}
}
@article{Cavanaugh2014,
abstract = {Regional warming associated with climate change is linked with altered range and abundance of species and ecosystems worldwide. However, the ecological impacts of changes in the frequency of extreme events have not been as well documented, especially for coastal and marine environments. We used 28 y of satellite imagery to demonstrate that the area of mangrove forests has doubled at the northern end of their historic range on the east coast of Florida. This expansion is associated with a reduction in the frequency of "extreme" cold events (days colder than -4 °C), but uncorrelated with changes in mean annual temperature, mean annual precipitation, and land use. Our analyses provide evidence for a threshold response, with declining frequency of severe cold winter events allowing for poleward expansion of mangroves. Future warming may result in increases in mangrove cover beyond current latitudinal limits of mangrove forests, thereby altering the structure and function of these important coastal ecosystems.},
author = {Cavanaugh, K C and Kellner, J R and Forde, A J and Gruner, D S and Parker, J D and Rodriguez, W and Feller, I C},
doi = {10.1073/pnas.1315800111},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2014{\_}Cavanaugh{\_}poleward{\_}expansion.pdf:pdf},
journal = {Proceedings of the National Academy of Sciences},
number = {2},
pages = {723--727},
title = {{Poleward expansion of mangroves is a threshold response to decreased frequency of extreme cold events}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1315800111},
volume = {111},
year = {2014}
}
@misc{CDMO14,
annote = {$\backslash$url{\{}http://cdmo.baruch.sc.edu/{\}}. (Accessed January, 2014)},
author = {{CDMO (Centralized Data Management Office)}},
title = {{National Estuarine Research Reserve System}},
year = {2014}
}
@techreport{CEC97,
address = {Montreal, Quebec},
author = {{CEC (Commission for Environmental Cooperation)}},
title = {{Ecological regions of {\{}N{\}}orth {\{}A{\}}merica: Toward a common perspective}},
year = {1997}
}
@article{Chambers87,
author = {Chambers, P A},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {9},
pages = {1666--1669},
title = {{Nearshore occurrence of submersed aquatic macrophytes in relation to wave action}},
volume = {44},
year = {1987}
}
@article{Champely97,
author = {Champely, S and Doledec, S},
journal = {Water Research},
number = {11},
pages = {2849--2857},
title = {{How to separate long-term trends from periodic variation in water quality monitoring}},
volume = {31},
year = {1997}
}
@article{Chandra05,
author = {Chandra, S and Zanden, M Jake Vander and Heyvaert, A C and Richards, B C and Allen, B C and Goldman, C R},
journal = {Limnology and Oceanography},
number = {5},
pages = {1368--1376},
title = {{The effects of cultural eutrophication on the coupling between pelagic primary producers and benthic producers}},
volume = {50},
year = {2005}
}
@article{Chang08,
author = {Chang, H},
journal = {Water Research},
number = {13},
pages = {3285--3304},
title = {{Spatial analysis of water quality trends in the {\{}H{\}}an {\{}R{\}}iver basin, {\{}S{\}}outh {\{}K{\}}orea}},
volume = {42},
year = {2008}
}
@article{Chang13,
author = {Chang, N B and Xuan, Z and Yang, Y J},
journal = {Remote Sensing of Environment},
pages = {100--110},
title = {{Exploring spatiotemporal patterns of phosphorus concentrations in a coastal bay with {\{}MODIS{\}} images and machine learning models}},
volume = {134},
year = {2013}
}
@manual{chang15,
annote = {R package version 0.11.1},
author = {Chang, Winston and Cheng, Joe and Allaire, J J and Xie, Yihui and McPherson, Jonathan},
title = {{shiny: Web Application Framework for R}},
url = {http://cran.r-project.org/package=shiny},
year = {2015}
}
@article{Chase06,
author = {Chase, J M and Knight, T M},
journal = {Biological Invasions},
number = {8},
pages = {1643--1649},
title = {{Effects of eutrophication and snails on {\{}E{\}}urasian watermilfoil ($\backslash$textit{\{}{\{}M{\}}yriophyllum spicatum{\}}) invasion}},
volume = {8},
year = {2006}
}
@article{Chen14,
author = {Chen, K and Hughes, R M and Xu, S and Zhang, J and Cai, D and Wang, B},
doi = {10.1016/j.ecolind.2013.07.006},
journal = {Ecological Indicators},
pages = {142--151},
title = {{Evaluating performance of macroinvertebrate-based adjusted and unadjusted multi-metric indices ({\{}MMI{\}}) using multi-season and multi-year samples}},
volume = {36},
year = {2014}
}
@article{Chen07,
author = {Chen, Z and Muller-Karger, F E and Hu, C},
journal = {Remote Sensing of Environment},
number = {2},
pages = {249--259},
title = {{Remote sensing of water clarity in {\{}T{\}}ampa {\{}B{\}}ay}},
volume = {109},
year = {2007}
}
@article{Cheng94,
author = {Cheng, B and Titterington, D M},
journal = {Statistical Science},
number = {1},
pages = {2--54},
title = {{Neural networks: A review from a statistical perspective}},
volume = {9},
year = {1994}
}
@manual{Cheng15,
annote = {R package version 1.0.0},
author = {Cheng, Joe and Xie, Yihui},
title = {{leaflet: Create Interactive Web Maps with the JavaScript 'Leaflet' Library}},
url = {http://cran.r-project.org/package=leaflet},
year = {2015}
}
@article{Cheruvelil08,
author = {Cheruvelil, K S and Soranno, P A},
journal = {Aquatic Botany},
number = {3},
pages = {219--227},
title = {{Relationships between lake macrophyte cover and lake and landscape features}},
volume = {88},
year = {2008}
}
@techreport{Chipman09,
address = {Madison, Wisconsin},
author = {Chipman, J W and Olmanson, L G and Gitelson, A A},
institution = {North American Lake Management Society in collaboration with Dartmouth College, University of Minnesota, University of Nebraska and University of Wisconsin for the United States Environmental Protection Agency},
pages = {126},
title = {{Remote sensing methods for lake management: A guide for resource managers and decision-makers}},
year = {2009}
}
@techreport{Chirhart03,
address = {St. Paul, Minnesota},
author = {Chirhart, J},
institution = {Biological Monitoring Program, Minnesota Pollution Control Agency},
pages = {45},
title = {{Development of a macroinvertebrate index of biological integrity ({\{}MIBI{\}}) for rivers and streams of the {\{}S{\}}t. {\{}C{\}}roix river basin in {\{}M{\}}innesota}},
year = {2003}
}
@article{Choice14,
author = {Choice, Z D and Frazer, T K and Jacoby, C A},
journal = {Marine Pollution Bulletin},
number = {1},
pages = {94--102},
title = {{Light requirements of seagrasses determined from historical records of light attenuation along the {\{}G{\}}ulf coast of peninsular {\{}F{\}}lorida}},
volume = {81},
year = {2014}
}
@article{Christensen96,
author = {Christensen, D L and Herwig, B R and Schindler, D E and Carpenter, S R},
journal = {Ecological Applications},
number = {4},
pages = {1143--1149},
title = {{Impacts of lakeshore residential development on coarse woody debris in north temperate lakes}},
volume = {6},
year = {1996}
}
@misc{Cintron1984,
author = {Cintron, G and Novelli, Y S},
booktitle = {The mangrove ecosystem: research methods},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1984{\_}Cintron{\_}methods{\_}for.pdf:pdf},
pages = {91--113},
title = {{Methods for studying mangrove structure}},
year = {1984}
}
@article{Clark01,
author = {Clark, James S and Carpenter, Steven R and Barber, Mary and Collins, Scott and Dobson, Andy and Foley, Jonathan A and Lodge, David M and Pascual, Mercedes and Pielke, Roger and Pizer, William and Pringle, Cathy and Reid, Walter V and Rose, Kenneth A and Sala, Osvaldo and Schlesinger, William H and Wall, Diana H and Wear, David},
journal = {Science},
number = {5530},
pages = {657--660},
title = {{Ecological forecasts: an emerging imperative}},
volume = {293},
year = {2001}
}
@article{Clarke93,
author = {Clarke, K R},
journal = {Australian Journal of Ecology},
number = {1},
pages = {117--143},
title = {{Non-parametric multivariate analyses of changes in community structure}},
volume = {18},
year = {1993}
}
@article{Clayton06,
author = {Clayton, J and Edwards, T},
journal = {Hydrobiologia},
pages = {147--151},
title = {{Aquatic plants as environmental indicators of ecological condition in {\{}N{\}}ew {\{}Z{\}}ealand lakes}},
volume = {570},
year = {2006}
}
@article{Cleve08,
author = {Cleve, C and Kelly, M and Kearns, F R and Moritz, M},
journal = {Computers, Environment and Urban Systems},
number = {4},
pages = {317--326},
title = {{Classification of the wildland-urban interface: A comparison of pixel- and object-based classifications using high-resolution aerial photography}},
volume = {32},
year = {2008}
}
@article{Cleveland79,
author = {Cleveland, W S},
journal = {Journal of the American Statistical Association},
number = {368},
pages = {829--836},
title = {{Robust locally weighted regression and smoothing scatterplots}},
volume = {74},
year = {1979}
}
@incollection{Cloern15,
address = {California},
author = {Cloern, J E},
booktitle = {Ecosystems of California: A Source Book},
editor = {Mooney, H and Zavaleta, E},
pages = {359--387},
publisher = {University of California Press},
title = {{Life on the edge: {\{}C{\}}alifornia's estuaries}},
year = {2015}
}
@article{Cloern01,
author = {Cloern, J E},
journal = {Marine Ecology Progress Series},
pages = {223--253},
title = {{Our evolving conceptual model of the coastal eutrophication problem}},
volume = {210},
year = {2001}
}
@article{Cloern96,
author = {Cloern, J E},
journal = {Review of Geophysics},
number = {2},
pages = {127--168},
title = {{Phytoplankton bloom dynamics in coastal ecosystems: {\{}A{\}} review with some general lessons from sustained investigation of {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay, {\{}C{\}}alifornia}},
volume = {34},
year = {1996}
}
@misc{Cloern2016,
abstract = {Time series of environmental measurements are essential for detecting, measuring and understanding changes in the Earth system and its biological communities. Observational series have accumulated over the past 2-5 decades from measurements across the world's estuaries, bays, lagoons, inland seas and shelf waters influenced by runoff. We synthesize information contained in these time series to develop a global view of changes occurring in marine systems influenced by connectivity to land. Our review is organized around four themes: (i) human activities as drivers of change; (ii) variability of the climate system as a driver of change; (iii) successes, disappointments and challenges of managing change at the sea-land interface; and (iv) discoveries made from observations over time. Multidecadal time series reveal that many of the world's estuarine-coastal ecosystems are in a continuing state of change, and the pace of change is faster than we could have imagined a decade ago. Some have been transformed into novel ecosystems with habitats, biogeochemistry and biological communities outside the natural range of variability. Change takes many forms including linear and nonlinear trends, abrupt state changes and oscillations. The challenge of managing change is daunting in the coastal zone where diverse human pressures are concentrated and intersect with different responses to climate variability over land and over ocean basins. The pace of change in estuarine-coastal ecosystems will likely accelerate as the human population and economies continue to grow and as global climate change accelerates. Wise stewardship of the resources upon which we depend is critically dependent upon a continuing flow of information from observations to measure, understand and anticipate future changes along the world's coastlines.},
author = {Cloern, J E and Abreu, P C and Carstensen, J and Chauvaud, L and Elmgren, R and Grall, Jacques and Greening, H S and Johansson, J O R and Kahru, M and Sherwood, E T and Xu, J and Yin, K},
booktitle = {Global Change Biology},
doi = {10.1111/gcb.13059},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2015 Tech Pubs/TBEP{\_}07{\_}15{\_}Cloern{\_}et{\_}al-2015-Global{\_}Change{\_}Biology.pdf:pdf},
isbn = {1354-1013},
issn = {13652486},
keywords = {Climate variability,Ecosystems,Environmental change,Estuarine-coastal,Global change,Human disturbance},
number = {2},
pages = {513--529},
pmid = {26242490},
title = {{Human activities and climate variability drive fast-paced change across the world's estuarine-coastal ecosystems}},
volume = {22},
year = {2016}
}
@article{Cloern83,
author = {Cloern, J E and Alpine, A E and Cole, B E and Wong, R L J and Arthur, J F and Ball, M D},
journal = {Estuarine, Coastal and Shelf Science},
number = {4},
pages = {415--426},
title = {{River discharge controls phytoplankton dynamics in the northern {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay estuary}},
volume = {16},
year = {1983}
}
@article{Cloern95,
author = {Cloern, J E and Grenz, C and Vidergar-Lucas, L},
journal = {Limnology and Oceanography},
number = {7},
pages = {1313--1321},
title = {{An empirical model of the phytoplankton:carbon ratio - the conversion factor between productivity and growth rate}},
volume = {40},
year = {1995}
}
@article{Cloern12b,
author = {Cloern, J E and Jassby, A D},
journal = {Reviews of Geophysics},
number = {4},
pages = {1--33},
title = {{Drivers of change in estuarine-coastal ecosystems: Discoveries from four decades of study in {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {50},
year = {2012}
}
@article{Cloern10,
author = {Cloern, J E and Jassby, A D},
journal = {Estuaries and Coasts},
number = {2},
pages = {230--241},
title = {{Patterns and scales of phytoplankton variability in estuarine-coastal ecosystems}},
volume = {33},
year = {2010}
}
@article{Cloern12,
author = {Cloern, J E and Jassby, A D and Carstensen, J and Bennett, W A and Kimmerer, W and {Mac Nally}, R and Schoellhamer, D H and Winder, M},
journal = {Limnology and Oceanography},
number = {2},
pages = {665--668},
title = {{Perils of correlating {\{}CUSUM{\}}-transformed variables to infer ecological relationships ({\{}Breton et al. 2006{\}}; {\{}Glibert 2010{\}})}},
volume = {57},
year = {2012}
}
@article{Cloern07,
author = {Cloern, J E and Jassby, A D and Thompson, J K and Hieb, K A},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {47},
pages = {18561--18565},
title = {{A cold phase of the {\{}E{\}}ast {\{}P{\}}acific triggers new phytoplankton blooms in {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {104},
year = {2007}
}
@article{Cloern05,
author = {Cloern, J E and Schraga, T S and Lopez, C B and Knowles, N and Labiosa, R G and Dugdale, R},
journal = {Geophysical Research Letters},
number = {14},
pages = {L14608},
title = {{Climate anomalies generate an exceptional dinoflagellate bloom in {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {32},
year = {2005}
}
@techreport{CPE97,
address = {Palatka, Florida},
author = {{Coastal Planning and Engineering}},
institution = {Coastal Planning and Engineering},
number = {Contract 95W142},
title = {{{\{}I{\}}ndian {\{}R{\}}iver {\{}L{\}}agoon bathymetric survey. {\{}A{\}} final report to {\{}S{\}}t. {\{}J{\}}ohn's {\{}R{\}}iver {\{}W{\}}ater {\{}M{\}}anagement {\{}D{\}}istrict}},
year = {1997}
}
@article{Cohen98,
author = {Cohen, A N and Carlton, J T},
journal = {Science},
number = {5350},
pages = {555--558},
title = {{Accelerating invasion rate in a highly invaded estuary}},
volume = {279},
year = {1998}
}
@article{Cohen60,
author = {Cohen, J},
journal = {Educational Psychology Measurement},
number = {1},
pages = {37--46},
title = {{A coefficient of agreement for nominal scales}},
volume = {20},
year = {1960}
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author = {Cohn, T A and Caulder, D L and Gilroy, E J and Zynjuk, L D and Summers, R M},
journal = {Water Resources Research},
number = {9},
pages = {2353--2363},
title = {{The validity of a simple statistical model for estimating fluvial constituent loads: An empirical study involving nutrient loads entering {\{}C{\}}hesapeake {\{}B{\}}ay}},
volume = {28},
year = {1992}
}
@article{Cohn89,
author = {Cohn, T A and DeLong, L L and Gilroy, E J and Hirsch, R M and Wells, D K},
journal = {Water Resources Research},
number = {5},
pages = {937--942},
title = {{Estimating constituent loads}},
volume = {25},
year = {1989}
}
@article{Cole84,
author = {Cole, B E and Cloern, J E},
journal = {Marine Ecology Progress Series},
number = {1},
pages = {15--24},
title = {{Significance of biomass and light availability to phytoplankton productivity in {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {17},
year = {1984}
}
@article{Collins13,
author = {Collins, J R and Raymond, P A and Bohlen, W F and Howard-Strobel, M M},
journal = {Estuaries and Coasts},
number = {1},
pages = {74--97},
title = {{Estimates of new and total productivity in {\{}C{\}}entral {\{}L{\}}ong {\{}I{\}}sland {\{}S{\}}ound from in situ measurements of nitrate and dissolved oxygen}},
volume = {36},
year = {2013}
}
@article{Coloso11,
author = {Coloso, J J and Cole, J J and Pace, M L},
journal = {Ecosystems},
number = {6},
pages = {935--948},
title = {{Difficulty in discerning drivers of lake ecosystem metabolism with high-frequency data}},
volume = {14},
year = {2011}
}
@article{Congalton91,
author = {Congalton, R G},
journal = {Remote Sensing of Environment},
number = {1},
pages = {35--46},
title = {{A review of assessing the accuracy of classifications of remotely sensed data}},
volume = {37},
year = {1991}
}
@article{Connell78,
author = {Connell, J H},
journal = {Science},
pages = {1302--1310},
title = {{Diversity in tropical rain forests and coral reefs}},
volume = {199},
year = {1978}
}
@book{Cook99,
address = {New York, New York},
author = {Cook, R D and Weisberg, S},
pages = {593},
publisher = {Wiley},
title = {{Applied Regression Including Computing and Graphics}},
year = {1999}
}
@article{Cornwell14,
author = {Cornwell, J C and Glibert, P M and Owens, M S},
journal = {Estuaries and Coasts},
number = {5},
pages = {1120--1133},
title = {{Nutrient fluxes from sediments in the {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay {\{}D{\}}elta}},
volume = {37},
year = {2014}
}
@misc{Cottam1956,
author = {Cottam, G and Curtis, J T},
booktitle = {Ecology},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1956{\_}Cottam{\_}Distance{\_}Measures.pdf:pdf},
number = {3},
pages = {451--460},
title = {{The Use of Distance Measures in Phytosociological Sampling}},
volume = {37},
year = {1956}
}
@misc{CPC13,
annote = {$\backslash$url{\{}http://www.cpc.ncep.noaa.gov/products/analysis{\_}monitoring/ensostuff/ensoyears.shtml{\}}. (Accessed September, 2013)},
author = {{CPC (Climate Prediction Center)}},
title = {{{\{}N{\}}ational {\{}W{\}}eather {\{}S{\}}ervice {\{}C{\}}limate {\{}P{\}}rediction {\{}C{\}}enter: Cold and warm episodes by season}},
year = {2013}
}
@techreport{Crauder16,
address = {Reston, Virginia},
author = {Crauder, J S and Thompson, J K and Parchaso, F and Anduaga, R I and Pearson, S A and Gehrts, K and Fuller, H and Wells, E},
institution = {US Geological Survey},
number = {Open-File Report 2016-1005},
title = {{Bivalve effects on the food web supporting delta smelt - A long-term study of bivalve recruitment, biomass, and grazing rate patterns with varying freshwater outflow}},
year = {2016}
}
@techreport{Cronin75,
address = {Baltimore, Maryland},
author = {Cronin, W B and Pritchard, D W},
institution = {Chesapeake Bay Institute, The Johns Hopkins University},
number = {42, Reference 75-3},
title = {{Additional statistics on the dimensions of the {\{}C{\}}hesapeake {\{}B{\}}ay and its tributaries: Cross-section widths and segment volumes per meter depth}},
year = {1975}
}
@article{Cross13,
author = {Cross, T K and Jacobson, P C},
journal = {Lake and Reservoir Management},
number = {1},
pages = {1--12},
title = {{Landscape factors influencing lake phosphorus concentrations across {\{}M{\}}innesota}},
volume = {29},
year = {2013}
}
@techreport{Cross06,
address = {St. Paul, Minnesota},
author = {Cross, T and McInerny, M},
institution = {Fisheries and Wildlife Division, Minnesota Department of Natural Resources},
number = {537},
title = {{Relationships between aquatic plant cover and fish populations based on {\{}M{\}}innesota lake survey data}},
year = {2006}
}
@book{Cryer08,
address = {New York, New York},
author = {Cryer, J D and Chan, K S},
edition = {second},
pages = {491},
publisher = {Springer-Verlag},
title = {{Time Series Analysis with Applications in R}},
year = {2008}
}
@manual{Csardi15,
annote = {R package version 2.1.0},
author = {Csardi, Gabor},
title = {{cranlogs: Download Logs from the 'RStudio' 'CRAN' Mirror}},
url = {https://github.com/metacran/cranlogs},
year = {2015}
}
@article{Cullen-unsworth2013,
author = {Cullen-unsworth, Leanne and Unsworth, Richard},
doi = {10.1080/00139157.2013.785864},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Cullen-Unsworth{\_}Seagrass{\_}Meadows.pdf:pdf},
isbn = {0013-9157},
issn = {0013-9157},
journal = {Environmental Magazine},
number = {3},
pages = {37--41},
title = {{Seagrass Meadows , E and Sustainability}},
volume = {55},
year = {2013}
}
@article{Cutler07,
author = {Cutler, D R and Jr., T C Edwards and Beard, K H and Cutler, A and Hess, K T and Gibson, J and Lawler, J J},
doi = {10.1890/07-0539.1},
journal = {Ecology},
number = {11},
pages = {2783--2792},
title = {{Random forests for classification in ecology}},
volume = {88},
year = {2007}
}
@article{Cvetkovic10,
author = {Cvetkovic, M and Wei, A and Chow-Fraser, P},
journal = {Journal of Great Lakes Research},
pages = {64--73},
title = {{Relative importance of macrophyte community versus water quality variables for predicting fish assemblages in coastal wetlands of the {\{}L{\}}aurentian {\{}G{\}}reat {\{}L{\}}akes}},
volume = {36},
year = {2010}
}
@article{Dafforn2016,
author = {Dafforn, K A A and Johnston, E L A and Ferguson, A C and Humphrey, C L D and Monk, W E},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Daffron{\_}Big{\_}Data-Ecosystem-Assessments{\_}MF15108.pdf:pdf},
pages = {393--413},
title = {{Big data opportunities and challenges for assessing multiple stressors across scales in aquatic ecosystems}},
year = {2016}
}
@article{Dahdouh-Guebas2005,
abstract = {The increasing anthropogenic pressure on natural environments results in impacts that affect tropical forest areas and their biodiversity [1, 2]. Adverse impacts on terrestrial and oceanic environments often compound in the intertidal area, where mangrove forest ecosystems thrive. In tropical coastal areas of many developing countries where people depend on wood and other mangrove forest products and services, forest degradation leads to socioeconomic problems. At the same time, increasing freshwater needs in these areas are expected to cause additional problems [3-5]. On the basis of remote sensing and ground truthing complemented by colonial archival material from the Dutch East India Company (1602-1800), we report that changes to the historic system of inland freshwater management have increased dramatically in recent times. Hydrological changes, such as interbasin transfers, have resulted in a qualitative ecological and socioeconomic degradation in three coastal lagoons in southern Sri Lanka. Variations in river hydrology have caused changes in the areas suitable as mangrove habitat and, thus, have resulted in an altered distribution. However, increases in mangrove area can mask the degradation of the site in terms of floristic composition, significance of the species, and biodiversity (this effect is termed "cryptic ecological degradation"). It is important that such changes be carefully monitored to ensure biological and socioeconomic sustainability. {\textcopyright} 2005 Elsevier Ltd All rights reserved.},
author = {Dahdouh-Guebas, F and Hettiarachchi, S and {Lo Seen}, D and Batelaan, O and Sooriyarachchi, S and Jayatissa, L P and Koedam, N},
doi = {10.1016/j.cub.2005.01.053},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2005{\_}Dahdouh-Guebas{\_}transitions{\_}in.pdf:pdf},
journal = {Current Biology},
number = {6},
pages = {579--586},
title = {{Transitions in ancient inland freshwater resource management in Sri Lanka affect biota and human populations in and around coastal lagoons}},
volume = {15},
year = {2005}
}
@article{Dahm16,
author = {Dahm, C N and Parker, A E and Adelson, A E and Christman, M A and Bergamaschi, B A},
journal = {San Francisco Estuary and Watershed Science},
number = {4},
pages = {1--36},
title = {{Nutrient dynamics of the {\{}D{\}}elta: Effects on primary producers}},
volume = {14},
year = {2016}
}
@article{Dale02,
author = {Dale, M R T and Dixon, P and Fortin, M J and Legendre, P and Myers, D E and Rosenberg, M S},
journal = {Ecography},
number = {5},
pages = {558--577},
title = {{Conceptual and mathematical relationships among methods for spatial analysis}},
volume = {25},
year = {2002}
}
@article{Dalyander2016,
abstract = {Coastal ecosystem management typically relies on subjective interpretation of scientific understanding, with limited methods for explicitly incorporating process knowledge into decisions that must meet multiple, potentially competing stakeholder objectives. Conversely, the scientific community lacks methods for identifying which advancements in system understanding would have the highest value to decision-makers. A case in point is barrier island restoration, where decision-makers lack tools to objectively use system understanding to determine how to optimally use limited contingency funds when project construction in this dynamic environment does not proceed as expected. In this study, collaborative structured decision-making (SDM) was evaluated as an approach to incorporate process understanding into mid-construction decisions and to identify priority gaps in knowledge from a management perspective. The focus was a barrier island restoration project at Ship Island, Mississippi, where sand will be used to close an extensive breach that currently divides the island. SDM was used to estimate damage that may occur during construction, and guide repair decisions within the confines of limited availability of sand and funding to minimize adverse impacts to project objectives. Sand was identified as more limiting than funds, and unrepaired major breaching would negatively impact objectives. Repairing minor damage immediately was determined to be generally more cost effective (depending on the longshore extent) than risking more damage to a weakened project. Key gaps in process-understanding relative to project management were identified as the relationship of island width to breach formation; the amounts of sand lost during breaching, lowering, or narrowing of the berm; the potential for minor breaches to self-heal versus developing into a major breach; and the relationship between upstream nourishment and resiliency of the berm to storms. This application is a prototype for using structured decision-making in support of engineering projects in dynamic environments where mid-construction decisions may arise; highlights uncertainty about barrier island physical processes that limit the ability to make robust decisions; and demonstrates the potential for direct incorporation of process-based models in a formal adaptive management decision framework.},
author = {Dalyander, P. Soupy and Meyers, Michelle and Mattsson, Brady and Steyer, Gregory and Godsey, Elizabeth and McDonald, Justin and Byrnes, Mark and Ford, Mark},
doi = {10.1016/j.jenvman.2016.08.078},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Dalyander{\_}J{\_}Env{\_}Mgmt.pdf:pdf},
issn = {10958630},
journal = {Journal of Environmental Management},
keywords = {Adaptive management,Barrier islands,Ecosystem restoration,Gulf of Mexico,Mississippi Coastal Improvements Program,Structured decision-making},
pages = {497--509},
pmid = {27623362},
publisher = {Elsevier Ltd},
title = {{Use of structured decision-making to explicitly incorporate environmental process understanding in management of coastal restoration projects: Case study on barrier islands of the northern Gulf of Mexico}},
url = {http://dx.doi.org/10.1016/j.jenvman.2016.08.078},
volume = {183},
year = {2016}
}
@article{Danz07,
author = {Danz, Nicholas P and Niemi, Gerald J and Regal, Ronald R and Hollenhorst, Tom and Johnson, Lucinda B and Hanowski, JoAnn M and Axler, Richard P and Ciborowski, Jan J H and Hrabik, Thomas and Brady, Valerie J and Kelly, John R and Morrice, John A and Brazner, John C and Howe, Robert W and Johnston, Carol A and Host, George E},
journal = {Environmental Management},
number = {5},
pages = {631--647},
title = {{Integrated measures of anthropogenic stress in the {\{}US Great Lakes{\}} basin}},
volume = {39},
year = {2007}
}
@article{Davanzo96,
author = {D'Avanzo, C and Kremer, J N and Wainwright, S C},
journal = {Marine Ecology Progress Series},
number = {1-3},
pages = {263--274},
title = {{Ecosystem production and respiration in response to eutrophication in shallow temperate estuaries}},
volume = {141},
year = {1996}
}
@incollection{Davidson2016,
author = {Davidson, Nick C},
booktitle = {The Wetland Book},
doi = {10.1007/978-94-007-6173-5},
editor = {Finlayson, C M and Everard, M and Irvine, K and McInnes, R J and Middleton, B A and van Dam, A A and Davidson, N C},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Davidson{\_}wetland{\_}losses.pdf:pdf},
isbn = {978-94-007-6173-5},
publisher = {Springer Nertherlands},
title = {{Wetland Losses and the Status of Wetland-Dependent Species}},
url = {http://link.springer.com/10.1007/978-94-007-6173-5},
year = {2016}
}
@article{Davies06,
author = {Davies, S P and Jackson, S K},
journal = {Ecological Applications},
number = {4},
pages = {1251--1266},
title = {{The biological condition gradient: A descriptive model for interpreting change in aquatic ecosystems}},
volume = {16},
year = {2006}
}
@article{Dawes10,
author = {Dawes, C and Avery, W},
journal = {Florida Scientist},
number = {3-4},
pages = {185--195},
title = {{Epiphytes of the seagrass {\{}$\backslash$textit{\{}Halodule wrightii{\}}{\}} in {\{}H{\}}illsborough {\{}B{\}}ay, {\{}F{\}}lorida, a 14 year study in an estuary recovering from eutrophication}},
volume = {73},
year = {2010}
}
@article{DeDeckere2011,
author = {de Deckere, Eric and de Cooman, Ward and Leloup, Vicky and Meire, Patrick and Schmitt, Claudia and von der Ohe, Peter C},
doi = {10.1007/s11368-010-0328-x},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2011{\_}Deckere{\_}Development{\_}of.pdf:pdf},
journal = {Journal of Soils and Sediments},
keywords = {EQS,Macrobenthos,Priority substances,SEC,SQG,Sediment quality guidelines,TRIAD},
number = {3},
pages = {504--517},
title = {{Development of sediment quality guidelines for freshwater ecosystems}},
volume = {11},
year = {2011}
}
@article{DeMutsert2017,
abstract = {A coupled ecosystem modeling approach was used to evaluate how select combinations of large-scale river diversions in the lower Mississippi River Deltaic Plain may affect the distribution, biomass, and landings of fish and shellfish over decades relative to a future without action. These river diversions are controlled openings in the riverbank of the Mississippi River designed to reintroduce sediment, water, and nutrients into hydrologically isolated coastal wetlands in order to mitigate wetland loss. We developed a spatial ecosystem model using Ecopath with Ecosim (EwE) software, and prepared it to receive output from a Delft3D hydrodynamic model coupled to primary production models. The Delft3D model provided environmental drivers including salinity, temperature, Chl a, total suspended solids, and change in wetland cover as a result of simulated river diversions over decadal model runs. Driver output was averaged either daily, monthly, or annually depending on the parameter. A novel oyster-specific subroutine is introduced in this paper to incorporate information at daily intervals in Ecospace, while Ecospace runs on a monthly time step. The ecosystem model simulates biomass and distribution of fish and shellfish species, and landings of targeted fisheries species, as a result of environmental changes projected for a preliminary set of management scenarios designed to evaluate and screen select combinations of river diversions. Abundant local field samples and landings data allowed for model calibration and validation. The results of simulations indicate that inflow of Mississippi River water in estuaries may cause local shifts in species assemblages. These changes were in some cases direct effects of decreased salinity, such as locally reduced Spotted Seatrout biomass. Changes in some other species in the affected areas resulted from indirect effects; for example, reduced Chl a (as a result of increased TSS) resulted in near-field reductions of Gulf Menhaden. The simulations also showed that local biomass reductions were mostly the result of redistribution, since the scenario with the proposed diversions open had minimal impact on the total biomass or landings of species simulated in the Mississippi River Delta as compared to a future without action. The model and its output were used as a decision support tool to help evaluate and compare alternative management actions. The results of this study played a role in the decision by the Coastal Protection and Restoration Authority to prioritize moving forward to conduct more detailed analyses through engineering and design of the two middle diversions but not the two lower diversions that were tested in this study.},
author = {de Mutsert, Kim and Lewis, Kristy and Milroy, Scott and Buszowski, Joe and Steenbeek, Jeroen},
doi = {10.1016/j.ecolmodel.2017.06.029},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}de{\_}Musert{\_}et{\_}al{\_} EcoPath{\_}MS{\_}River{\_}Diversions{\_}fisheries.pdf:pdf},
issn = {03043800},
journal = {Ecological Modelling},
keywords = {Coastal restoration,Delta management,Ecopath with Ecosim,Ecospace,Fisheries,Model coupling},
pages = {14--26},
publisher = {Elsevier B.V.},
title = {{Using ecosystem modeling to evaluate trade-offs in coastal management: Effects of large-scale river diversions on fish and fisheries}},
url = {http://dx.doi.org/10.1016/j.ecolmodel.2017.06.029},
volume = {360},
year = {2017}
}
@article{DeKeyser03,
author = {DeKeyser, E and Kirby, D R and Ell, M J},
journal = {Ecological Indicators},
number = {2},
pages = {119--133},
title = {{An index of plant community integrity: Development of the methodology for assessing prairie wetland plant commmunities}},
volume = {3},
year = {2003}
}
@article{Denman03,
author = {Denman, K L},
journal = {Progress in Oceanography},
number = {3-4},
pages = {429--452},
title = {{Modelling planktonic ecosystems: parameterizing complexity}},
volume = {57},
year = {2003}
}
@article{Dennison87,
author = {Dennison, W C},
journal = {Aquatic Botany},
number = {1},
pages = {15--26},
title = {{Effects of light on seagrass photosynthesis, growth and depth distribution}},
volume = {27},
year = {1987}
}
@article{Dennison93,
author = {Dennison, W C and Orth, R J and Moore, K A and Stevenson, J C and Carter, V and Kollar, S and Bergstrom, P W and Batiuk, R A},
journal = {Bioscience},
number = {2},
pages = {86--94},
title = {{Assessing water quality with submersed aquatic vegetation}},
volume = {43},
year = {1993}
}
@article{Diaz11,
author = {Diaz, R J and Rosenberg, R},
journal = {International Journal of Water Resources Development},
number = {1},
pages = {71--82},
title = {{Introduction to environmental and economic consequences of hypoxia}},
volume = {27},
year = {2011}
}
@article{Diaz08,
author = {Diaz, R J and Rosenberg, R},
journal = {Science},
pages = {926--929},
title = {{Spreading dead zones and consequences for marine ecosystems}},
volume = {321},
year = {2008}
}
@article{Diaz95,
author = {Diaz, R J and Rosenberg, R},
journal = {Oceanography and Marine Biology},
pages = {245--303},
title = {{Marine benthic hypoxia: A review of its ecological effects and the behavioural responses of benthic macrofauna}},
volume = {33},
year = {1995}
}
@article{Diefenderfer16,
abstract = {This study adapts and applies the evidence-based approach for causal inference, a medical standard, to the restoration and sustainable management of large-scale aquatic ecosystems. Despite long-term investments in restoring aquatic ecosystems, it has proven difficult to adequately synthesize and evaluate program outcomes, and no standard method has been adopted. Complex linkages between restorative actions and ecosystem responses at a landscape scale make evaluations problematic and most programs focus on monitoring and analysis. Herein, we demonstrate a new transdisciplinary approach integrating techniques from evidence-based medicine, critical thinking, and cumulative effects assessment. Tiered hypotheses about the effects of landscape-scale restorative actions are identified using an ecosystem conceptual model. The systematic literature review, a health sciences standard since the 1960s, becomes just one of seven lines of evidence assessed collectively, using critical thinking strategies, causal criteria, and cumulative effects categories. As a demonstration, we analyzed data from 166 locations on the Columbia River and estuary representing 12 indicators of habitat and fish response to floodplain restoration actions intended to benefit culturally and economically important, threatened and endangered salmon. Synthesis of the lines of evidence demonstrated that hydrologic reconnection promoted macrodetritis export, prey availability, and juvenile fish access and feeding. Upon evaluation, the evidence was sufficient to infer cross-boundary, indirect, compounding, and delayed cumulative effects, and suggestive of nonlinear, landscape-scale, and spatial density effects. Therefore, on the basis of causal inferences regarding foodweb functions, we concluded that the restoration program is having a cumulative beneficial effect on juvenile salmon. The lines of evidence developed are transferable to other ecosystems: modeling of cumulative net ecosystem improvement, physical modeling of ecosystem controlling factors, meta-analysis of restoration action effectiveness, analysis of data on target species, research on critical ecological uncertainties, evidence-based review of the literature, and change analysis on the landscape setting. As with medicine, the science of ecological restoration needs scientific approaches to management decisions, particularly because the consequences affect species extinctions and the availability of ecosystem services. This evidencebased approach will enable restoration in complex coastal, riverine, and tidal-fluvial ecosystems like the lower Columbia River to be evaluated when data have accumulated without sufficient synthesis.},
author = {Diefenderfer, Heida L and Johnson, Gary E and Thom, Ronald M and Buenau, Kate E and Weitkamp, Laurie A and Woodley, Christa M and Borde, Amy B and Kropp, Roy K},
doi = {10.1002/ecs2.1242},
editor = {Peters, D. P. C.},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Diefenderfer{\_}et{\_}al-Evaluation{\_}of{\_}Cumulative{\_}Restoration{\_}Effects.pdf:pdf},
issn = {21508925},
journal = {Ecosphere},
month = {mar},
number = {3},
pages = {e01242},
title = {{Evidence-based evaluation of the cumulative effects of ecosystem restoration}},
url = {http://doi.wiley.com/10.1002/ecs2.1242 http://dx.doi.org/10.1002/ecs2.1242},
volume = {7},
year = {2016}
}
@article{Dix08,
author = {Dix, N G and Phlips, E J and Gleeson, R A},
journal = {Journal of Coastal Research},
number = {SI},
pages = {26--37},
title = {{Water quality changes in the {\{}G{\}}uana {\{}T{\}}olomato {\{}M{\}}atanzas {\{}N{\}}ational {\{}E{\}}stuarine {\{}R{\}}esearch {\{}R{\}}eserve, {\{}F{\}}lorida, associated with four tropical storms}},
volume = {55},
year = {2008}
}
@techreport{Dixon95,
address = {Sarasota, Florida},
author = {Dixon, L K and Leverone, J R},
institution = {Number 425, Mote Marine Lab},
pages = {77},
title = {{Light requirements of $\backslash$textit{\{}Thalassia testudinum{\}} in {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida}},
year = {1995}
}
@article{Dodds09,
author = {Dodds, W K and Bouska, W W and Eitzmann, J L and Pilger, T J and Pitts, K L and Riley, A J and Schloesser, J T and Thornbrugh, D J},
journal = {Environmental Science and Technology},
number = {1},
pages = {12--19},
title = {{Eutrophication of {\{}U.S.{\}} freshwaters: Analysis of potential economic damages}},
volume = {43},
year = {2009}
}
@article{Dodson00,
author = {Dodson, S I and Arnott, S E and Cottingham, K L},
journal = {Ecology},
number = {10},
pages = {2662--2679},
title = {{The relationship in lake communities between primary productivity and species richness}},
volume = {81},
year = {2000}
}
@article{Dolph11,
author = {Dolph, C L and Huff, D D and Chizinski, C J and Vondracek, B},
journal = {Freshwater Biology},
pages = {1652--1669},
title = {{Implications of community concordance for assessing stream intregrity at three nested spatial scales in {\{}M{\}}innesota, {\{}U.S.A{\}}}},
volume = {56},
year = {2011}
}
@article{Dolph10,
author = {Dolph, C L and Sheshukov, A Y and Chizinski, C J and Vondracek, B},
journal = {Ecological Indicators},
number = {2},
pages = {527--537},
title = {{The index of biological integrity and the bootstrap: Can random sampling error affect stream impairment decisions?}},
volume = {10},
year = {2010}
}
@article{Doran07,
author = {Doran, H and Bates, D and Bliese, P},
journal = {Journal of Statistical Software},
number = {2},
pages = {1--18},
title = {{Estimating the multilevel {\{}R{\}}asch model: {\{}W{\}}ith the lme4 package}},
volume = {20},
year = {2007}
}
@techreport{Dortch07,
address = {Vicksburg, Mississippi},
author = {Dortch, M S and Zakikhani, M and Noel, M R and Kim, S C},
institution = {Engineer Research and Development Center},
pages = {889},
title = {{Application of a water quality model to {\{}M{\}}ississippi {\{}S{\}}ound to evaluate impacts of freshwater diversions}},
year = {2007}
}
@article{Dortch90,
author = {Dortch, W},
journal = {Marine Ecology Progress Series},
number = {1/2},
pages = {183--201},
title = {{The interaction between ammonium and nitrate uptake in phytoplankton}},
volume = {61},
year = {1990}
}
@manual{Dowle14,
annote = {R package version 1.9.4},
author = {Dowle, M and Short, T and Lianoglou, S and Srinivasan, A and Saporta, R and Antonyan, E},
title = {{data.table: Extension of data.frame}},
url = {http://cran.r-project.org/package=data.table},
year = {2014}
}
@article{Downs1998,
author = {Downs, S G and MacLeod, C L and Lester, J N},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1998{\_}Downs{\_}Mercury{\_}in.pdf:pdf},
journal = {Water, Air, and Soil Pollution},
pages = {149--187},
title = {{Mercury in precipitation and its relation to bioaccumulation in fish: a literature review}},
volume = {108},
year = {1998}
}
@article{Drake02,
author = {Drake, M T and Pereira, D L},
journal = {North American Journal of Fisheries Management},
number = {4},
pages = {1105--1123},
title = {{Development of a fish-based index of biotic integrity for small inland lakes in central {\{}M{\}}innesota}},
volume = {22},
year = {2002}
}
@article{Drake05,
author = {Drake, M T and Valley, R D},
journal = {North American Journal of Fisheries Management},
number = {3},
pages = {1095--1111},
title = {{Validation and application of a fish-based index of biotic integrity for small central {\{}M{\}}innesota lakes}},
volume = {25},
year = {2005}
}
@article{Droop73,
author = {Droop, M R},
journal = {Journal of Phycology},
pages = {264--272},
title = {{Some thoughts on nutrient limitation in algae}},
volume = {9},
year = {1973}
}
@article{Duan83,
author = {Duan, N},
journal = {Journal of the American Statistical Association},
number = {383},
pages = {605--610},
title = {{Smearing estimate: A nonparametric retransformation method}},
volume = {78},
year = {1983}
}
@article{Duarte95,
author = {Duarte, C M},
journal = {Ophelia},
pages = {87--112},
title = {{Submerged aquatic vegetation in relation to different nutrient regimes}},
volume = {41},
year = {1995}
}
@article{Duarte91,
author = {Duarte, C M},
journal = {Aquatic Botany},
number = {4},
pages = {363--377},
title = {{Seagrass depth limits}},
volume = {40},
year = {1991}
}
@article{Duarte09,
author = {Duarte, C M and Conley, D J and Carstensen, J and S{\'{a}}nchez-Camacho, M},
journal = {Estuaries and Coasts},
number = {1},
pages = {29--36},
title = {{Return to $\backslash$textit{\{}Neverland{\}}: Shifting baseline affect eutrophication restoration targets}},
volume = {32},
year = {2009}
}
@article{Duarte86,
author = {Duarte, C M and Kalff, J and Peters, R H},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
pages = {1900--1908},
title = {{Patterns in biomass and cover of aquatic macrophytes in lakes}},
volume = {43},
year = {1986}
}
@article{Dugdale67,
author = {Dugdale, R C and Goering, J J},
journal = {Limnology and Oceanography},
pages = {196--206},
title = {{Uptake of new and regenerated nitrogen in primary productivity}},
volume = {12},
year = {1967}
}
@article{Dugdale07,
author = {Dugdale, R C and Wilkerson, F P and Hogue, V E and Marchi, A},
journal = {Estuarine, Coastal, and Shelf Science},
pages = {17--29},
title = {{The role of ammonium and nitrate in spring bloom development in {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {73},
year = {2007}
}
@article{Durand02,
author = {Durand, P and Gascuel-Odoux, C and Cordier, M O},
journal = {Agronomie},
number = {2},
pages = {217--228},
title = {{Parameterisation of hydrological models: a review and lessons learned from studies of an agricultural catchment ({\{}N{\}}aisin, {\{}F{\}}rance}},
volume = {22},
year = {2002}
}
@book{Dyer73,
address = {London, United Kingdom},
author = {Dyer, K R},
pages = {156},
publisher = {Wiley},
title = {{Estuaries: A Physical Introduction}},
year = {1973}
}
@article{Edwards08,
author = {Edwards, L J and Muller, K E and Wolfinger, R D and Qaqish, B F and Schabenberger, O},
journal = {Statistics in Medicine},
number = {29},
pages = {6137--6157},
title = {{An {\{}R{\}}{\$}{\^{}}2{\$} statistic for fixed effects in the linear mixed model}},
volume = {27},
year = {2008}
}
@book{Efron93,
address = {New York, New York},
author = {Efron, B and Tibshirani, R},
edition = {first},
pages = {436},
publisher = {Chapman and Hall},
title = {{An Introduction to the Bootstrap}},
year = {1993}
}
@article{Eiswerth00,
author = {Eiswerth, M E and Donaldson, S G and Johnson, W S},
journal = {Weed Technology},
number = {3},
pages = {511--518},
title = {{Potential environmental impacts and economic damages of {\{}E{\}}urasian watermilfoil ($\backslash$textit{\{}{\{}M{\}}yriophyllum spicatum{\}}) in western {\{}N{\}}evada and northeastern {\{}C{\}}alifornia}},
volume = {14},
year = {2000}
}
@article{Eldridge10,
author = {Eldridge, P M and Roelke, D L},
journal = {Ecological Modelling},
number = {7},
pages = {1028--1042},
title = {{Origins and scales of hypoxia on the {\{}L{\}}ouisiana shelf: importance of seasonal plankton dynamics and river nutrients and discharge}},
volume = {221},
year = {2010}
}
@article{Ellenius00,
author = {Ellenius, J and Groth, T},
journal = {International Journal of Medical Informatics},
number = {2-3},
pages = {181--202},
title = {{Methods for selection of adequate neural network structures with application to early assessment of chest pain patients by biochemical monitoring}},
volume = {57},
year = {2000}
}
@article{Ellison2004,
abstract = {Abstract Bayesian inference is an important statistical tool that is increasingly being used by ecologists. In a Bayesian analysis, information available before a study is conducted is summarized in a quantitative model or hypothesis: the prior probability distribution. Bayes' Theorem uses the prior probability distribution and the likelihood of the data to generate a posterior probability distribution. Posterior probability distributions are an epistemological alternative to P-values and provide a direct measure of the degree of belief that can be placed on models, hypotheses, or parameter estimates. Moreover, Bayesian information-theoretic methods provide robust measures of the probability of alternative models, and multiple models can be averaged into a single model that reflects uncertainty in model construction and selection. These methods are demonstrated through a simple worked example. Ecologists are using Bayesian inference in studies that range from predicting single-species population dynamics to understanding ecosystem processes. Not all ecologists, however, appreciate the philosophical underpinnings of Bayesian inference. In particular, Bayesians and frequentists differ in their definition of probability and in their treatment of model parameters as random variables or estimates of true values. These assumptions must be addressed explicitly before deciding whether or not to use Bayesian methods to analyse ecological data.},
author = {Ellison, Aaron M.},
doi = {10.1111/j.1461-0248.2004.00603.x},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2004{\_}Ellison{\_}Bayesian inference in ecology.pdf:pdf},
isbn = {1461-023X},
issn = {1461023X},
journal = {Ecology Letters},
keywords = {Bayes' Theorem,Bayesian inference,Epistemology,Information criteria,Model averaging,Model selection},
number = {6},
pages = {509--520},
pmid = {87324813},
title = {{Bayesian inference in ecology}},
volume = {7},
year = {2004}
}
@article{Elsdon09,
author = {Elsdon, T S and Connell, S D},
journal = {Aquatic Biology},
number = {2},
pages = {157--166},
title = {{Spatial and temporal monitoring of coastal water quality: refining the way we consider, gather, and interpret patterns}},
volume = {5},
year = {2009}
}
@article{Emerson13,
author = {Emerson, J W and Green, W A and Schloerke, B and Crowley, J and Cook, D and Hofmann, H and Wickham, H},
journal = {Journal of Computational and Graphical Statistics},
number = {1},
pages = {79--91},
title = {{The generalized pairs plot}},
volume = {22},
year = {2013}
}
@article{Engel94,
author = {Engel, S and Nichols, S A},
journal = {Journal of Freshwater Ecology},
number = {2},
pages = {97--109},
title = {{Aquatic macrophyte growth in a turbid windswept lake}},
volume = {9},
year = {1994}
}
@article{Enright09,
author = {Enright, C and Culberson, S D},
journal = {San Francisco Estuary and Watershed Science},
number = {2},
pages = {1--28},
title = {{Salinity trends, variability, and control in the northern reach of the {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary}},
volume = {7},
year = {2009}
}
@article{Enwright2016,
abstract = {In the 21st century, accelerated sea- level rise and continued coastal development are expected to greatly alter coastal landscapes across the globe. Historically, many coastal ecosystems have responded to sea- level fluctu- ations via horizontal and vertical movement on the landscape. However, anthropogenic activities, including urbanization and the construction of flood- prevention infrastructure, can produce barriers that impede ecosystem migration. Here we show where tidal saline wetlands have the potential to migrate landward along the northern Gulf of Mexico coast, one of the most sea- level rise sensitive and wetland- rich regions of the world. Our findings can be used to identify migration corridors and develop sea- level rise adaptation strategies to help ensure the continued availability of wetland- associated ecosystem goods and services.},
author = {Enwright, Nicholas M. and Griffith, Kereen T. and Osland, Michael J.},
doi = {10.1002/fee.1282},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016-Enwright{\_}et{\_}al-Barriers and opportunities for landward migration of coastal wetlands with sea level rise.pdf:pdf},
issn = {15409309},
journal = {Frontiers in Ecology and the Environment},
month = {aug},
number = {6},
pages = {307--316},
title = {{Barriers to and opportunities for landward migration of coastal wetlands with sea-level rise}},
url = {http://doi.wiley.com/10.1002/fee.1282},
volume = {14},
year = {2016}
}
@article{Eppley69,
author = {Eppley, R W and Rogers, J N and McCarthy, J},
journal = {Limnology and Oceanography},
number = {6},
pages = {912--920},
title = {{Half-saturation constants for uptake of nitrate and ammonium by marine phytoplankton}},
volume = {14},
year = {1969}
}
@techreport{EQB00,
address = {St. Paul, Minnesota},
annote = {$\backslash$url{\{}http://www.gda.state.mn.us/pdf/2000/eqb/wtr{\_}mrk.pdf{\}}},
author = {{EQB (Environmental Quality Board)}},
institution = {Minnesota Planning, Environmental Quality Board},
pages = {49},
title = {{{\{}M{\}}innesota watermarks: Gauging the flow of progress 2000-2010}},
year = {2000}
}
@misc{ERDAS10,
annote = {{\{}ERDAS, Hexagon Group{\}}, Atlanta, Georgia},
author = {{ERDAS (Earth Resource Data Analysis System)}},
title = {{ERDAS Imagine}},
year = {2010}
}
@article{Eshleman2013,
abstract = {We evaluated long-term surface water nitrate and atmospheric nitrogen (N) deposition trends for a group of nine predominantly forested Appalachian Mountain watersheds during a recent multidecadal period (1986–2009) in which regional NOx emissions have been progressively reduced. Statistical analysis showed unexpected linear declines in both annual surface water nitrate-N concentrations (mean =46.4{\%}) and yields (mean =47.7{\%}) among the watersheds corresponding to comparable declines in annual wet N deposition (mean =34.4{\%}) resulting from U.S. NOx emission control programs during the same time period. Nitrate-N concentration trends were robust across a large geographical region and appeared insensitive to watershed size across several orders of magnitude—suggesting that the improvements in water quality are probably propagated to surface and estuarine waters downstream. Surface waters are thus responding to declining atmospheric N deposition in much the same way they responded to declining sulfur deposition—although only one watershed showed a 1:1 relationship. Application of a kinetic N saturation model indicated that all nine forested watersheds are exhibiting signs of N saturation as evidenced by a limited, but variable, efficiency of demand for N. Further reductions in N deposition would be expected to produce additional reductions in streamwater N loads.},
author = {Eshleman, Keith N and Sabo, Robert D and Kline, Kathleen M},
doi = {dx.doi.org/10.1021/es4028748},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Eshleman{\_}Surface{\_}Water.pdf:pdf},
journal = {Environmental Science {\&} Technology},
number = {21},
pages = {12193--12200},
title = {{Surface Water Quality Is Improving due to Declining Atmospheric N Deposition}},
volume = {47},
year = {2013}
}
@misc{ESRI12,
annote = {{\{}ESRI{\}}, Redlands, California},
author = {{ESRI (Environmental Systems Research Institute)}},
title = {{ArcGIS v10.1}},
year = {2012}
}
@article{Esselman12,
author = {Esselman, P C and Infante, D M and Wang, L and Wu, D and Cooper, A R and Taylor, W W},
journal = {Ecological Restoration},
number = {1-2},
pages = {133--151},
title = {{An index of cumulative disturbance to river fish habitats of the conterminous {\{}U{\}}nited {\{}S{\}}tates from landscape anthropogenic activities}},
volume = {29},
year = {2012}
}
@article{Esterby96,
author = {Esterby, S R},
journal = {Hydrological Processes},
number = {2},
pages = {127--149},
title = {{Review of methods for the detection and estimation of trends with emphasis on water quality applications}},
volume = {10},
year = {1996}
}
@article{Estrada10,
author = {Estrada, V and Diaz, M S},
journal = {Environmental Modelling and Software},
pages = {1539--1551},
title = {{Global sensitivity analysis in the development of first principle-based eutrophication models}},
volume = {25},
year = {2010}
}
@article{Fahnenstiel95,
author = {Fahnenstiel, G L and McCormick, M J and Lang, G A and Redalje, D G and Lohrenz, S E and Markowitz, M and Wagoner, B and Carrick, H J},
journal = {Marine Ecology Progress Series},
number = {1-3},
pages = {229--239},
title = {{Taxon-specific growth and loss rates for dominant phytoplankton populations from the northern {\{}G{\}}ulf of {\{}M{\}}exico}},
volume = {117},
year = {1995}
}
@incollection{Fanning85,
address = {Tampa, Florida, USA},
author = {Fanning, K A and Bell, L M},
booktitle = {Proceedings of the Tampa Bay Area Scientific Information Symposium},
editor = {Treat, S F and Simon, J L and Lewis, R R and Whitman, R L},
pages = {109--129},
publisher = {Florida Sea Grant Report No. 65, Bellwether Press},
title = {{Nutrients in {\{}T{\}}ampa {\{}B{\}}ay}},
year = {1985}
}
@article{Fasham06,
author = {Fasham, M J R and Flynn, K J and Pondaven, P and Anderson, T R and Boyd, P W},
journal = {Deep-Sea Research I},
pages = {333--366},
title = {{Development of a robust marine ecosystem model to predict the role of iron in biogeochemical cycles: A comparison of results for iron-replete and iron-limited areas, and the {\{}SOIREE{\}} iron-enrichment experiment}},
volume = {53},
year = {2006}
}
@book{Fassett57,
address = {Madison, Wisconsin},
author = {Fassett, N C},
pages = {416},
publisher = {University of Wisconsin Press},
title = {{A Manual of Aquatic Plants}},
year = {1957}
}
@article{Feller1996,
abstract = {Despite several thousand publications concerning mangrove forests, a clear understanding of the dynamics in mangrove ecosystems is just beginning to emerge. Of the several hypotheses advanced to account for species zonation, several warrant further attention, but others should be laid to rest. In particular, hypotheses concerning zonation as plant succession and the tidal sorting of propagules clearly are not supported by the available data. Geomorphological factors establish much, but not all, of the framework within which mangrove forests develop. Climatic factors, particularly rainfall, are important determinants of species richness, stand structure, and growth dynamics in mangrove forests. Two groups of mangroves can be identified based on salinity tolerance data, one has a very broad range (0-80‰) and the other has a narrower range ({\textless}40‰) of tolerance. Physiological responses to other environmental gradients in the intertidal zone (e.g., soil texture, redox potential, nutrients) do not appear to be sufficient to influence observed zonation patterns. However, more data are needed to address this question adequately. Biotic factors such as predation on propagules are important influences on the distributional patterns of some groups of mangroves and in certain geographic regions. Competitive interactions may be important in determining some aspects of forest structure, but much more experimental and long-term observational work is needed. A more important consideration is that the dynamics of mangrove forest systems fit within current theories and paradigms developed for other vegetation systems. Ideas of gap-phase dynamics, natural disturbance, and forest mosaics are applicable to mangrove ecosystems and will provide a fruitful avenue for further research.},
author = {Feller, Ic and Sitnik, M},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Feller{\_}mangrove ecology.pdf:pdf},
pages = {1--135},
title = {{Mangrove ecology: a manual for a field course}},
url = {http://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:MANGROVE+ECOLOGY+:+A+Manual+for+a+Field+Course{\#}0},
year = {1996}
}
@article{Feng02,
author = {Feng, C X and Wang, X},
journal = {Journal of Intelligent Manufacturing},
number = {3},
pages = {189--199},
title = {{Digitizing uncertainty modeling for reverse engineering applications: regression versus neural networks}},
volume = {13},
year = {2002}
}
@article{Fennel13,
author = {Fennel, K and Hu, J and Laurent, A and Marta-Almeida, M and Hetland, R},
journal = {Journal of Geophysical Research: Oceans},
number = {2},
pages = {990--1002},
title = {{Sensitivity of hypoxia predictions for the northern {\{}G{\}}ulf of {\{}M{\}}exico to sediment oxygen consumption and model nesting}},
volume = {118},
year = {2013}
}
@article{Fetscher13,
author = {Fetscher, A E and Stancheva, R and Kociolek, J P and Sheath, R G and Stein, E D and Mazor, R D and Ode, P R and Busse, L B},
doi = {10.1007/s10811-013-0088-2},
journal = {Journal of Applied Phycology},
number = {1},
pages = {433--450},
title = {{Development and comparison of stream indices of biotic integrity using diatoms vs. non-diatom algae vs. a combination}},
volume = {26},
year = {2013}
}
@article{Feyrer03,
author = {Feyrer, F and Herbold, B and Matern, S A and Moyle, P B},
journal = {Environmental Biology of Fishes},
number = {3},
pages = {277--288},
title = {{Dietary shifts in a stressed fish assemblage: Consequences of a bivalve invasion in the {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary}},
volume = {67},
year = {2003}
}
@article{Figuerola12,
author = {Figuerola, B and Maceda-Veiga, A and Sostoa, A De},
journal = {Hydrobiologia},
number = {1},
pages = {75--86},
title = {{Assessing the effects of sewage effluents in a {\{}M{\}}editerranean creek: Fish population features and biotic indices}},
volume = {694},
year = {2012}
}
@techreport{FLDEP12,
address = {Tallahassee, Florida},
author = {{Florida Department of Environmental Protection (FDEP)}},
institution = {Florida Department of Environmental Protection},
pages = {118},
title = {{Site-specific information in support of establishing numeric nutrient criteria for {\{}C{\}}hoctawhatchee {\{}B{\}}ay}},
year = {2012}
}
@article{Flynn05,
author = {Flynn, K J},
journal = {Journal of Plankton Research},
number = {12},
pages = {1205--1210},
title = {{Castles built on sand: dysfunctionality in plankton models and the inadequacy of dialogue between biologists and modellers}},
volume = {27},
year = {2005}
}
@article{Flynn03,
author = {Flynn, K J},
journal = {Progress in Oceanography},
number = {2},
pages = {249--279},
title = {{Modelling multi-nutrient interactions in phytoplankton; balancing simplicity and realism}},
volume = {56},
year = {2003}
}
@article{Fore94,
author = {Fore, L S and Karr, J R and Conquest, L L},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {5},
pages = {1077--1087},
title = {{Statistical properties of an index of biological integrity used to evaluate water resources}},
volume = {51},
year = {1994}
}
@article{Fore09,
author = {Fore, L S and Karr, J R and Fisher, W S and Bradley, P and Davis, W S},
journal = {Marine Pollution Bulletin},
number = {10},
pages = {1421--1423},
title = {{Heeding a call to action for {\{}US{\}} coral reefs: The untapped potential of the {\{}C{\}}lean {\{}W{\}}ater {\{}A{\}}ct}},
volume = {58},
year = {2009}
}
@article{Foreman89,
author = {Foreman, M G G and Henry, R F},
journal = {Advances in Water Resources},
number = {3},
pages = {109--120},
title = {{The harmonic analysis of tidal model time series}},
volume = {12},
year = {1989}
}
@book{Fox11,
address = {Thousand Oaks, California},
author = {Fox, J and Weisberg, S},
pages = {449},
publisher = {{\{}SAGE{\}} Publications Inc.},
title = {{An {\{}R{\}} Companion to Applied Regression}},
year = {2011}
}
@article{Fox2017,
abstract = {The conservation and management of military training lands has long evolved around the unique criteria for maintaining a viable fighting force. In lieu of this primary mission, landscapes have often experienced accelerated degradation and loss of structural and functional capabilities for providing desired ecosystem services (including the basic training mission). In an effort to aid military land managers as well as anyone who makes and implements decisions for natural resource management; we support an innovative approach towards the integration of evidence and the application of diagnosis and prognosis for the decision-making process through the use of Bayesian Networks. Illustrated below is an example for utilizing Bayesian Networks in the decision support process. We utilized data and experience from ongoing efforts at the Fort Hood Military Installation to build the initial network; then integrate expert input from authors and engineers in propagating the node relationships. Through this approach, we demonstrate how military land managers can integrate varying streams of evidence, including empirical, model generated or expert opinion, into a network for decision support. The example below is developed based upon land management issues within the U.S. Army, but the process can be adapted and implemented across most all ecosystems under some form of land management.},
author = {Fox, William E. and Medina-Cetina, Zenon and Angerer, Jay and Varela, Patricia and {Ryang Chung}, Ji},
doi = {10.1016/j.swaqe.2017.03.001},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Fox{\_}WQ{\_}Natural{\_}Resource{\_}management{\_}in{\_}TX.pdf:pdf},
issn = {22126139},
journal = {Sustainability of Water Quality and Ecology},
pages = {39--52},
publisher = {Elsevier B.V.},
title = {{Water Quality {\&} natural resource management on military training lands in Central Texas: Improved decision support via Bayesian Networks}},
url = {http://dx.doi.org/10.1016/j.swaqe.2017.03.001},
volume = {9-10},
year = {2017}
}
@article{Francis06,
author = {Francis, T B and Schindler, D E},
journal = {AMBIO: A Journal of the Human Environment},
number = {6},
pages = {274--280},
title = {{Degradation of littoral habitats by residential development: {\{}W{\}}oody debris in lakes of the {\{}P{\}}acific {\{}N{\}}orthwest and {\{}M{\}}idwest, {\{}U{\}}nited {\{}S{\}}tates}},
volume = {35},
year = {2006}
}
@article{Franks97,
author = {Franks, S W and Beven, K J and Quinn, P F and Wright, I R},
journal = {Agricultural and Forest Meteorology},
number = {1-2},
pages = {63--75},
title = {{On the sensitivity of soil-vegetation-atmosphere transfer ({\{}SVAT{\}}) schemes: Equifinality and the problem of robust calibration}},
volume = {86},
year = {1997}
}
@article{Frieden14,
author = {Frieden, J C and Peterson, E E and Webb, J A and Negus, P M},
journal = {Environmental Modelling {\&} Sofware},
pages = {320--330},
title = {{Improving the predictive power of spatial statistical models of stream macroinvertebrates using weighted autocovariance functions}},
volume = {60},
year = {2014}
}
@article{Fries08,
author = {Fries, D P and Ivanov, S Z and Bhanushali, P H and Wilson, J A and Broadbent, H A and Sanderson, A C},
journal = {Oceanography},
number = {4},
pages = {150--155},
title = {{Broadband, low-cost, coastal sensor nets}},
volume = {20},
year = {2008}
}
@article{Frissell86,
author = {Frissell, C A and Liss, W J and Warren, C E and Hurley, M D},
journal = {Environmental Management},
number = {2},
pages = {199--214},
title = {{A hierarchical framework for stream habitat classification: Viewing streams in a watershed context}},
volume = {10},
year = {1986}
}
@manual{Fritsch12,
annote = {R package version 1.32},
author = {Fritsch, Stefan and Guenther, Frauke},
title = {{neuralnet: Training of neural networks}},
url = {http://cran.r-project.org/package=neuralnet},
year = {2012}
}
@article{Fry11,
author = {Fry, J and Xian, G and Jin, S and Dewitz, J and Homer, C and Yang, L and Barnes, C and Herold, N and Wickham, J},
journal = {Photogrammetric Engineering and Remote Sensing},
number = {9},
pages = {858--864},
title = {{Completion of the 2006 {\{}National Land Cover Database{\}} for the conterminous {\{}United States{\}}}},
volume = {77},
year = {2011}
}
@article{Fu1994,
author = {Fu, J M and Winchester, J W},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1994{\_}Fu{\_}Sources{\_}of.pdf:pdf},
journal = {Geochimica et Cosmochimic Acta},
number = {6},
pages = {1581--1590},
title = {{Sources of nitrogen in three watersheds of northern Florida, USA: Mainly atmospheric deposition}},
volume = {58},
year = {1994}
}
@article{Gaarder27,
author = {Gaarder, T and Gran, H H},
journal = {Rapports et Proc{\'{e}}s-Verbaux des R{\'{e}}unions du Conseil Permanent International pour l'Exploration de le Mer},
pages = {1--48},
title = {{Investigations of the production of plankton in the Oslo Fjord}},
volume = {42},
year = {1927}
}
@article{Gaeta11,
author = {Gaeta, J W and Gaurascio, M J and Sass, G G and Carpenter, S R},
journal = {Ecology of Freshwater Fish},
number = {1},
pages = {92--101},
title = {{Lakeshore residential development and growth of largemouth bass ($\backslash$textit{\{}Micropterus salmoides{\}}): A cross-lakes comparison}},
volume = {20},
year = {2011}
}
@incollection{Galatowitsch2016,
author = {Galatowitsch, Susan M},
booktitle = {The Wetland Book},
doi = {10.1007/978-94-007-6173-5},
editor = {Finlayson, C M and Everard, M and Irvine, K and McInnes, R J and Middleton, B A and van Dam, A A and Davidson, N C},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Galatowitcsh{\_}Natural{\_}and.pdf:pdf},
isbn = {978-94-007-6173-5},
pages = {1--10},
publisher = {Springer Nertherlands},
title = {{Natural and Anthropogenic Drivers of Wetland Change}},
url = {http://link.springer.com/10.1007/978-94-007-6173-5},
year = {2016}
}
@article{Gallagher07,
author = {Gallagher, M and Doherty, J},
journal = {Environmental Modelling and Software},
number = {7},
pages = {1000--1020},
title = {{Parameter estimation and uncertainty analysis for a watershed model}},
volume = {22},
year = {2007}
}
@article{Ganju16,
author = {Ganju, N K and Brush, M J and {B. Rashleigh} and Aretxabaleta, A L and del Barrio, P and Grear, J S and Harris, L A and Lake, S J and McCardell, G and O'Donnell, J and Ralston, D K and Signell, R P and Testa, J M and Vaudrey, J M P},
journal = {Estuaries and Coasts},
number = {2},
pages = {311--332},
title = {{Progress and challenges in coupled hydrodynamic-ecological estuarine modeling}},
volume = {39},
year = {2016}
}
@article{Garcia13,
author = {Garc{\'{i}}a, S and Luengo, J and S{\'{a}}ez, J A and L{\'{o}}pez, V and Herrera, F},
journal = {IEEE Transactions on Knowledge and Data Engineering},
number = {4},
pages = {734--750},
title = {{A survey of discretization techniques: Taxonomy and empirical analysis in supervised learning}},
volume = {25},
year = {2013}
}
@techreport{Garrison05,
address = {Madison, Wisconsin},
author = {Garrison, P J and Marshall, D W and Thompson, L S and Cicero, P L and Dearlove, P D},
institution = {Wisconsin Department of Natural Resources, Jefferson County Land and Water Conservation Department, and Lake Ripley Management District},
number = {PUB-SS-1006},
pages = {18},
title = {{Effects of pier shading on littoral zone habitat and communities in lakes {\{}R{\}}ipley and {\{}R{\}}ock, {\{}J{\}}efferson county, {\{}W{\}}isconsin}},
year = {2005}
}
@article{Garson91,
author = {Garson, G D},
journal = {Artificial Intelligence Expert},
number = {4},
pages = {46--51},
title = {{Interpreting neural network connection weights}},
volume = {6},
year = {1991}
}
@article{Geider98,
author = {Geider, R J and MacIntyre, H L and Kana, T M},
journal = {Limnology and Oceanography},
number = {4},
pages = {679--694},
title = {{A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature}},
volume = {43},
year = {1998}
}
@article{Geider97,
author = {Geider, R J and MacIntyre, H L and Kana, T M},
journal = {Marine Ecology Progress Series},
pages = {187--200},
title = {{A dynamic model of phytoplankton growth and acclimation: responses of the balanced growth rate and the chlorophyll $\backslash$textit{\{}a{\}}:carbon ratio to light, nutrient-limitation and temperature}},
volume = {148},
year = {1997}
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@article{Gelbrecht05,
author = {Gelbrecht, J and Lengsfeld, H and Pothig, R and Opitz, D},
journal = {Journal of Hydrology},
pages = {151--165},
title = {{Temporal and spatial variation of phosphorus input, retention and loss in a small catchment of {\{}NE{\}} {\{}Germany{\}}}},
volume = {304},
year = {2005}
}
@techreport{Genet06,
address = {St. Paul, Minnesota},
author = {Genet, J and Bourdaghs, M},
institution = {Biological Monitoring Program, Minnesota Pollution Control Agency},
pages = {136},
title = {{Development and validation of indices of biological integrity ({\{}IBI{\}}) for depressional wetlands in the temperate prairies ecoregion}},
year = {2006}
}
@techreport{Genet04,
address = {St. Paul, Minnesota},
author = {Genet, J and Chirhart, J},
institution = {Biological Monitoring Program, Minnesota Pollution Control Agency},
pages = {23},
title = {{Development of a macroinvertebrate index of biological integrity ({\{}MIBI{\}}) for rivers and streams of the {\{}U{\}}pper {\{}M{\}}ississippi river basin in {\{}M{\}}innesota}},
year = {2004}
}
@article{Genkai-Cato05,
author = {Genkai-Cato, M and Carpenter, S R},
journal = {Ecology},
number = {1},
pages = {210--219},
title = {{Eutrophication due to phosphorus recycling in relation to lake morphometry, temperature, and macrophytes}},
volume = {86},
year = {2005}
}
@techreport{Gernes02,
address = {St. Paul, Minnesota},
author = {Gernes, M C and Helgen, J C},
institution = {Biological Monitoring Program, Minnesota Pollution Control Agency},
pages = {86},
title = {{Indexes of biological integrity ({\{}IBI{\}}) for large depressional wetlands in {\{}M{\}}innesota}},
year = {2002}
}
@incollection{Gershenfeld93,
address = {Santa Fe, New Mexico},
author = {Gershenfeld, N A and Weigend, A S},
booktitle = {Time Series Prediction: Forecasting the Future and Understanding the Past},
edition = {Second},
editor = {Weigend, A S and Gershenfeld, N A},
pages = {1--70},
publisher = {Addison-Wesley},
title = {{The future of time series: Learning and understanding}},
year = {1993}
}
@article{Gevrey03,
author = {Gevrey, M and Dimopoulos, I and Lek, S},
journal = {Ecological Modelling},
number = {3},
pages = {249--264},
title = {{Review and comparison of methods to study the contribution of variables in artificial neural network models}},
volume = {160},
year = {2003}
}
@incollection{Gevrey06,
address = {Berlin, Germany},
author = {Gevrey, M and Lek, S and Oberdorff, T},
booktitle = {Ecological Informatics: Scope, Techniques and Applications},
edition = {2nd},
editor = {Recknagel, F},
pages = {293--306},
publisher = {Springer-Verlag},
title = {{Utility of sensitivity analysis by artificial neural network models to study patterns of endemic fish species}},
year = {2006}
}
@book{Gilbert87,
address = {New York, USA},
author = {Gilbert, R O},
pages = {320},
publisher = {Van Nostrand Reinhold},
title = {{Statistical Methods for Environmental Pollution Monitoring}},
year = {1987}
}
@article{Gilman2007,
abstract = {Three mangrove restoration methods were tested at Nu'uuli, Tutuila Island, American Samoa. Since clearing 27 years ago converted the mangrove into a mudflat, the ecosystem was sufficiently altered that it could not self-correct; the ecosystem showed no natural regrowth despite an ample supply of propagules. While several years of monitoring may ultimately be required to determine the project's success, and several decades could be required to fully return the full suite of functions, the project's low-cost, nontechnical restoration techniques, using readily available materials, have proven to be modestly successful, with 38{\%} sapling survival after six months. Several years of monitoring will be necessary to determine if the restoration site's small elevation deficit relative to a reference site ultimately requires modifying the site's physical structure to correct the hydrology. Direct community participation in the project was critical to reduce the risk of human disturbance of the restoration site. One year project costs were about USD {\$}2,150 or USD {\$}13,030 ha(-1). Labor comprised 84{\%} of expenses; replicating the restoration project in developing countries would cost less due to lower wage levels. Six months after initial restoration activities, there was a highly significant difference between Bruguiera qmnorrhiza and Rhizophora mangle sapling survival, with 21 {\%} and 45{\%} of the original 42 R. mangle and 95 B. gmnorrhiza saplings remaining, respectively. The lower R. mangle survival may have resulted from an unavoidable need to source saplings from an area with different environmental conditions than the restoration site. Saplings were transplanted into tires fined with sediment as a simple, low-cost method to raise the elevation of the sediment surface. Saplings were also transplanted adjacent to rebar and without any support mechanism. There was no significant difference in sapling survival by treatment for individual or combined species. The restoration project is a model for the community-based, simple, low-cost approaches to ecological restoration needed in the region. Pilot projects using similar techniques may be worth pursuing at the other 15 Pacific Island countries and territories where mangroves are indigenous.},
author = {Gilman, E and Ellison, J},
doi = {10.1007/BF02841961},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}Gilman{\_}Efficacy{\_}of.pdf:pdf},
journal = {Estuaries and coasts},
number = {4},
pages = {641--651},
title = {{Efficacy of Alternative Low-cost Approaches to Mangrove Restoration , American Samoa}},
url = {http://www.springerlink.com/index/V8804T77H1333U0G.pdf},
volume = {30},
year = {2007}
}
@article{Gittleman90,
author = {Gittleman, J L and Kot, M},
journal = {Systematic Biology},
number = {3},
pages = {227--241},
title = {{Adaptation: statistics and a null model for estimating phylogenetic effects}},
volume = {39},
year = {1990}
}
@article{Glasgow04,
author = {Glasgow, H B and Burkholder, J M and Reed, R E and Lewitus, A J and Kleinman, J E},
journal = {Journal of Experimental Marine Biology and Ecology},
number = {1-2},
pages = {409--448},
title = {{Real-time remote monitoring of water quality: a review of current applications, and advancements in sensor, telemetry, and computing technologies}},
volume = {300},
year = {2004}
}
@article{Glibert10,
author = {Glibert, P M},
journal = {Reviews in Fisheries Science},
number = {2},
pages = {211--232},
title = {{Long-term changes in nutrient loading and stoichiometry and their relationships with changes in the food web and dominant pelagic fish species in the {\{}S{\}}an {\{}F{\}}ranciso {\{}E{\}}stuary, {\{}C{\}}alifornia}},
volume = {18},
year = {2010}
}
@article{Glibert14,
author = {Glibert, P M and Dugdale, R C and Wilkerson, F and Parker, A E and Alexander, J and Antell, E and Blaser, S and Johnson, A and Lee, J and Lee, T and Murasko, S and Strong, S},
journal = {Journal fo Experimental Marine Biology and Ecology},
pages = {8--18},
title = {{Major - but rare - spring blooms in San Francisco Bay Delta, California, a result of long-term drought, increased residence time, and altered nutrient loads and forms}},
volume = {460},
year = {2014}
}
@article{Glibert13,
author = {Glibert, P M and Hinkle, D C and Sturgis, B and Jesien, R V},
journal = {Estuaries and Coasts},
title = {{Eutrophication of a {\{}M{\}}aryland/{\{}V{\}}irginia coastal lagoon: A tipping point, ecosytem changes, and potential causes}},
year = {2013}
}
@article{Goh95,
author = {Goh, A T C},
journal = {Artificial Intelligence in Engineering},
number = {3},
pages = {143--151},
title = {{Back-propagation neural networks for modeling complex systems}},
volume = {9},
year = {1995}
}
@article{Goldberg83,
author = {Goldberg, D E and Werner, P A},
journal = {American Journal of Botany},
number = {7},
pages = {1098--1104},
title = {{Equivalence of competitors in plant communities: {\{}A{\}} null hypothesis and a field experimental approach}},
volume = {70},
year = {1983}
}
@techreport{Goodwin87,
address = {Denver, Colorado},
author = {Goodwin, C R},
institution = {US Geological Survey},
number = {Water-Supply Paper 2282},
title = {{Tidal-flow, circulation, and flushing changes caused by dredge and fill in {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida}},
url = {http://pubs.usgs.gov/wsp/2282/report.pdf},
year = {1987}
}
@article{Grabe2005,
author = {Grabe, Stephen A},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2005{\_}Grabe{\_}Distribution{\_}of.pdf:pdf},
pages = {57--68},
title = {{Distribution of Myodocopid Ostracods in Tampa Bay , Florida, and association with abiotic variables}},
volume = {17},
year = {2005}
}
@article{Greene09,
author = {Greene, R M and Lehrter, J C and Hagy, J D},
journal = {Ecological Applications},
number = {5},
pages = {1161--1175},
title = {{Multiple regression models for hindcasting and forecasting midsummer hypoxia in the {\{}G{\}}ulf of {\{}M{\}}exico}},
volume = {19},
year = {2009}
}
@article{Greening2011,
abstract = {Recovery of seagrass coverage in Tampa Bay, Florida, to levels observed in 1950 (15,380 ha) is a long-term goal adopted by local, state, federal, and private partners participating in the Tampa Bay Estuary Program. Nitrogen controls initiated in 1980 and continuing through present (from wastewater treatment facilities, stormwater treatment, fertilizer manu - facturers, and power plants) resulted in a 60{\%} total nitrogen load reduction compared to the mid-1970s. As a result, annual water clarity targets (measured as light attenuation and chlorophyll- a concentrations) are being met, and seagrass coverage in 2008 was the highest recorded since 1950 (but still 3,380 ha lower than 1950 coverage). However, seagrass coverage in all areas of the bay is not increasing at the same rate. Wave energy and tidal scour affect longshore sandbars, and in turn seagrass recovery in some areas. Localized water quality factors, including colored dissolved organic matter and turbidity may have impacts on seagrass growth in other areas. Have we had an effect on seagrass recovery in Tampa Bay? Yes, but it will take more than maintaining a successful nutrient management strategy to reach the recovery goal. A multiscale adaptive research and application approach is currently underway to ensure continuation of the upward trend in Tampa Bay seagrass coverage.},
author = {Greening, H S and Cross, L and Sherwood, E T},
doi = {10.3368/er.29.1-2.82},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2011 Tech Pubs/TBEP{\_}11{\_}11{\_}Greening{\_}et{\_}al-Ecol{\_}Restoration{\_}29.pdf:pdf},
issn = {15434079},
journal = {Ecological Restoration},
keywords = {Multiscale restoration strategy,Nutrient management,Seagrass restoration,Tampa bay,Water quality improvements},
number = {1-2},
pages = {82--93},
title = {{A multiscale approach to seagrass recovery in Tampa Bay, Florida}},
volume = {29},
year = {2011}
}
@article{Greening2014,
abstract = {In subtropical Tampa Bay, Florida, USA, we evaluated restoration trajectories before and after nutrient management strategies were implemented using long-term trends in nutrient loading, water quality, primary production, and seagrass extent. Following citizen demands for action, reduction in wastewater nutrient loading of approximately 90{\%} in the late 1970s lowered external total nitrogen (TN) loading by more than 50{\%} within three years. Continuing nutrient management actions from public and private sectors were associated with a steadily declining TN load rate and with concomitant reduction in chlorophyll-a concentrations and ambient nutrient concentrations since the mid-1980s, despite an increase of more than 1M people living within the Tampa Bay metropolitan area. Water quality (chlorophyll-a concentration, water clarity as indicated by Secchi disk depth, total nitrogen concentration and dissolved oxygen) and seagrass coverage are approaching conditions observed in the 1950s, before the large increases in human population in the watershed. Following recovery from an extreme weather event in 1997-1998, water clarity increased significantly and seagrass is expanding at a rate significantly different than before the event, suggesting a feedback mechanism as observed in other systems. Key elements supporting the nutrient management strategy and concomitant ecosystem recovery in Tampa Bay include: 1) active community involvement, including agreement about quantifiable restoration goals; 2) regulatory and voluntary reduction in nutrient loadings from point, atmospheric, and nonpoint sources; 3) long-term water quality and seagrass extent monitoring; and 4) a commitment from public and private sectors to work together to attain restoration goals. A shift from a turbid, phytoplankton-based system to a clear water, seagrass-based system that began in the 1980s following comprehensive nutrient loading reductions has resulted in a present-day Tampa Bay which looks and functions much like it did in the relatively pre-disturbance 1950s period.},
author = {Greening, H S and Janicki, A and Sherwood, E T and Pribble, R and Johansson, J O R},
doi = {10.1016/j.ecss.2014.10.003},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2014 Tech Pubs/TBEP{\_}06{\_}14{\_}Greening{\_}et{\_}al{\_}2014{\_}Ecosystem{\_}Responses{\_}ECSS{\_}s2.0-S0272771414002819.pdf:pdf},
isbn = {0272-7714},
issn = {02727714},
journal = {Estuarine, Coastal and Shelf Science},
keywords = {Ecosystem recovery,Eutrophication,Florida,Seagrass,Tampa bay,USA,Watershed management},
month = {dec},
pages = {A1--A16},
title = {{Ecosystem responses to long-term nutrient management in an urban estuary: Tampa Bay, Florida, USA}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0272771414002819},
volume = {151},
year = {2014}
}
@incollection{Greening2016,
author = {Greening, H and Janicki, A and Sherwood, E T},
booktitle = {The Wetland Book},
doi = {10.1007/978-94-007-6173-5},
editor = {Finlayson, C M and Everard, M and Irvine, K and McInnes, R J and Middleton, B A and van Dam, A A and Davidson, N C},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Tiner{\_}Estuarine Marsh.pdf:pdf},
isbn = {978-94-007-6173-5},
pages = {1--12},
publisher = {Springer Nertherlands},
title = {{Seagrass Recovery in Tampa Bay, Florida (USA)}},
url = {http://link.springer.com/10.1007/978-94-007-6173-5},
year = {2016}
}
@article{Greening2006,
abstract = {Hurricanes, typhoons, and other cyclonic disturbances often produce sudden, massive disturbances in estuaries and other coastal ecosystems around the world. Compared with other ecological disturbances, such as prairie and forest fires, tree falls, and coral bleaching events, the effects of hurricanes are usually studied in isolation of each other and rarely as repeated or even ecologically predictable events across an area of sustained hurricane activity. Studies of their effects have rarely contributed to the growing body of theory on ecological disturbance and ecosystem resiliency and they are conspicuously absent from ecological textbooks. Since 1996, there has been an increase in the frequency of hurricane landfalls in the southeastern United States that is predicted to continue for some years into the future (Goldenberg et al. 2001; Emanuel 2005; Webster et al. 2005). Coupled with the availability of results from many water quality and biological monitoring programs now in place in these coastal systems, the increase in hurricane activity now provides an opportunity to begin the systematic investigation of how a series of hurricanes might produce cumulative and perhaps even irreversible effects on coastal ecosystems. One particular example that is highlighted in this special issue of Estuaries and Coasts is the occurrence of four major hurricanes to make landfall in Florida in a two-month period of 2004. In some localities, sequential hurricanes made landfall in close proximity to each other, while in other regions of coastal Florida, the repeated heavy rains associated with the multiple hurricanes had effects that were distinct from the wind and storm surge effects often associated with hurricanes. This special issue of Estuaries and Coasts, which reports investigations of hurricane-mediated disturbances, is an opportunity to describe the individual and cumulative effects of storms on coastal environments and component flora and fauna, to put effects of extreme events in the context of long-term monitoring data sets in multiple estuaries, to examine effects of storms on estuarine management, and to provide the impetus for synthesis and generalization. Although the articles in this issue focus primarily on new findings related to the effects of the 2004 hurricanes on coastal systems, the effects of earlier hurricanes are summarized, and some preliminary reports on effects of the 2005 hurricanes are given.},
author = {Greening, Holly and Doering, Peter and Corbett, Catherine},
doi = {10.1007/BF02798646},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}Greening{\_}Hurricane{\_}Impacts.pdf:pdf},
isbn = {1559-2723},
issn = {1559-2723},
journal = {Estuaries and Coasts},
number = {6},
pages = {877--879},
title = {{Hurricane impacts on coastal ecosystems}},
url = {http://link.springer.com/10.1007/BF02798646},
volume = {29},
year = {2006}
}
@article{Greening06,
abstract = {Coastal waters have been significantly influenced by increased inputs of nutrients that have accompanied population growth in adjacent drainage basins. In Tampa Bay, Florida, USA, the population has quadrupled since 1950. By the late 1970s, eutrophic conditions including phytoplankton and macroalgal blooms and seagrass losses were evident. The focus of improving Tampa Bay is centered on obtaining sufficient water quality necessary for restoring seagrass habitat, estimated to have been 16,400 ha in 1950 but reduced to 8800 ha by 1982. To address these problems, targets for nutrient load reductions along with seagrass restoration goals were developed and actions were implemented to reach adopted targets. Empirical regression models were developed to determine relationships between chlorophyll a concentrations and light attenuation adequate for sustainable seagrass growth. Additional empirical relationships between nitrogen loading and chlorophyll a concentrations were developed to determine how Tampa Bay responds to changes in loads. Data show that when nitrogen load reduction and chlorophyll a targets are met, seagrass cover increases. After nitrogen load reductions and maintenance of chlorophyll a at target levels, seagrass acreage has increased 25{\%} since 1982, although more than 5000 ha of seagrass still require recovery. The cooperation of scientists, managers, and decision makers participating in the Tampa Bay Estuary Program's Nitrogen Management Strategy allows the Tampa Bay estuary to continue to show progress towards reversing many of the problems that once plagued its waters. These results also highlight the importance of a multi-entity watershed management process in maintaining progress towards science-based natural resource goals.},
author = {Greening, Holly and Janicki, Anthony},
doi = {10.1007/s00267-005-0079-4},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}Greening{\_}Toward{\_}Reversal.pdf:pdf},
isbn = {0026700500794},
issn = {0364-152X},
journal = {Environmental Management},
keywords = {,Eutrophication,Nutrient management,Seagrass,Tampa Bay},
month = {aug},
number = {2},
pages = {163--178},
pmid = {16788855},
title = {{Toward reversal of eutrophic conditions in a subtrophical estuary: Water quality and seagrass response to nitrogen loading reductions in {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida, {\{}USA{\}}}},
url = {http://link.springer.com/10.1007/s00267-005-0079-4},
volume = {38},
year = {2006}
}
@article{Greenwood2007,
abstract = {We used 183-m seines to study the effects of canopy damage by Hurricane Char-ley (August 2004) on the use of red mangrove Rhizophora mangle Linnaeus shore-lines by large-bodied ({\textgreater} {\~{}}100 mm SL) fishes in Charlotte Harbor (Florida, USA). No significant relationship was found between proportion of the shoreline that was damaged and fish-assemblage structure in the year following the hurricane; how-ever, temperature, water depth, and salinity did influence fish-assemblage struc-ture. Post-hurricane fish assemblages were not notably different from pre-hurricane (1996–2004) assemblages. Despite wide-ranging loss of canopy, defoliation, and mortality of red mangroves, prop-root structure remained largely intact, which may have minimized gross changes in the assemblages of large-bodied fish along the mangrove shorelines during the first post-hurricane year. The effects of habitat damage on the fish assemblages may yet be manifested due to continued deteriora-tion of existing prop-root structure and the apparent slow rate of recolonization of red mangroves in the area. Also, the effect of widespread mangrove mortality on the many other mangrove functions (e.g., primary productivity, food-web, and nutrient dynamics) may ultimately lead to system-level changes that affect the abundance and condition of large-bodied fish. Mangrove shorelines are important habitats for fishes (Kathiresan and Bingham, 2001), mostly because they provide areas that are valuable for feeding and refuge from predation (Manson et al., 2005a). Evidence suggests that mangrove carbon does not directly contribute to fish diets, but instead that mangroves form substrates for vari-ous epibionts (both primary producers and consumers) that fish may eat (Kieckbusch et al., 2004). Refuge from predators may be provided by canopy shade and prop-root structural complexity (Laegdsgaard and Johnson, 2001, Cocheret de la Morini{\`{e}}re et al., 2004, Ellis and Bell, 2004). There is debate over the value of mangroves as nursery habitat, but juveniles of some species appear to be mangrove-dependent (reviewed by Manson et al., 2005a). Very few studies have documented clear links between fishery catches of finfish and extent of mangroves in adjacent areas (Manson et al., 2005b). Correlations tend to be relatively weak and merely imply enhanced nursery function without directly addressing causative factors (Manson et al., 2005a). Two recent fish-ery-independent studies suggested relatively high fish abundance and species rich-ness in mangrove areas with low anthropogenic degradation (Dankwa and Gordon, 2002, Singkran and Sudara, 2005), although both studies had confounding variables (e.g., distance to sea) that may compromise the overall conclusions. One of the most destructive natural threats to mangroves is the passage of hur-ricanes. Hurricane-associated wind effects include defoliation, snapping of trunks/ limbs, and uprooting, all of which can lead to immediate or delayed mortality of mangroves (Baldwin et al., 2001, Sherman et al., 2001). Susceptibility to damage, mortality rates, and potential for regeneration all vary depending upon mangrove species, location (e.g., fringe or inland), and tree size (Roth, 1992, Imbert et al., 1996, McCoy et al., 1996, Baldwin et al., 2001, Sherman et al., 2001). Regardless,},
author = {Greenwood, Marin F D and Idelberger, Charles F and Stevens, Philip W},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}greenwood{\_}Habitat{\_}associations.pdf:pdf},
journal = {Bulletin of Marine Science},
number = {3},
pages = {805--821},
title = {{Habitat associations of large-bodied mangrove-shoreline fishes in a southwest Florida estuary and the effects of hurricane damage}},
volume = {80},
year = {2007}
}
@article{Greve05,
author = {Greve, T and Krause-Jensen, D},
journal = {Marine Biology},
number = {3},
pages = {803--812},
title = {{Stability of eelgrass ($\backslash$textit{\{}{\{}Z{\}}ostera marine {\{}L{\}}.{\}}) depth limits: influence of habitat type}},
volume = {147},
year = {2005}
}
@article{Griffith2008,
abstract = {To use bioassessments to help diagnose or identify the specific environmental stressors affecting estuaries, we need a better understanding of the relationships among sediment chemistry guidelines, ambient toxicity tests, and community metrics. However, this relationship is not simple because metrics generally assess the responses at the community level of biological organization whereas sediment guidelines and ambient toxicity tests generally assess or are based on the responses at the organism level. The relationship may be further complicated by the influence of other chemical and physical variables that affect the bioavailability and toxicity of chemical contaminants in the environment. Between 1990 and 1993, the U.S. Environmental Protection Agency (USEPA) conducted an Environmental Monitoring and Assessment Program (EMAP) survey of estuarine sites in the Virginian Province of the eastern United States. The surveys collected data on benthic assemblages, physical and chemical habitat characteristics, and sediment chemistry and toxicity. We characterized these estuarine sites as affected by sediment contamination based on the exceedence of sediment guidelines or on ambient sediment toxicity tests (i.e., 10-day Ampelisca abdita survival). Then, benthic invertebrate metrics were compared among affected and unaffected sites to identify metrics sensitive to the contamination. A number of benthic invertebrate metrics differed between groups of sites segregated using the organism-level measures whereas other metrics did not. The difference among metrics appears to depend on the sensitivity of the individual metrics to the stressor gradient represented by metals or persistent organic toxics in sediments because the insensitive metrics do not effectively quantify the changes in the benthic invertebrate assemblage associated with these stressors. The significant relationships suggest that a relationship exists between the organismlevel effects assessed by chemistry or ambient toxicity tests and the community-level effects assessed by community metrics and that the organism-level effects are predictive, to some extent, of community-level effects.},
author = {Griffith, Michael B and Kravitz, Michael},
doi = {10.1007/s12237-007-9003-x},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2008{\_}Griffith{\_}Relationships{\_}among.pdf:pdf},
journal = {Estuaries and Coasts},
keywords = {Ambient sediment toxicity tests,Community metrics,Community-level effects,Estuarine systems,Organism-level effects,Sediment guidelines},
number = {1},
pages = {101--114},
title = {{Relationships among exceedences of sediment guidelines, the results of ambient sediment toxicity tests, and community metrics in estuarine systems}},
volume = {31},
year = {2008}
}
@article{Gross2017,
abstract = {As more success is achieved in restoring lakes and estuaries from the impacts of nutrient pollution, there is increased opportunity to evaluate the scientific, social, and policy factors associated with achieving restoration goals. We examined case studies where deliberate actions to reduce nutrient pollution and restore ecosystems resulted in ecological recovery. Prospective cases were identified from scientific literature and technical documents for lakes and estuaries with: (1) scientific evidence of nutrient pollution; (2) restoration actions taken to mitigate nutrient pollution; and (3) documented ecological improvement. Using these criteria, we identified 9 estuaries and 7 lakes spanning countries, climatic regions, physical types, depths, and watershed areas. Among 16 case studies ultimately included, 8 achieved improvements short of stated restoration goals. Five more were successful initially, but condition subsequently declined. Three of the case studies achieved their goals fully and are currently managing to maintain the restored condition. We examined each case to identify both common attributes of nutrient management, grouped into ‘themes', and variations on those attributes, which were coded into categorical variables based on thorough review of documents associated with each case. The themes and variables were organized into a broad conceptual model illustrating how they relate to each other and to nutrient management outcomes. We then explored relationships among the themes and variables using multiple correspondence analysis (MCA). Results of the MCA suggested that the attributes most associated with achieving restoration goals include: (1) leadership by a dedicated watershed management agency; (2) governance through a bottom-up collaborative process; (3) a strategy that set numeric targets based on a specific ecological goal; and (4) actions to reduce nutrient loads from all sources. While our study did not provide a comprehensive road map to successful nutrient management, it suggested attributes that could be emulated in future efforts. The quantitative approach that was applied could be used to provide ongoing analysis as new examples of nutrient management success emerge.},
author = {Gross, Catharine and Hagy, James D.},
doi = {10.1016/j.jenvman.2016.11.018},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Gross{\_}Hagy{\_}Attributes{\_}of{\_}Successful{\_}Nutrient{\_}Management.pdf:pdf},
isbn = {0301-4797},
issn = {10958630},
journal = {Journal of Environmental Management},
keywords = {Ecological restoration,Multiple correspondence analysis,Nutrient pollution,Watershed management,Watershed partnership},
pages = {122--136},
publisher = {Elsevier Ltd},
title = {{Attributes of successful actions to restore lakes and estuaries degraded by nutrient pollution}},
url = {http://dx.doi.org/10.1016/j.jenvman.2016.11.018},
volume = {187},
year = {2017}
}
@phdthesis{Hagydiss,
address = {College Park, Maryland},
author = {Hagy, J D},
school = {University of Maryland},
title = {{Eutrophication, hypoxia, and trophic transfer efficiency in {\{}C{\}}hesapeake {\{}B{\}}ay}},
year = {2002}
}
@mastersthesis{Hagythes,
address = {College Park, Maryland},
author = {Hagy, J D},
pages = {205},
school = {University of Maryland},
title = {{Residence times and net ecosystem processes in {\{}P{\}}atuxent {\{}R{\}}iver estuary}},
year = {1996}
}
@techreport{Hagy08,
address = {Gulf Breeze, Florida},
author = {Hagy, J D and Kurtz, J C and Greene, R M},
institution = {US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Gulf Ecology Division},
number = {EPA/600/R-08/004},
title = {{An approach for developing numeric nutrient criteria for a {\{}G{\}}ulf {\{}C{\}}oast estuary}},
year = {2008}
}
@article{Hagy06,
author = {Hagy, J D and Lehrter, J C and Murrell, M C},
journal = {Estuaries and Coasts},
number = {6A},
pages = {919--925},
title = {{Effects of hurricanee {\{}I{\}}van on water quality in {\{}P{\}}ensacola {\{}B{\}}ay, {\{}F{\}}lorida}},
volume = {29},
year = {2006}
}
@article{Hagy07,
author = {Hagy, J D and Murrell, M C},
journal = {Estuarine Coastal and Shelf Science},
pages = {239--253},
title = {{Susceptibility of a northern {\{}G{\}}ulf of {\{}M{\}}exico estuary to hypoxia: An analysis using box models}},
volume = {74},
year = {2007}
}
@article{Hakanson2010,
abstract = {This work presents empirical data from several databases. Empirical data ultimately form the basis for most ecological/environmental studies, and this work uses what may be the most comprehensive data set ever compiled concerning relationships between chlorophyll-a concentrations, nitrogen, phosphorus, and salinity, since the data in this study concerns about 500 lakes and coastal areas. The focus has been on how variations between systems in median summer values of chlorophyll-a concentrations (Chl) depend on variations in total nitrogen, total phosphorus, and salinity. The salinities range from 0 to 275 PSS78 in hypersaline systems; the median salinity is 12.5. The range in nutrients is from ultraoligotrophic (totalP, or TP, is less than 1  g/L) to hypertrophic systems (TP is greater than 1000  g/L). The chlorophyll values vary from 0.12 to 60  g/L. Results showed that there is a minimum in the Chl/TP ratio in the salinity range between 2 and 5, followed by an increase up to a salinity range of 10–15, and then a continuous reduction in the Chl/TP ratio until a minimum value of about 0.012 is reached in hypersaline systems. We have also identified a threshold value for the salinity. In systems dominated by freshwater influences, the ratio of Chl to total nitrogen, or TN, increases steadily from about 0.008 in lakes to 0.02 when the salinity is 10. At higher salinities than 10, the Chl/TN ratio decreases in a nonlinear fashion. We have also presented several empirical models to predict chlorophyll concentrations from levels of TP, TN, and salinity. The model predicting Chl from TP and salinity is generally the best one. The next best model according to the criteria (r2 value, median error, and standard deviation for the error) is the model using TN and salinity. Models not including salinity predict chlorophyll less well. },
author = {H{\aa}kanson, Lars and Eklund, Jenny M.},
doi = {10.2112/08-1121.1},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2010{\_}Hakanson{\_}Relationships{\_}Between.pdf:pdf},
isbn = {0749-0208},
issn = {0749-0208},
journal = {Journal of Coastal Research},
pages = {412--423},
pmid = {50676513},
title = {{Relationships Between Chlorophyll, Salinity, Phosphorus, and Nitrogen in Lakes and Marine Areas}},
url = {http://www.bioone.org/doi/abs/10.2112/08-1121.1},
volume = {263},
year = {2010}
}
@article{Hale04,
author = {Hale, J A and Frazer, T K and Tomasko, D A and Hall, M O},
journal = {Estuaries},
number = {1},
pages = {36--43},
title = {{Changes in the distribution of seagrass species along {\{}F{\}}lorida's central gulf coast: {\{}I{\}}verson and {\{}B{\}}ittaker revisited}},
volume = {27},
year = {2004}
}
@article{Hall00,
author = {Hall, L W and Giddings, J M},
journal = {Human and Ecological Risk Assessment},
number = {4},
pages = {679--710},
title = {{The need for multiple lines of evidence for predicting site-specific ecological effects}},
volume = {6},
year = {2000}
}
@article{Hall90,
author = {Hall, M O and Durako, M J and Fourqurean, J W and Zieman, J C},
journal = {Estuaries},
number = {2B},
pages = {445--459},
title = {{Decadal changes in seagrass distribution and abundance in {\{}F{\}}lorida {\{}B{\}}ay}},
volume = {22},
year = {1990}
}
@article{Halliday12,
author = {Halliday, S J and Wade, A J and Skeffington, R A and Neal, C and Reynolds, B and Rowland, P and Neal, M and Norris, D},
journal = {Science of the Total Environment},
pages = {186--200},
title = {{An analysis of long-term trends, seasonality and short-term dynamics in water quality data from {\{}P{\}}lynlimon, {\{}W{\}}ales}},
volume = {434},
year = {2012}
}
@article{Hammerstrom93,
author = {Hammerstrom, D},
journal = {IEEE Spectrum},
number = {7},
pages = {46--53},
title = {{Working with neural networks}},
volume = {30},
year = {1993}
}
@article{Hampton13,
author = {Hampton, S E and Strasser, C A and Tewksbury, J J and Gram, W K and Budden, A E and Batcheller, A L and Duke, C S and Porter, J H},
journal = {Frontiers in Ecology and the Environment},
number = {3},
pages = {156--162},
title = {{Big data and the future of ecology}},
volume = {11},
year = {2013}
}
@article{Haraguchi15,
author = {Haraguchi, L and Carstensen, J and Abreu, P C and Odebrecht, C},
journal = {Estuarine, Coastal and Shelf Science},
number = {SI},
pages = {76--87},
title = {{Long-term changes of the phytoplankton community and biomass in the subtropical shallow {\{}P{\}}atos {\{}L{\}}agoon {\{}E{\}}stuary, {\{}B{\}}razil}},
volume = {162},
year = {2015}
}
@article{Harding94,
author = {Harding, L W},
journal = {Marine Ecology Progress Series},
pages = {267--291},
title = {{Long-term trends in the distribution of phytoplankton in {\{}C{\}}hesapeake {\{}B{\}}ay - roles of light, nutrients, and streamflow}},
volume = {104},
year = {1994}
}
@article{Harding13,
author = {Harding, L W and Batiuk, R A and Fisher, T R and Gallegos, C L and Mallone, T C and Miller, W D and Mulholland, M R and w. Paerl, H and Perry, E S and Tango, P},
journal = {Estuaries and Coasts},
number = {1},
pages = {134--148},
title = {{Scientific bases for numerical chlorophyll criteria in {\{}C{\}}hesapeake {\{}B{\}}ay}},
volume = {37},
year = {2013}
}
@article{Harding16,
author = {Harding, L W and Gallegos, C L and Perry, E S and Miller, W D and Adolf, J E and Mallonee, M E and Paerl, H W},
journal = {Estuaries and Coasts},
pages = {664--681},
title = {{Long-term trends of nutrients and phytoplankton in {\{}C{\}}hesapeake {\{}B{\}}ay}},
volume = {39},
year = {2016}
}
@article{Hartigan79,
author = {Hartigan, J A and Wong, M A},
journal = {Applied Statistics},
number = {1},
pages = {100--108},
title = {{A K-means clustering algorithm}},
volume = {28},
year = {1979}
}
@book{Harvey89,
address = {Cambridge, United Kingdom},
author = {Harvey, A C},
pages = {572},
publisher = {Cambridge University Press},
title = {{Forecasting, Structural Time Series Models and the Kalman Filter}},
year = {1989}
}
@article{Harvey00,
author = {Harvey, L D D},
journal = {Climatic Change},
number = {3},
pages = {225--263},
title = {{Upscaling in global change research}},
volume = {44},
year = {2000}
}
@article{Hassett2005,
abstract = {Restoration of aquatic ecosystems is a high priority regionally and globally, yet only recently have such efforts adopted holistic approaches that include the restoration of streams and rivers flowing to coastal areas. As the largest estuary in the US, the Chesapeake Bay has been the focus of one of the most high-profile restoration programs ever undertaken in North America. While the primary emphasis has been on tidal waters, freshwater tributary clean-up strategies have recently been developed. We have compiled the first comprehensive database of over 4700 existing river and stream restoration projects in the Chesapeake Bay Watershed (CBW) to examine where dollars are being spent, what issues motivate restoration, and what approaches are used. By conservative estimates, in excess of {\$}400 million has been invested in restoration projects since 1990. The majority of projects were implemented to restore forest vegetation in riparian areas and improve water quality. Although the CBW has an extremely high density of restoration activities relative to other regions of the US, only 5.4{\%} of the project records indicated that related monitoring of project performance has occurred. To provide cost-effective management solutions, we recommend that a centralized tracking system be developed that includes restoration projects associated with both tidal and non-tidal waterways, along with a substantial increase in investment in the comprehensive monitoring of individual projects following implementation.},
author = {Hassett, Brooke and Palmer, Margaret and Bernhardt, Emily and Smith, Sean and Carr, Jamie and Hart, David},
doi = {10.1890/1540-9295(2005)003[0259:RWPBPT]2.0.CO;2},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2005{\_}Hassett{\_}et{\_}al-CB{\_}Watershed{\_}Restoration{\_}Project.pdf:pdf},
isbn = {1540-9295},
issn = {15409309},
journal = {Frontiers in Ecology and the Environment},
number = {5},
pages = {259--267},
title = {{Restoring watersheds project by project: Trends in Chesapeake Bay tributary restoration}},
volume = {3},
year = {2005}
}
@book{Hastie90,
address = {London, New York},
author = {Hastie, T and Tibshirani, R},
pages = {335},
publisher = {Chapman and Hall},
title = {{Generalized Additive Models}},
year = {1990}
}
@book{Hastie09,
address = {New York},
author = {Hastie, T and Tibshirani, R and Friedman, J},
edition = {2nd},
pages = {745},
publisher = {Springer},
title = {{The elements of statistical learning: data mining, inference, and prediction}},
year = {2009}
}
@techreport{Hauxwell10,
address = {Madison, Wisconsin},
author = {Hauxwell, J and Knight, S and Wagner, K and Mikulyuk, A and Nault, M and Porzky, M and Chase, S},
institution = {Wisconsin Department of Natural Resources},
number = {PUB SS-1068 2010},
title = {{Recommended baseline monitoring of aquatic plants in {\{}W{\}}isconsin: Sampling design, field and laboratory procedures, data entry and analysis, and applications}},
year = {2010}
}
@article{Hawkins00,
author = {Hawkins, C P and Norris, R H and Gerritsen, J and Hughes, R M and Jackson, S K and Johnson, R K and Stevenson, R J},
journal = {Journal of the North American Benthological Society},
number = {3},
pages = {541--556},
title = {{Evaluation of the use of landscape classifications for the prediction of freshwater biota: Synthesis and recommendations}},
volume = {19},
year = {2000}
}
@incollection{Hay08,
address = {Heidelberg, Berlin, New York},
author = {Hay, G J and Castilla, G},
booktitle = {Object-Based Image Analysis: Spatial Concepts for Knowledge-Driven Remote Sensing Applications},
editor = {Blaschke, T and Lang, S and Hay, G J},
pages = {75--89},
publisher = {Springer-Verlag},
title = {{Geographic object-based image analysis ({\{}GEOBIA{\}}): A new name for a new discipline}},
year = {2008}
}
@article{Heiskary08,
author = {Heiskary, S and Wilson, B},
journal = {Lake and Reservoir Management},
number = {3},
pages = {282--297},
title = {{Minnesota's approach to lake nutrient criteria development}},
volume = {24},
year = {2008}
}
@book{Helsel12,
address = {Hoboken New Jersey},
author = {Helsel, D R},
edition = {2nd},
pages = {344},
publisher = {John Wiley {\&} Sons, Inc.},
title = {{Statistics for Censored Environmental Data Using Minitab and R}},
year = {2012}
}
@article{Hestir13,
author = {Hestir, E L and Schoellhamer, D H and Morgan-King, T and Ustin, S L},
journal = {Marine Geology},
number = {1},
pages = {304--313},
title = {{A step decrease in sediment concentration in a highly modifed tidal river delta following the 1983 {\{}E{\}}l Ni{\~{n}}o floods}},
volume = {345},
year = {2013}
}
@article{Heugens01,
author = {Heugens, E H W and Hendriks, A J and Dekker, T and van Straalen, N M and Admiraal, W},
journal = {Critical Reviews in Toxicology},
number = {3},
pages = {247--284},
title = {{A review of the effects of multiple stressors on aquatic organisms and analysis of uncertainty factors for use in risk assessment}},
volume = {31},
year = {2001}
}
@article{Hickey2017,
abstract = {Ecological (poleward) regime shifts are a predicted response to climate change and have been well documented in terrestrial and more recently ocean species. Coastal zones are amongst the most susceptible ecosystems to the impacts of climate change, yet studies particularly focused on mangroves are lacking. Recent studies have highlighted the critical ecosystem services mangroves provide, yet there is a lack of data on temporal global population response. This study tests the notion that mangroves are migrating poleward at their biogeographical limits across the globe in line with climate change. A coupled systematic approach utilising literature and land surface and air temperature data was used to determine and validate the global poleward extent of the mangrove population. Our findings indicate that whilst temperature (land and air) have both increased across the analysed time periods, the data we located showed that mangroves were not consistently extending their latitudinal range across the globe. Mangroves, unlike other marine and terrestrial taxa, do not appear to be experiencing a poleward range expansion despite warming occurring at the present distributional limits. Understanding failure for mangroves to realise the global expansion facilitated by climate warming may require a focus on local constraints, including local anthropogenic pressures and impacts, oceanographic, hydrological, and topographical conditions. Keywords},
author = {Hickey, Sharyn M and Phinn, Stuart R and Callow, Nik J and {Van Niel}, Kimberly P and Hansen, Jeff E and Duarte, Carlos M},
doi = {10.1007/s12237-017-0211-8},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}hickey{\_}is{\_}climate.pdf:pdf},
journal = {Estuaries and Coasts},
keywords = {Climate change,Global change,Mangroves,Range shifts,Temperature},
number = {5},
pages = {1215--1226},
publisher = {Estuaries and Coasts},
title = {{Is Climate Change Shifting the Poleward Limit of Mangroves?}},
volume = {40},
year = {2017}
}
@book{Hilborn97,
address = {Princeton, New Jersey},
author = {Hilborn, R and Mangel, M},
pages = {315},
publisher = {Princeton University Press},
title = {{The Ecological Detective: Confronting Models with Data}},
year = {1997}
}
@article{Hill17,
author = {Hill, R A and Fox, E W and Leibowitz, S G and Olsen, A R and Thornbrugh, D J and Weber, M H},
doi = {10.1002/eap.1617},
journal = {Ecological Applications},
number = {8},
pages = {2397--2415},
title = {{Predictive mapping of the biotic condition of conterminous {\{}U.S.{\}} rivers and streams}},
volume = {27},
year = {2017}
}
@article{Hill16,
author = {Hill, R A and Weber, M H and Leibowitz, S G and Olsen, A R and Thornbrugh, D J},
doi = {10.1111/1752-1688.12372},
journal = {Journal of the American Water Resources Assocation},
pages = {120--128},
title = {{The {\{}S{\}}tream-{\{}C{\}}atchment ({\{}S{\}}tream{\{}C{\}}at) dataset: A database of watershed metrics for the conterminous {\{}U{\}}nited {\{}S{\}}tates}},
volume = {52},
year = {2016}
}
@article{Hirsch14b,
author = {Hirsch, R M},
journal = {Journal of the American Water Resources Association},
number = {6},
pages = {1401--1424},
title = {{Large biases in regression-based constituent flux estimates: causes and diagnostic tools}},
volume = {50},
year = {2014}
}
@article{Hirsch91,
author = {Hirsch, R M and Alexander, R B and Smith, R A},
journal = {Water Resources Research},
pages = {803--813},
title = {{Selection of methods for the detection and estimation of trends in water quality}},
volume = {27},
year = {1991}
}
@article{Hirsch15,
author = {Hirsch, R M and Archfield, S A and {De Cicco}, L A},
journal = {Environmental Modelling and Software},
pages = {148--166},
title = {{A bootstrap method for estimating uncertainty of water quality trends}},
volume = {73},
year = {2015}
}
@techreport{Hirsch14,
address = {Reston, Virginia},
annote = {$\backslash$url{\{}http://pubs.usgs.gov/tm/04/a10/{\}}},
author = {Hirsch, R M and {De Cicco}, L},
institution = {US Geological Survey},
number = {Techniques and Methods book 4, ch. A10},
pages = {94},
title = {{User guide to {\{}E{\}}xploration and {\{}G{\}}raphics for {\{}R{\}}iv{\{}E{\}}r {\{}T{\}}rends ({\{}EGRET{\}}) and data{\{}R{\}}etrieval: {\{}R{\}} packages for hydrologic data}},
year = {2014}
}
@article{Hirsch10,
author = {Hirsch, R M and Moyer, D L and Archfield, S A},
journal = {Journal of the American Water Resources Association},
number = {5},
pages = {857--880},
title = {{Weighted regressions on time, discharge, and season ({\{}WRTDS{\}}), with an application to {\{}C{\}}hesapeake {\{}B{\}}ay river inputs}},
volume = {46},
year = {2010}
}
@article{Hirsch82,
author = {Hirsch, R M and Slack, J R and Smith, R A},
journal = {Water Resources Research},
pages = {107--121},
title = {{Techniques of trend analysis for monthly water quality data}},
volume = {18},
year = {1982}
}
@incollection{Hoang06,
address = {Berlin, Germany},
author = {Hoang, H and Recknagel, F and Marshall, J and Choy, S},
booktitle = {Ecological Informatics: Scope, Techniques and Applications},
edition = {2nd},
editor = {Recknagel, F},
pages = {239--251},
publisher = {Springer-Verlag},
title = {{Elucidation of hypothetical relationships between habitat conditions and macroinvertebrate assemblages in freshwater streams by artificial neural networks}},
year = {2006}
}
@article{Hoang01,
author = {Hoang, H and Recknagel, F and Marshall, J and Choy, S},
journal = {Ecological Modelling},
number = {1-3},
pages = {195--206},
title = {{Predictive modelling of macroinvertebrate assemblages for stream habitat assessments in {\{}Q{\}}ueensland ({\{}A{\}}ustraila)}},
volume = {195},
year = {2001}
}
@article{Hobbs2001,
abstract = {The extent of human-induced change and damage to Earth's ecosystems renders ecosystem repair an essen- tial part of our future survival strategy, and this de- mands that restoration ecology provide effective con- ceptual and practical tools for this task. We argue that restoration ecology has to be an integral component of land management in today's world, and to be broadly applicable, has to have a clearly articulated conceptual basis. This needs to recognize that most ecosystems are dynamic and hence restoration goals cannot be based on static attributes. Setting clear and achiev- able goals is essential, and these should focus on the desired characteristics for the system in the future, rather than in relation to what these were in the past. Goal setting requires that there is a clear understand- ing of the restoration options available (and the rela- tive costs of different options). The concept of restora- tion thresholds suggests that options are determined by the current state of the system in relation to biotic and abiotic thresholds. A further important task is the development of effective and easily measured success criteria. Many parameters could be considered for in- clusion in restoration success criteria, but these are of- ten ambiguous or hard to measure. Success criteria need to relate clearly back to specific restoration goals. If restoration ecology is to be successfully prac- ticed as part of humanity's response to continued eco- system change and degradation, restoration ecologists need to rise to the challenges of meshing science},
author = {Hobbs, R J and Harris, J a},
doi = {10.1046/j.1526-100x.2001.009002239.x},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2001{\_}Hobbs{\_}Restoration{\_}Ecology.pdf:pdf},
isbn = {1526-100X},
issn = {1061-2971},
journal = {Restoration Ecology},
keywords = {conceptual framework,dynamic ecosystems,ecosystem repair,restoration goals,suc-,thresholds},
month = {jun},
number = {2},
pages = {239--246},
pmid = {2272},
title = {{Restoration Ecology: Repairing the Earth's Ecosystems in the New Millennium}},
url = {http://doi.wiley.com/10.1046/j.1526-100x.2001.009002239.x},
volume = {9},
year = {2001}
}
@article{Hodur97,
author = {Hodur, R M},
journal = {Monthly Weather Review},
pages = {1414--1430},
title = {{The {\{}N{\}}aval {\{}R{\}}esearch {\{}L{\}}aboratory's {\{}C{\}}oupled {\{}O{\}}cean/{\{}A{\}}tmosphere {\{}M{\}}esoscale {\{}P{\}}rediction {\{}S{\}}ystem ({\{}COAMPS{\}})}},
volume = {125},
year = {1997}
}
@article{Holmes99,
author = {Holmes, R M and Amino, A and Kerouel, R and Hooker, B A and Peterson, B J},
journal = {Journal of Fisheries and Aquatic Sciences},
number = {10},
pages = {1801--1808},
title = {{A simple precise method for measuring ammonium in marine and freshwater ecosystems}},
volume = {56},
year = {1999}
}
@article{Holmes70,
author = {Holmes, R W},
journal = {Limnology and Oceanography},
number = {5},
pages = {688--694},
title = {{The secchi disk in turbid coastal waters}},
volume = {15},
year = {1970}
}
@article{Homer07,
author = {Homer, C and Dewitz, J and Fry, J and Coan, M and Hossain, N and Larson, C and Herold, N and McKerrow, A and VanDriel, J N and Wickham, J},
journal = {Photogrammetric Engineering and Remote Sensing},
number = {4},
pages = {337--341},
title = {{Completion of the 2001 {\{}National Land Cover Database{\}} for the conterminous {\{}United States{\}}}},
volume = {73},
year = {2007}
}
@incollection{Hopkinson05,
address = {Oxford, United Kingdom},
author = {Hopkinson, C S and Smith, E M},
booktitle = {Respiration in Aquatic Ecosystems},
editor = {Giorgio, P A Del and Williams, P},
pages = {122--146},
publisher = {Oxford Press},
title = {{Estuarine respiration: an overview of benthic, pelagic, and whole system respiration}},
year = {2005}
}
@article{Hornik91,
author = {Hornik, K},
journal = {Neural Networks},
number = {2},
pages = {251--257},
title = {{Approximation capabilities of multilayer feedforward networks}},
volume = {4},
year = {1991}
}
@article{Horppila01,
author = {Horppila, J and Nurminen, L},
journal = {Freshwater Biology},
number = {11},
pages = {1447--1455},
title = {{The effect of an emergent macrophyte ($\backslash$textit{\{}{\{}T{\}}ypha angustifolia{\}}) on sediment resuspension in a shallow north temperate lake}},
volume = {46},
year = {2001}
}
@article{Host05,
author = {Host, G E and Schuldt, J and Ciborowski, J J H and Johnson, L B and Hollenhorst, T and Richards, C},
journal = {International Journal of Remote Sensing},
number = {23},
pages = {5325--5341},
title = {{Use of {\{}GIS{\}} and remotely sensed data for a priori identification of reference areas for {\{}G{\}}reat {\{}L{\}}akes coastal ecosystems}},
volume = {26},
year = {2005}
}
@article{Howard15,
author = {Howard, J K and Klausmeyer, K R and Fesenmyer, K A and Furnish, J and Gardali, T and Grantham, T and Katz, J V E and Kupferberg, S and McIntyre, P and Moyle, P B and Ode, P R and Peek, R and Qui{\~{n}}ones, R M and Rehn, A C and Santos, N and Schoenig, S and Serpa, L and Shedd, J D and Slusark, J and Viers, J H and Wright, A and Morrison, S A},
doi = {10.1371/journal.pone.0130710},
journal = {PLOS ONE},
number = {7},
pages = {e0130710},
title = {{Patterns of freshwater species richness, endemism, and vulnerability in {\{}C{\}}alifornia}},
volume = {10},
year = {2015}
}
@techreport{Howard09,
address = {San Francisco, CA},
author = {Howard, J and Revenga, C},
institution = {The Nature Conservancy of California},
pages = {29 + Appendices},
title = {{California's freshwater biodiveristy in a continental context. {\{}S{\}}cience for {\{}C{\}}onservation {\{}T{\}}echnical {\{}B{\}}rief {\{}S{\}}eries}},
year = {2000}
}
@article{Howarth96,
author = {Howarth, R W and Billen, G and Swaney, D and Townsend, A and Jaworski, N and Lajtha, K and Downing, J A and Elmgren, R and Caraco, N and Jordan, T and Berendse, F and Freney, J and Kudeyarov, V and Murdoch, P and Zhao-Liang, Z},
journal = {Biogeochemistry},
number = {1},
pages = {75--139},
title = {{Regional nitrogen budgets and riverine {\{}N{\}} {\&} {\{}P{\}} fluxes for the drainages to the {\{}N{\}}orth {\{}A{\}}tlantic {\{}O{\}}cean: natural and human influences}},
volume = {35},
year = {1996}
}
@article{Howarth14,
author = {Howarth, R W and Hayn, M and Marino, R M and Ganju, N and Foreman, K and McGlathery, K and Giblin, A E and Berg, P and Walker, J D},
journal = {Biogeochemistry},
number = {1-3},
pages = {1--20},
title = {{Metabolism of a nitrogen-enriched coastal marine lagoon during the summertime}},
volume = {118},
year = {2014}
}
@article{Hughes09,
author = {Hughes, A R and Williams, S L and Duarte, C M and Heck, K L and Waycott, M},
journal = {Frontiers in Ecology and the Environment},
number = {5},
pages = {242--246},
title = {{Associations of concern: declining seagrasses and threatened dependent species}},
volume = {7},
year = {2009}
}
@article{Hunt02,
author = {Hunt, J and Annett, C A},
journal = {North American Journal of Fisheries Management},
number = {4},
pages = {1201--1208},
title = {{Effects of habitat manipulation on reproducive success of individual largemouth bass in an {\{}O{\}}zark reservoir}},
volume = {22},
year = {2002}
}
@article{Hutchison2014,
abstract = {Understanding spatial variation in carbon storage in natural habitats is critical for climate change mitigation efforts such as REDD. Terrestrial forests are being mapped with increasing accuracy, but the distribution of ``blue carbon'' in marine ecosystems remains poorly understood. We reviewed the literature to obtain field data on carbon storage and fluxes in mangroves world-wide. Using this material we developed a climate-based model for potential mangrove above-ground biomass (AGB) with almost four times the explanatory power of the only previous published model. From this model, we present the first ever global map of potential mangrove AGB and estimate a total global mangrove AGB of 2.83 Pg, with an average of 184.8 t ha−1. Data on other carbon stocks and fluxes confirm the importance of mangroves in carbon accounting. The map highlights the high variability in mangrove AGB and indicates areas that should be prioritised for mangrove conservation and restoration.},
author = {Hutchison, James and Manica, Andrea and Swetnam, Ruth and Balmford, Andrew and Spalding, Mark},
doi = {10.1111/conl.12060},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Hutchison{\_}predicting{\_}global.pdf:pdf},
journal = {Conservation Letters},
keywords = {Above ground biomass,Bioclim,Biomass,Blue carbon,Carbon,Carbon storage,Ecosystem services,Global model,Mangrove,REDD},
number = {3},
pages = {233--240},
title = {{Predicting global patterns in mangrove forest biomass}},
volume = {7},
year = {2014}
}
@article{Hyndman08,
author = {Hyndman, R J and Khandakar, Y},
journal = {Journal of Statistical Software},
number = {3},
pages = {1--22},
title = {{Automatic time series forecasting: The forecast package for R}},
volume = {26},
year = {2008}
}
@article{Ibarra03,
author = {Ibarra, A A and Gevrey, M and Park, Y S and Lim, P and Lek, S},
journal = {Ecological Modelling},
number = {3},
pages = {281--290},
title = {{Modelling the factors that influence fish guilds composition using a back-propagation network: Assessment of metrics for indices of biotic integrity}},
volume = {160},
year = {2003}
}
@article{Idso74,
author = {Idso, S B and Gilbert, R G},
journal = {Journal of Applied Ecology},
number = {1},
pages = {399--401},
title = {{On the universality of the {\{}P{\}}oole and {\{}A{\}}tkins secchi disk-light extinction equation}},
volume = {11},
year = {1974}
}
@misc{IEP16,
annote = {$\backslash$url{\{}http://www.water.ca.gov/dayflow/{\}}},
author = {IEP},
title = {{Dayflow: An estimate of daily average Delta outflow. Interagency Ecological Program for the San Francisco Estuary}},
year = {2016}
}
@misc{IEP13,
annote = {$\backslash$url{\{}http://water.ca.gov/bdma/meta/discrete.cfm{\}}},
author = {IEP},
title = {{IEP Bay-Delta Monitoring and Analysis Section, Discrete Water Quality Metadata}},
year = {2013}
}
@article{Iverson86,
author = {Iverson, R L and Bittaker, H F},
journal = {Estuarine, Coastal and Shelf Science},
number = {5},
pages = {577--602},
title = {{Seagrass distribution and abundance in eastern {\{}G{\}}ulf of {\{}M{\}}exico coastal waters}},
volume = {22},
year = {1986}
}
@techreport{Jabusch16,
address = {Richmond, CA},
author = {Jabusch, T and Bresnahan, P and Trowbridge, P and Novick, E and Wong, A and Salomon, M and Senn, D},
institution = {San Francisco Estuary Institute},
title = {{Summary and evaluation of {\{}D{\}}elta subregions for nutrient monitoring and assessment}},
url = {http://sfbaynutrients.sfei.org/books/dsp-nutrient-monitoring-and-assessment},
year = {2016}
}
@techreport{Jabusch09,
address = {Richmond, CA},
author = {Jabusch, T and Gilbreath, A N},
institution = {San Francisco Estuary Institute},
title = {{Summary of current water quality monitoring programs in the {\{}D{\}}elta}},
url = {http://www.waterboards.ca.gov/centralvalley/water{\_}issues/delta{\_}water{\_}quality/delta{\_}regional{\_}monitoring/studies{\_}reports/drmp{\_}wq{\_}monitoring{\_}progs{\_}sum.pdf},
year = {2009}
}
@article{Jackson93,
author = {Jackson, D A},
journal = {Hydrobiologia},
pages = {9--26},
title = {{Multivariate analysis of benthic invertebrate communities: The implication of choosing particular data standardizations, measures of association, and ordination methods}},
volume = {268},
year = {1993}
}
@article{Jackson01,
author = {Jackson, D A and Peres-Neto, P R and Olden, J D},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {1},
pages = {157--170},
title = {{What controls who is where in freshwater fish communities - the roles of biotic, abiotic, and spatial factors}},
volume = {58},
year = {2001}
}
@article{Jain00,
author = {Jain, A K and Duin, R P W and Mao, J C},
journal = {{\{}IEEE{\}} Transactions on Pattern Analysis and Machine Intelligence},
number = {1},
pages = {4--37},
title = {{Statistical pattern recognition: A review}},
volume = {22},
year = {2000}
}
@techreport{Janicki96,
address = {St. Petersburg, Florida},
author = {Janicki, A and Wade, D},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/1996 Tech Pubs/TBEP{\_}06{\_}96ExternalTNLoads.pdf:pdf},
institution = {Tampa Bay National Estuary Program},
number = {06-96},
pages = {200},
title = {{Estimating critical external nitrogen loads for the {\{}T{\}}ampa {\{}B{\}}ay estuary: An empirically based approach to setting management targets}},
year = {1996}
}
@article{Jassby08,
author = {Jassby, A D},
journal = {San Francisco Estuary and Watershed Science},
number = {1},
pages = {1--24},
title = {{Phytoplankton in the {\{}U{\}}pper {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary: Recent biomass trends, their causes, and their trophic significance}},
volume = {6},
year = {2008}
}
@article{Jassby00,
author = {Jassby, A D and Cloern, J E},
journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
pages = {323--352},
title = {{Organic matter sources and rehabilitations of the {\{}S{\}}acramento-{\{}S{\}}an {\{}J{\}}oaquin {\{}D{\}}elta ({\{}C{\}}alifornia, {\{}USA{\}})}},
volume = {10},
year = {2000}
}
@article{Jassby02,
author = {Jassby, A D and Cloern, J E and Cole, B E},
journal = {Limnology and Oceanography},
number = {3},
pages = {698--712},
title = {{Annual primary production: Patterns and mechanisms of change in a nutrient-rich tidal ecosystem}},
volume = {47},
year = {2002}
}
@manual{Jassby14,
annote = {R package version 0.4-1},
author = {Jassby, Alan D and Cloern, James E},
title = {{wq: Exploring water quality monitoring data}},
url = {http://cran.r-project.org/package=wq},
year = {2014}
}
@article{Jennings99,
author = {Jennings, M J and Bozek, M A and Hatzenbeler, G R and Emmons, E E and Staggs, M D},
journal = {North American Journal of Fisheries Management},
number = {1},
pages = {18--27},
title = {{Cumulative effects of incremental shoreline habitat modification on fish assemblages in north temperate lakes}},
volume = {19},
year = {1999}
}
@article{Jennings03,
author = {Jennings, M J and Emmons, E E and Hatzenbeler, G R and Edwards, C and Bozek, M A},
journal = {Lake and Reservoir Management},
number = {3},
pages = {272--279},
title = {{Is littoral habitat affected by residential development and land use in watersheds of {\{}W{\}}isconsin lakes?}},
volume = {19},
year = {2003}
}
@incollection{Jensen09,
address = {Los Angeles, California},
author = {Jensen, J R and Im, J and Hardin, P and Jensen, R R},
booktitle = {The SAGE Handbook of Remote Sensing},
editor = {Warner, T A and Nellis, M D and Foody, G M},
pages = {269--281},
publisher = {SAGE Publications},
title = {{Image classification}},
year = {2009}
}
@book{Jeppesen98,
address = {New York, New York},
editor = {Jeppesen, E and S{\o}ndergaard, M and S{\o}ndergaard, M and Christoffersen, K},
publisher = {Springer-Verlag},
title = {{The Structuring Role of Submerged Macrophytes in Lakes, Ecological Studies, Vol. 131}},
year = {1998}
}
@article{Johansson91,
address = {Tampa, Florida, USA},
author = {Johansson, J O R},
editor = {Treat, S F and Clark, P A},
journal = {Proceedings of the Tampa Bay Area Scientific Information Symposium 2},
pages = {157--176},
publisher = {Tampa Bay Area Study Group Project at Scholar Commons},
title = {{Long-term trends of nitrogen loading, water quality and biological indicators in {\{}H{\}}illsborough {\{}B{\}}ay, {\{}F{\}}lorida}},
year = {1991}
}
@article{Johansson92,
author = {Johansson, J O R and {Lewis III}, R R},
journal = {Marine Coastal Eutrophication},
pages = {1199--1215},
title = {{Recent improvements in water quality and biological indicators in {\{}H{\}}illsborough {\{}B{\}}ay, a highly impacted subdivision of {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida, {\{}USA{\}}}},
volume = {Proceeding},
year = {1992}
}
@article{Johnstone85,
author = {Johnstone, I M and Coffey, B T and Howard-Williams, C},
journal = {Journal of Environmental Management},
number = {3},
pages = {263--279},
title = {{The role of recreational boat traffic in interlake dispersal of macrophytes: A {\{}N{\}}ew {\{}Z{\}}ealand case study}},
volume = {20},
year = {1985}
}
@article{Jones94,
author = {Jones, C G and Lawton, J H and Shachak, M},
journal = {OIKOS},
number = {3},
pages = {373--386},
title = {{Organisms as ecosystem engineers}},
volume = {69},
year = {1994}
}
@article{Jordan03,
author = {Jordan, T E and Weller, D E and Correll, D L},
journal = {Estuaries and Coasts},
number = {2A},
pages = {226--243},
title = {{Sources of nutrient inputs to the {\{}P{\}}atuxent {\{}R{\}}iver estuary}},
volume = {26},
year = {2003}
}
@article{Schoolmaster13,
author = {Jr., D R Schoolmaster and Grace, J B and Schweiger, E W and Guntenspergen, G R and Mitchell, B R and Miller, K M and Little, A M},
journal = {Ecological Indicators},
pages = {14--23},
title = {{An algorithmic and information-theoretic approach to multimetric index construction}},
volume = {26},
year = {2013}
}
@article{Rykiel96,
author = {Jr., E J Rykiel},
journal = {Ecological Modelling},
number = {3},
pages = {229--244},
title = {{Testing ecological models: the meaning of validation}},
volume = {90},
year = {1996}
}
@article{Jurca12,
author = {Jurca, T and Donohue, L and Laketic, D and Radulovic, S and Irvine, K},
journal = {Fundamental and Applied Limnology},
number = {2},
pages = {175--184},
title = {{Importance of the shoreline diversity features for littoral macroinvertebrate assemblages}},
volume = {180},
year = {2012}
}
@article{Justic87,
author = {Just{\'{i}}c, D and Legov{\'{i}}c, T and Rottini-Sandrini, L},
journal = {Estuarine, Coastal and Shelf Science},
number = {4},
pages = {435--445},
title = {{Trends in oxygen content 1911--1984 and occurrence of benthic mortality in the northern {\{}A{\}}driatic {\{}S{\}}ea}},
volume = {25},
year = {1987}
}
@article{Kahle13,
author = {Kahle, David and Wickham, Hadley},
journal = {The R Journal},
number = {1},
pages = {144--161},
title = {{ggmap: Spatial Visualization with ggplot2}},
url = {http://journal.r-project.org/archive/2013-1/kahle-wickham.pdf},
volume = {5},
year = {2013}
}
@article{Kanninen13,
author = {Kanninen, A and Hellsten, S and H{\"{a}}m{\"{a}}l{\"{a}}inen, H},
journal = {Ecological Indicators},
pages = {29--43},
title = {{Comparing stressor-specific indices and general measures of taxonomic composition for assessing the status of boreal lacustrine macrophyte communities}},
volume = {27},
year = {2013}
}
@article{Karr81,
author = {Karr, J R},
journal = {Fisheries},
number = {6},
pages = {21--27},
title = {{Assessment of biotic integrity using fish communities}},
volume = {6},
year = {1981}
}
@book{Karr99,
address = {Washington, DC},
author = {Karr, J R and Chu, E W},
pages = {206},
publisher = {Island Press},
title = {{Restoring Life in Running Waters: Better Biological Monitoring}},
year = {1999}
}
@article{KarrDud81,
author = {Karr, J R and Dudley, D R},
journal = {Environmental Management},
pages = {55--68},
title = {{Ecological perspective on water quality goals}},
volume = {5},
year = {1981}
}
@techreport{Karr86,
address = {Champaign, Illinois},
author = {Karr, J R and Fausch, K D and Angermeier, P L and Yant, P R and Schlosser, I J},
institution = {Illinois Natural History Survey},
number = {Special Publication 5},
title = {{Assessing biological integrity in running waters: a method and its rationale}},
year = {1986}
}
@incollection{Karul06,
address = {Berlin, Germany},
author = {Karul, C and Soyupak, S},
booktitle = {Ecological Informatics: Scope, Techniques and Applications},
edition = {2nd},
editor = {Recknagel, F},
pages = {309--323},
publisher = {Springer-Verlag},
title = {{A comparison between neural network based and multiple regression models for {\{}C{\}}hlorophyll-$\backslash$textit{\{}a{\}} estimation}},
year = {2006}
}
@article{Kauffman2012,
abstract = {This report describes the approaches necessary for the measurement, monitoring and reporting of structure, biomass and carbon stocks in mangrove forests. Mangroves are coastal ecosystems providing numerous ecosystem services affecting both marine and terrestrial resources. In addition, they contain substantial carbon stocks and, due to high rates of deforestation, are significant sources of carbon emissions. Because of their value as carbon stocks and sinks and their numerous other benefits, mangroves could be excellent candidates for carbon mitigation programmes including Reducing Emissions from Deforestation and Forest Degradation, and Enhancing Forest Carbon Stocks in Developing Countries (REDD+). This publication outlines biologically relevant and statistically valid approaches to the efficient and accurate assessment of ecosystem structure, biomass and carbon stocks of mangrove forests},
author = {Kauffman, Jb and Donato, Dc},
doi = {10.17528/cifor/003749},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2012{\_}Kauffman{\_}Protocols{\_}for.pdf:pdf},
issn = {978-1-4020-4948-4},
journal = {Center for International Forestry},
pages = {11},
title = {{Protocols for the measurement, monitoring and reporting of structure, biomass and carbon stocks in mangrove forests}},
url = {http://www.amazonico.org/speclab/SiteAssets/SitePages/Methods/Mangrove-biomass-CIFOR.pdf},
volume = {Working pa},
year = {2012}
}
@article{Keddy82,
author = {Keddy, P A},
journal = {Aquatic Botany},
number = {1},
pages = {41--58},
title = {{Quantifying within-lake gradients of wave energy - interrelationships of wave energy, substrate particle size and shoreline plants in {\{}A{\}}xe {\{}L{\}}ake, {\{}O{\}}ntario}},
volume = {14},
year = {1982}
}
@article{Kell03,
author = {Kell, D B and Oliver, S G},
journal = {BioEssays},
number = {1},
pages = {99--105},
title = {{Here is the evidence, now what is the hypothesis? {\{}T{\}}he complementary roles of inductive and hypothesis-driven science in the post-genomic era}},
volume = {26},
year = {2003}
}
@misc{Kelley14,
annote = {$\backslash$url{\{}http://dankelley.github.com/oce/{\}}},
author = {Kelley, Dan and Richards, Clark},
title = {{oce: Analysis of Oceanographic data, {\{}R{\}} package version 0.9-15}},
year = {2014}
}
@article{Kelling09,
author = {Kelling, S and Hochachka, W M and Fink, D and Riedewald, M and Caruana, R and Ballard, G and Hooker, G},
journal = {BioScience},
number = {7},
pages = {613--620},
title = {{Data-intensive science: A new paradigm for biodiversity studies}},
volume = {59},
year = {2009}
}
@article{Kemp80,
author = {Kemp, W M and Boynton, W R},
journal = {Estuarine and Coastal Marine Science},
number = {4},
pages = {407--431},
title = {{Influence of biological and physical processes on dissolved oxygen dynamics in an estuarine system: Implications for the measurement of community metabolism}},
volume = {11},
year = {1980}
}
@article{Kemp05,
author = {Kemp, W M and Boynton, W R and Adolf, J E and Boesch, D F and Boicourt, W C and Brush, G and Cornwell, J C and Fisher, T R and Glibert, P M and Hagy, J D and Harding, L W and Houde, E D and Kimmel, D G and Miller, W D and Newell, R I E and Roman, M R and Smith, E M and Stevenson, J C},
journal = {Marine Ecology Progress Series},
pages = {1--29},
title = {{Eutrophication of {\{}C{\}}hesapeake {\{}B{\}}ay: historical trends and ecological interactions}},
volume = {303},
year = {2005}
}
@incollection{Kemp12,
address = {New York},
author = {Kemp, W M and Testa, J M},
booktitle = {Treatise on Estuarine and Coastal Science},
editor = {Wolanski, E and McLusky, D S},
pages = {83--118},
publisher = {Academic Press},
title = {{Metabolic balance between ecosystem production and consumption}},
year = {2012}
}
@article{Kemp09,
author = {Kemp, W M and Testa, J M and Conley, D J and Gilbert, D and Hagy, J D},
journal = {Biogeosciences},
number = {12},
pages = {2985--3008},
title = {{Temporal responses of coastal hypoxia to nutrient loading and physical controls}},
volume = {6},
year = {2009}
}
@article{Kemp04,
abstract = {We developed an algorithm for calculating habitat suitability for seagrasses and related submerged aquatic vegetation (SAV) at coastal sites where monitoring data are available for five water quality variables that govern light availability at the leaf surface. We developed independent estimates of the minimum light required for SAV survival both as a percentage of surface light passing through the water column to the depth of SAV growth (PLW min) and as a percentage of light reaching leaves through the epiphyte layer (PLL min). Values were computed by applying, as inputs to this algorithm, statistically derived values for water quality variables that correspond to thresholds for SAV presence in Chesapeake Bay. These estimates of PLW min and PLL min compared well with the values established from a literature review. Calculations account for tidal range, and total light attenuation is partitioned into water column and epiphyte contributions. Water column attenuation is further partitioned into effects of chlorophyll a (chl a), total suspended solids (TSS) and other substances. We used this algorithm to predict potential SAV presence throughout the Bay where calcu-lated light available at plant leaves exceeded PLL min . Predictions closely matched results of aerial photographic moni-toring surveys of SAV distribution. Correspondence between predictions and observations was particularly strong in the mesohaline and polyhaline regions, which contain 75–80{\%} of all potential SAV sites in this estuary. The method also allows for independent assessment of effects of physical and chemical factors other than light in limiting SAV growth and survival. Although this algorithm was developed with data from Chesapeake Bay, its general structure allows it to be calibrated and used as a quantitative tool for applying water quality data to define suitability of specific sites as habitats for SAV survival in diverse coastal environments worldwide.},
author = {Kemp, W. Michael and Batleson, Richard and Bergstrom, Peter and Carter, Virginia and Gallegos, Charles L. and Hunley, William and Karrh, Lee and Koch, Evamaria W. and Landwehr, Jurate M. and Moore, Kenneth A. and Murray, Laura and Naylor, Michael and Rybicki, Nancy B. and {Court Stevenson}, J. and Wilcox, David J.},
doi = {10.1007/BF02803529},
isbn = {0160-8347},
issn = {0160-8347},
journal = {Estuaries},
month = {jun},
number = {3},
pages = {363--377},
title = {{Habitat requirements for submerged aquatic vegetation in Chesapeake Bay: Water quality, light regime, and physical-chemical factors}},
url = {http://link.springer.com/10.1007/BF02803529},
volume = {27},
year = {2004}
}
@book{Kendall83,
address = {New York, New York},
author = {Kendall, M and Stuart, A},
pages = {410--414},
publisher = {MacMillan Publishing Company},
title = {{The Advanced Theory of Statistics}},
volume = {3},
year = {1983}
}
@article{Kennard06,
author = {Kennard, M J and Harch, B D and Pusey, B J and Arthington, A H},
journal = {Hydrobiologia},
pages = {151--170},
title = {{Accurately defining the reference condition for summary biotic metrics: A comparison of four approaches}},
volume = {572},
year = {2006}
}
@article{Kenney12,
author = {Kenney, M A and Wilcock, P R and Hobbs, B F and Flores, N E and Mart{\'{i}}nez, D C},
doi = {10.1111/j.1752-1688.2011.00635.x},
journal = {Journal of the American Water Resources Association},
number = {3},
pages = {603--615},
title = {{Is urban stream restoration worth it?}},
volume = {48},
year = {2012}
}
@article{Kenworthy96,
author = {Kenworthy, W J and Fonseca, M S},
journal = {Estuaries},
number = {3},
pages = {740--750},
title = {{Light requirements of seagrasses $\backslash$textit{\{}Halodule wrightii{\}} and $\backslash$textit{\{}Syringodium filiforme{\}} derived from the relationship between diffuse light attenuation and maximum depth distribution}},
volume = {19},
year = {1996}
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author = {Kerans, B L and Karr, J R},
journal = {Ecological Applications},
number = {4},
pages = {768--785},
title = {{A benthic index of biotic integrity {\{}(B-IBI){\}} for rivers of the {\{}T{\}}ennessee {\{}V{\}}alley}},
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year = {1994}
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author = {Killick, R and Eckley, I A},
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number = {3},
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year = {2014}
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author = {Kim, C K and Park, K},
journal = {Journal of Marine Systems},
pages = {103--115},
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year = {2012}
}
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author = {Kimmerer, W},
journal = {Limnology and Oceanography},
number = {3},
pages = {793--798},
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volume = {50},
year = {2005}
}
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author = {Kimmerer, W J and Parker, A E and Lidstrom, U E and Carpenter, E J},
journal = {Estuaries and Coasts},
pages = {913--929},
title = {{Short-term and interannual variability in primary production in the low-salinity zone of the {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary}},
volume = {35},
year = {2012}
}
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author = {Kimmerer, W J and Thompson, J K},
journal = {Estuaries and Coasts},
pages = {1202--1218},
title = {{Phytoplankton growth balanced by clam and zooplankton grazing and net transport into the low-salinity zone of the {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary}},
volume = {37},
year = {2014}
}
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year = {2006}
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annote = {R package version 0.4.1},
author = {Klima, Grzegorz},
title = {{FCNN4R: Fast Compressed Neural Networks for R}},
year = {2015}
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year = {1999}
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address = {Stanford, California},
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annote = {$\backslash$url{\{}http://CRAN.R-project.org/package=quantreg{\}}},
author = {Koenker, R},
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year = {1999}
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address = {Bemidji, Minnesota},
author = {Krysel, C and Boyer, E M and Parson, C and Welle, P},
institution = {Legislative Commission on Minnesota Resources, Mississippi Headwaters Board, and Bemidji State University},
pages = {57},
title = {{Lakeshore property values and water quality: Evidence from property sales in the {\{}M{\}}ississippi headwaters region}},
year = {2003}
}
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annote = {R package version 6.0-52},
author = {Kuhn, Max},
title = {{caret: Classification and Regression Training}},
url = {http://cran.r-project.org/package=caret},
year = {2015}
}
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pages = {89--136},
title = {{Environmental influences on aquatic plants in freshwater ecosystems}},
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year = {2006}
}
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year = {1967}
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address = {Heidelberg, Berlin, New York},
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editor = {Blaschke, T and Lang, S and Hay, G J},
pages = {3--27},
publisher = {Springer-Verlag},
title = {{Object-based image analysis for remote sensing applications: Modeling reality - dealing with complexity}},
year = {2008}
}
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author = {Lauridsen, T L and Jeppesen, E and Andersen, F O},
journal = {Aquatic Botany},
number = {1},
pages = {1--15},
title = {{Colonization of submerged macrophytes in shallow fish manipulated lake {\{}V{\}}aeng: Impact of sediment composition and waterfowl grazing}},
volume = {46},
year = {1993}
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@article{Le17,
author = {Le, C and Lehrter, J C and Hu, C and MacIntyre, H and Beck, M W},
doi = {10.1002/2016JC012275},
journal = {Journal of Geophysical Research: Oceans},
number = {1},
pages = {555--569},
title = {{Satellite observation of particulate organic carbon dynamics on the {\{}L{\}}ouisiana continental shelf}},
volume = {122},
year = {2017}
}
@article{Le16,
author = {Le, C and Lehrter, J C and Schaeffer, B and Hu, C and Murrell, M C and {Hagy III}, J D and Greene, R M and Beck, M W},
doi = {10.1016/j.ecss.2016.02.003},
journal = {Estuarine Coastal and Shelf Science},
pages = {26--38},
title = {{Bio-optical water quality dynamics observed from {\{}MERIS{\}} in {\{}P{\}}ensacola {\{}B{\}}ay, {\{}F{\}}lorida}},
volume = {173},
year = {2016}
}
@incollection{Leber2013,
address = {New York, NY},
author = {Leber, K L},
booktitle = {Sustainable Food Production},
doi = {10.1007/978-1-4614-5797-8},
editor = {Christou, Paul and Savin, Roxana and Costa-Pierce, Barry A and Misztal, Ignacy and Whitelaw, C Bruce A},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Leber{\_}Marine{\_}Fisheries.pdf:pdf},
isbn = {978-1-4614-5796-1},
pages = {1139--1157},
publisher = {Springer New York},
title = {{Marine fisheries enhancement, coming of age in the new millenium}},
url = {http://link.springer.com/10.1007/978-1-4614-5797-8},
year = {2013}
}
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author = {Lee, Z P and Du, K P and Arnone, R},
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number = {C2},
pages = {1--15},
title = {{A model for the diffuse attenuation of downwelling irradiance}},
volume = {110},
year = {2005}
}
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address = {Amsterdam, Holland},
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publisher = {Elsevier},
title = {{Numerical Ecology}},
year = {1998}
}
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author = {Lehman, J T and Botkin, D B and Likens, G E},
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pages = {343--364},
title = {{The assumptions and rationales of a computer model of phytoplankton population dynamics}},
volume = {20},
year = {1975}
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author = {Lehman, P W},
journal = {Limnology and Oceanography},
number = {3},
pages = {580--590},
title = {{The influence of climate on phytoplankton community biomass in {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay {\{}E{\}}stuary}},
volume = {45},
year = {2000}
}
@article{Lehman92,
author = {Lehman, P W},
journal = {Estuaries},
number = {3},
pages = {335--348},
title = {{Environmental factors associated with long-term changes in chlorophyll concentration in the {\{}S{\}}acramento-{\{}S{\}}an {\{}J{\}}oaquin {\{}D{\}}elta and {\{}S{\}}uisun {\{}B{\}}ay, {\{}C{\}}alifornia}},
volume = {15},
year = {1992}
}
@article{Lehman05,
author = {Lehman, P W and Boyer, G and Hall, C and Waller, S and Gehrts, K},
journal = {Hydrobiologia},
pages = {87--99},
title = {{Distribution and toxicity of a new colonial $\backslash$textit{\{}{\{}M{\}}icrocystis aeruginosa{\}} bloom in the {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay {\{}E{\}}stuary, {\{}C{\}}alifornia}},
volume = {541},
year = {2005}
}
@article{Lehman15,
author = {Lehman, P W and Kendall, C and Guerin, M A and Young, M B and Silva, S R and Boyer, G L and Teh, S J},
journal = {Estuaries and Coasts},
number = {1},
pages = {165--178},
title = {{Characterization of the $\backslash$textit{\{}{\{}M{\}}icrocystis{\}} bloom and its nitrogen supply in {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary using stable isotopes}},
volume = {38},
year = {2015}
}
@article{Lehman10,
author = {Lehman, P W and Teh, S J and Boyer, G L and Nobriga, M L and Bass, E and Hogle, C},
journal = {Hydrobiologia},
number = {1},
pages = {229--248},
title = {{Initial impacts of $\backslash$textit{\{}{\{}M{\}}icrocystis aeruginosa{\}} blooms on the aquatic food web in the {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary}},
volume = {637},
year = {2010}
}
@article{Lehrter12,
author = {Lehrter, J C and Beddick, D L and Devereux, R and Yates, D F and Murrell, M C},
journal = {Biogeochemistry},
number = {1-3},
pages = {233--252},
title = {{Sediment-water fluxes of dissolved inorganic carbon, {\{}O{\}}{\$}{\_}2{\$}, nutrients, and {\{}N{\}}{\$}{\_}2{\$} from the hypoxic region of the {\{}L{\}}ousiana continental shelf}},
volume = {109},
year = {2012}
}
@article{Lehrter10,
author = {Lehrter, J C and Cebrian, J},
journal = {Ecological Applications},
number = {2},
pages = {508--524},
title = {{Uncertainty propagation in an ecosystem nutrient budget}},
volume = {20},
year = {2010}
}
@incollection{Lehrter17,
address = {New York},
author = {Lehrter, J C and Ko, D S and Lowe, L L and Penta, B},
booktitle = {Modeling Coastal Hypoxia: Numerical Simulations of Patterns, Controls, and Effect of Dissolved Oxygen Dynamics},
editor = {Justic et al.},
pages = {173--204},
publisher = {Springer},
title = {{Predicted effects of climate change on northern {\{}G{\}}ulf of {\{}M{\}}exico hypoxia}},
year = {2017}
}
@article{Lehrter13,
author = {Lehrter, J C and Ko, D S and Murrell, M C and {Hagy III}, J D and Schaeffer, B A and Greene, R M and Gould, R W and Penta, B},
journal = {Journal of Geophysical Research},
number = {10},
pages = {4822--4838},
title = {{Nutrient distributions, transports, and budgets on the inner margin of a river-dominated continental shelf}},
volume = {118},
year = {2013}
}
@article{Lek96,
author = {Lek, S and Delacoste, M and Baran, P and Dimopoulos, I and Lauga, J and Aulagnier, S},
journal = {Ecological Modelling},
number = {1},
pages = {39--52},
title = {{Application of neural networks to modelling nonlinear relationships in ecology}},
volume = {90},
year = {1996}
}
@incollection{Lek00b,
address = {Berlin, Germany},
author = {Lek, S and Giraudel, J L and Gu{\'{e}}gan, J F},
booktitle = {Artificial Neuronal Networks: Application to Ecology and Evolution},
editor = {Lek, S and Gu{\'{e}}gan, J F},
pages = {3--27},
publisher = {Springer-Verlag},
title = {{Neuronal Networks: Algorithms and architectures for ecologists and evolutionary ecologists}},
year = {2000}
}
@book{Lek00,
address = {Berlin, Germany},
author = {Lek, S and Gu{\'{e}}gan, J F},
publisher = {Springer-Verlag},
title = {{Artificial Neuronal Networks: Application to Ecology and Evolution}},
year = {2000}
}
@article{Lek99,
author = {Lek, S and Gu{\'{e}}gan, J F},
journal = {Ecological Modelling},
number = {2-3},
pages = {65--73},
title = {{Artificial neural networks as a tool in ecological modelling, an introduction}},
volume = {120},
year = {1999}
}
@article{Leopold2017,
abstract = {Mangrove water biogeochemistry has been frequently studied under tropical climates, but less is known regarding mangroves in semi-arid climates. In this study, we examine the carbon and nutrient biogeochemistry in a mangrove tidal creek and in the main branch of a semi-arid estuary in New Caledonia. Porewater seepage represents a source of nutrients (DON, NH4 +, and DIP), carbon (DOC and CO2), and alkalinity for the water column, but seawater dilution of the mangrove inputs is observed. Spatial and tidal variations in CO2 fluxes along the tidal creek suggest that porewater seepage is a driver of CO2 emission into the atmosphere. Large seasonal and spatial differences in the biogeochemical functioning of the main channel are observed and are mainly related to the seasonal rainfall pattern. During the rainy season, the watershed influences the entire estuary, which exhibits a typical positive circulation. During the dry season, the estuary turns into a salt-plug region with positive and negative circulations in the upper and lower reaches, respectively. In this case, the upper and lower reaches seem to function independently, and the biogeochemical functioning of their water column is not controlled by the same processes. Surprisingly, pCO2@27 °C values tend to be higher during the dry season, as do the total alkalinity (TAlk) values, while the pH values exhibit an opposite trend. Moreover, the TAlk values are higher in the lower reaches during the wet season and in the upper reaches during the dry season. These results indicate high in situ biogeochemical reactions and high porewater influence during the dry season, likely because of a low flushing rate and high water residence time after salt plug establishment. Although our results suggest that salt plugs may significantly affect the water column's biogeochemistry and may promote CO2 emissions of mangrove-derived carbon, further investigations, especially mass balance studies, are required to quantify their role in the biogeochemical functioning of such estuarine systems. {\textcopyright} 2016, Coastal and Estuarine Research Federation.},
author = {Leopold, Audrey and Marchand, Cyril and Deborde, Jonathan and Allenbach, Michel},
doi = {10.1007/s12237-016-0179-9},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Leopold{\_}water{\_}biogeochemistry.pdf:pdf},
journal = {Estuaries and Coasts},
keywords = {Estuary,Mangrove,New Caledonia,Semi-arid climate,Water column biogeochemistry},
number = {3},
pages = {773--791},
publisher = {Estuaries and Coasts},
title = {{Water Biogeochemistry of a Mangrove-Dominated Estuary Under a Semi-Arid Climate (New Caledonia)}},
volume = {40},
year = {2017}
}
@article{Leps15,
author = {Leps, M and Tonkin, J D and Dahm, V and Haase, P and Sundermann, A},
doi = {10.1016/j.scitotenv.2015.07.083},
journal = {Science of the Total Environment},
pages = {546--556},
title = {{Disentangling environmental drivers of benthic invertebrate assemblages: The role of spatial scale and riverscape heterogeneity in a multiple stressor environment}},
volume = {536},
year = {2015}
}
@article{Levin92,
author = {Levin, S A},
journal = {Ecology},
number = {6},
pages = {1943--1967},
title = {{The problem of pattern and scale in ecology}},
volume = {73},
year = {1992}
}
@article{Levins66,
author = {Levins, R},
journal = {American Scientist},
number = {4},
pages = {421--431},
title = {{The strategy of model building in population biology}},
volume = {54},
year = {1966}
}
@article{Lewis2001,
abstract = {The costs to successfully restore both the vegetative cover and ecological functions of a mangrove forest have been reported to range from USD{\$}225/ha to USD{\$}216,000/ha. Unpublished data would indicate that the even higher costs, as much as USD{\$}500,000/ha, has been spent on individual projects. These are obviously cost prohibitive amounts for most countries seeking to restore damaged mangroves. I divide the types of mangrove restoration projects into three categories: (1) planting alone, (2) hydrologic restoration, with and without planting, and (3) excavation or fill, with and without planting. The first type, planting only, although inexpensive (e.g.: USD{\$}100-200/ha) usually does not succeed due to a failure to appreciate the physiological tolerances of mangroves to tidal inundation. Even if it works, the result is often replacement of one productive marine habitat, like seagrass meadows with mangroves, a questionable trade-off. The second type, hydrologic restoration, can be done for similar costs, and with proper planning has a high success rate. Successful restoration of abandoned shrimp aquaculture ponds is an example of this method. Planting should only be done if natural recolonization fails, and can double the cost of a project. Scientific data indicates that using this method, ecological functions are quickly restored, with fish populations typically reaching reference site diversity and densities within 5 years. The third type, excavation and fill, is the most expensive due to the high costs of large scale earthmoving. It is only a viable option in more 2 developed countries, and may not be a cost-effective means of restoration except under limited circumstances.},
author = {Lewis, R R},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2001{\_}Lewis{\_}mangrove{\_}restoration.pdf:pdf},
journal = {Proceedings of the Mangrove Valuation Workshop, Universiti Sains Malaysia, Penang, 4-8 April, 2001. Beijer International Institute of Ecological Economics, Stockholm, Sweden},
keywords = {2001,4-,8 april,and benefits of successful,beijer international institute of,ecological economics,in review,mangrove restoration - costs,penang,proceedings of the mangrove,stockholm,sweden,universiti sains malaysia,valuation workshop},
pages = {18p.--18p.},
title = {{Mangrove Restoration - Costs and Benefits of Successful Ecological Restoration}},
url = {http://www.fao.org/forestry/10560-0fe87b898806287615fceb95a76f613cf.pdf},
year = {2001}
}
@unpublished{Lewis2014,
abstract = {This manual is designed as a much enhanced update of a previous EMR Manual – which illustrated the 5 basic steps of Ecological Mangrove Rehabilitation, as set out by Roy “Robin” Lewis III of Florida (Lewis et al. 2006). The purpose of this manual is to provide practitioners with activities, tools and options to be used in assessing, designing, implementing and monitoring a mangrove rehabilitation project.},
author = {Lewis, R R and Brown, B},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2014{\_}Lewis{\_}ecological{\_}Mangrove.pdf:pdf},
pages = {151},
title = {{Ecological Mangrove Rehabilitation: A Field Manual for Practitioners}},
url = {http://www.mangroverestoration.com},
year = {2014}
}
@techreport{Lewis88,
author = {Lewis, R R and Estevez, E D},
institution = {US Fish and Wildlife Service, Washington DC, USA},
number = {Biological Report 85(7.18)},
title = {{The ecology of {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida: An estuarine profile}},
year = {1988}
}
@incollection{Lewis85,
address = {Tampa, Florida, USA},
author = {Lewis, R R and Whitman, R L},
booktitle = {Proceedings of the Tampa Bay Area Scientific Information Symposium},
editor = {Treat, S F and Simon, J L and Lewis, R R and Whitman, R L},
pages = {10--18},
publisher = {Florida Sea Grant Report No. 65, Bellwether Press},
title = {{A new geographic description of the boundaries and subdivisions of {\{}T{\}}ampa {\{}B{\}}ay}},
year = {1985}
}
@article{Lewis2005,
abstract = {Great potential exists to reverse the loss of mangrove forests worldwide through the application of basic principles of ecological restoration using ecological engineering approaches, including careful cost evaluations prior to design and construction. Previous documented attempts to restore mangroves, where successful, have largely concentrated on creation of plantations of mangroves consisting of just a few species, and targeted for harvesting as wood products, or temporarily used to collect eroded soil and raise intertidal areas to usable terrestrial agricultural uses. I document here the importance of assessing the existing hydrology of natural extant mangrove ecosystems, and applying this knowledge to first protect existing mangroves, and second to achieve successful and cost-effective ecological restoration, if needed. Previous research has documented the general principle that mangrove forests worldwide exist largely in a raised and sloped platform above mean sea level, and inundated at approximately 30{\%}, or less of the time by tidal waters. More frequent flooding causes stress and death of these tree species. Prevention of such damage requires application of the same understanding of mangrove hydrology. ?? 2005 Elsevier B.V. All rights reserved.},
author = {Lewis, Roy R},
doi = {10.1016/j.ecoleng.2004.10.003},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2005{\_}Lewis{\_}ecological{\_}engineering.pdf:pdf},
journal = {Ecological Engineering},
keywords = {Ecological restoration,Mangrove forests,Mangroves,Restoration of mangrove forests},
number = {4 SPEC. ISS.},
pages = {403--418},
title = {{Ecological engineering for successful management and restoration of mangrove forests}},
volume = {24},
year = {2005}
}
@article{Lewis2007,
abstract = {Mangrove forest restoration projects commonly fail to achieve significant plant cover for two reasons: because there is a misunderstanding of mangrove forest hydrology, or, acceptance of the false assumption that simply planting mangroves is all that is required to establish a fully-functional mangrove ecosystem. Even restoration projects that meet a restoration goal within 3–5 yrs often fail to provide adequate habitat for fish and invertebrates. Here we discuss how fish and mangrove ecosystems are coupled in time and space, offer several restoration strategies that match these couplings, and provide simple sequential checklist of design tasks to use to prevent most failures. Tidal hydrology must be carefully designed to incorporate fish habitat, including tidal creeks, to provide access and low tide refuge for mobile nekton because the mangrove forest floor is generally flooded by tidal waters less than 30 percent of the time. A fully successful restoration design must mimic tidal stream morphology and hydrology along an estuarine gradient across a heterogeneous mixture of mangrove ecosystem communities.},
author = {Lewis, Roy R and Gilmore, R Grant},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}Lewis{\_}important{\_}considerations.pdf:pdf},
journal = {Bulletin of Marine Science},
number = {3},
pages = {823--837},
title = {{Important considerations to achieve successful mangrove forest restoration with optimum fish habitat}},
volume = {80},
year = {2007}
}
@article{Li03,
author = {Li, R and Di, K and Ma, R},
journal = {Marine Geodesy},
number = {1-2},
pages = {107--115},
title = {{{\{}3-D{\}} shoreline extraction from {\{}IKONOS{\}} satellite imagery}},
volume = {26},
year = {2003}
}
@article{Liaw02,
author = {Liaw, Andy and Wiener, Matthew},
journal = {R News},
number = {3},
pages = {18--22},
title = {{Classification and Regression by randomForest}},
url = {http://cran.r-project.org/doc/Rnews/},
volume = {2},
year = {2002}
}
@manual{Castejon14,
annote = {R package version 0.2-15},
author = {Limas, Manuel Castej{\'{o}}n and Mer{\'{e}}, Joaquin B Ordieres and Marcos, Ana Gonz{\'{a}}lez and {de Pis{\'{o}}n Ascacibar}, Francisco Javier Martinez and Espinoza, Alpha V Pern{\'{i}}a and El{\'{i}}as, Fernando Alba and Ramos, Jose Maria Perez},
title = {{AMORE: A MORE flexible neural network package}},
url = {http://cran.r-project.org/package=AMORE},
year = {2014}
}
@article{Lipp01,
author = {Lipp, E K and Schmidt, N and Luther, M E and Rose, J B},
journal = {Estuaries and Coasts},
number = {4},
pages = {491--497},
title = {{Determining the effects of {\{}E{\}}l {\{}N{\}}i{\~{n}}o-{\{}S{\}}outhern {\{}O{\}}scillation events on coastal water quality}},
volume = {24},
year = {2001}
}
@article{Lipton03,
author = {Lipton, D and Hicks, R},
journal = {Estuaries},
number = {2A},
pages = {310--315},
title = {{The cost of stress: low dissolved oxygen and eocnomic benefits of recreational striped bass ($\backslash$textit{\{}Morone saxatilis{\}}) fishing in the {\{}P{\}}atuxent {\{}R{\}}iver}},
volume = {26},
year = {2003}
}
@article{Liu11,
author = {Liu, H and Wang, L and Sherman, D J and Wu, Q and Su, H},
journal = {Journal of Geographic Information System},
number = {2},
pages = {99--119},
title = {{Algorithmic foundation and software tools for extracting shoreline features from remote sensing imagery and {\{}LiDAR{\}} data}},
volume = {3},
year = {2011}
}
@article{Liu2017,
author = {Liu, Tingting. and Opaluch, James J. and Uchida, Emi},
doi = {10.1002/2016WR019606},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Liu{\_}et{\_}alWater{\_}Resources{\_}Research.pdf:pdf},
issn = {00431397},
journal = {Water Resources Research},
month = {aug},
number = {8},
pages = {6454--6471},
title = {{The impact of water quality in Narragansett Bay on housing prices}},
url = {http://doi.wiley.com/10.1002/2016WR019606},
volume = {53},
year = {2017}
}
@article{Logez13,
author = {Logez, M and Pont, D},
journal = {Hydrobiologia},
number = {1},
pages = {417--436},
title = {{Global warming and potential shift in reference conditions: The case of functional fish-based metrics}},
volume = {704},
year = {2013}
}
@article{Lohrenz08,
author = {Lohrenz, S E and Redalje, D G and Cai, W J and Acker, J and Dagg, M},
journal = {Continental Shelf Research},
number = {12},
pages = {1466--1475},
title = {{A retrospective analysis of nutrients and phytoplankton productivity in the {\{}M{\}}ississippi {\{}R{\}}iver plume}},
volume = {28},
year = {2008}
}
@article{Lorenz07,
author = {Lorenz, D L and Delin, G N},
journal = {Ground Water},
number = {2},
pages = {196--208},
title = {{A regression model to estimate regional ground water recharge}},
volume = {45},
year = {2007}
}
@article{Lottig14,
author = {Lottig, N R and Wagner, T and Henry, E N and Cheruvelil, K S and Webster, K E and Downing, J A and Stow, C A},
journal = {PLoS ONE},
number = {4},
pages = {1--8},
title = {{Long-term citizen-collected data reveal geographical patterns and temporal trends in water clarity}},
volume = {9},
year = {2014}
}
@article{Lougheed02,
author = {Lougheed, V L and Chow-Fraser, P C},
journal = {Ecological Applications},
number = {2},
pages = {474--486},
title = {{Development and use of a zooplankton index of wetland quality in the {\{}L{\}}aurentian {\{}G{\}}reat {\{}L{\}}akes basin}},
volume = {12},
year = {2002}
}
@article{Lung03,
author = {Lung, W and Bai, S},
journal = {Estuaries},
number = {2A},
pages = {267--279},
title = {{A water quality model for the {\{}P{\}}atuxent estuary: Current conditions and predictions under changing land-use scenarios}},
volume = {26},
year = {2003}
}
@article{MacNally10,
author = {{Mac Nally}, R and Thompson, J R and Kimmerer, W J and Feyrer, F and Newman, K B and Sih, A and Bennett, W A and Brown, L and Fleishman, E and Culberson, S D and Castillo, G},
journal = {Ecological Applications},
number = {5},
pages = {1417--1430},
title = {{Analysis of pelagic species decline in the upper {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary using multivariate autoregressive modeling ({\{}MAR{\}})}},
volume = {20},
year = {2010}
}
@article{Mackay03,
author = {Mackay, S J and Arthington, A H and Kennard, M J and Pusey, B J},
journal = {Aquatic Botany},
pages = {169--186},
title = {{Spatial variation in the distribution and abundance of submersed macrophytes in an {\{}A{\}}ustralian subtropical river}},
volume = {77},
year = {2003}
}
@article{Mackay10,
author = {Mackay, S J and James, C S and Arthington, A H},
journal = {Ecological Indicators},
pages = {330--340},
title = {{Macrophytes as indicators of stream condition in the wet tropics region, {\{}N{\}}orthern {\{}Q{\}}ueensland, {\{}A{\}}ustralia}},
volume = {10},
year = {2010}
}
@techreport{Madsen99,
author = {Madsen, J D},
institution = {U.S. Army Engineer Center, Vicksburg, Missouri},
number = {TN APCRP-M1-02, APCRP Technical notes collection},
title = {{Point intercept and line intercept methods for aquatic plant management}},
year = {1999}
}
@article{Madsen97,
author = {Madsen, T V and Brix, H},
journal = {Oecologia},
number = {3},
pages = {320--327},
title = {{Growth, photosynthesis and acclimation by two submerged macrophytes in relation to temperature}},
volume = {110},
year = {1997}
}
@misc{Maechler05,
annote = {$\backslash$url{\{}http://CRAN.R-project.org/package=cluster{\}}},
author = {Maechler, M and Rousseeuw, P and Struyf, A and Hubert, M},
title = {{Cluster analysis and basics and extensions, {\{}R{\}} package.}},
year = {2005}
}
@article{Maier00,
author = {Maier, H R and Dandy, G C},
journal = {Environmental Modelling and Software},
number = {1},
pages = {101--124},
title = {{Neural networks for the prediction and forecasting of water resources variables: A review of modelling issues and applications}},
volume = {15},
year = {2000}
}
@article{Makela04,
author = {M{\"{a}}kel{\"{a}}, S and Huitu, E and Arvola, L},
journal = {Aquatic Botany},
pages = {253--269},
title = {{Spatial patterns in aquatic vegetation composition and environmental covariates along chains of lakes in the {\{}K{\}}okem{\"{a}}enjoki watershed ({\{}S{\}}. {\{}F{\}}inland)}},
volume = {80},
year = {2004}
}
@article{Malloy2007,
abstract = {The identification, remedial treatment, and monitoring of contaminated sediments are among the priorities for managers of the Tampa Bay Estuary. Tampa Bay, as an urbanized estuary, is subject to the input of watershed sources of chemical contaminants, including metals, pesticides, and organic chemicals. Although the use of biological indicators and their incorporation into multi-metric indices is not new, the refinement and applications of such techniques for determining environmental condition still require further development and exploration. We present a single Tampa Bay Benthic Index (TBBI) that was developed specifically for Tampa Bay. Stepwise discriminant analysis was applied to a comprehensive list of potential benthic metrics. Results from the stepwise procedure identified the metrics that best discriminated between "healthy" and "degraded" conditions, as defined by sediment contaminant effect levels and dissolved oxygen. Discriminant analysis was then applied to the resultant three variables to determine the linear combination for the index. {\textcopyright} 2006 Elsevier Ltd. All rights reserved.},
author = {Malloy, Kate J and Wade, David and Janicki, Anthony and Grabe, Stephen A and Nijbroek, Ravic},
doi = {10.1016/j.marpolbul.2006.06.011},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}Malloy{\_}development{\_}of.pdf:pdf},
journal = {Marine Pollution Bulletin},
keywords = {Benthic index,Biological indicators,Hypoxia,Sediment quality,Tampa Bay},
number = {1},
pages = {22--31},
title = {{Development of a benthic index to assess sediment quality in the Tampa Bay Estuary}},
volume = {54},
year = {2007}
}
@article{Manolakos07,
author = {Manolakos, E and Virani, H and Novotny, V},
journal = {Water Research},
pages = {4041--4050},
title = {{Extracting knowledge on the links between the water body stressors and biotic integrity}},
volume = {41},
year = {2007}
}
@article{Mantel67,
author = {Mantel, N},
journal = {Cancer Research},
number = {1},
pages = {209--220},
title = {{The detection of disease clustering and a generalized regression approach}},
volume = {27},
year = {1967}
}
@article{Maravelias03,
author = {Maravelias, C D and Haralabous, J and Papaconstantinou, C},
journal = {Marine Ecology Progress Series},
pages = {249--258},
title = {{Predicting demersal fish species distributions in the {\{}M{\}}editerranean {\{}S{\}}ea using artificial neural networks}},
volume = {255},
year = {2003}
}
@article{Marburg06,
author = {Marburg, A E and Turner, M G and Kratz, T K},
journal = {Journal of Ecology},
number = {3},
pages = {558--568},
title = {{Natural and anthropogenic variation in coarse wood among and within lakes}},
volume = {94},
year = {2006}
}
@techreport{Martin00,
address = {Mississippi},
author = {Martin, P J},
institution = {Naval Research Lab, Stennis Space Center},
number = {NRL/FR/7322-00-9962},
title = {{Description of the navy coastal ocean model version 1.0}},
year = {2000}
}
@article{Mateus15,
author = {Mateus, M D and Franz, G},
journal = {Water},
pages = {2060--2081},
title = {{Sensitivity analysis in a complex marine ecological model}},
volume = {7},
year = {2015}
}
@article{May03,
author = {May, C L and Koseff, J R and Lucas, L V and Cloern, J E and Schoellhamer, D H},
journal = {Marine Ecology Progress Series},
pages = {111--128},
title = {{Effects of spatial and temporal variability of turbidity on phytoplankton blooms}},
volume = {254},
year = {2003}
}
@article{Mazor16,
author = {Mazor, R D and Rehn, A C and Ode, P R and Engeln, M and Schiff, K C and Stein, E D and Gillett, D J and Herbst, D B and Hawkins, C P},
journal = {Freshwater Science},
number = {1},
pages = {249--271},
title = {{Bioassessment in complex environments: designing an index for consistent meaning in different settings}},
volume = {35},
year = {2016}
}
@article{McCormick01,
author = {McCormick, F H and Hughes, R M and Kaufmann, P R and Peck, D V and Stoddard, J L and Herlihy, A T},
journal = {Transactions of the American Fisheries Society},
number = {5},
pages = {857--877},
title = {{Development of an index of biotic integrity for the {\{}M{\}}id-{\{}A{\}}tlantic {\{}H{\}}ighlands region}},
volume = {130},
year = {2001}
}
@book{McCullagh89,
address = {London, United Kingdom},
author = {McCullagh, P and Nelder, J},
edition = {second},
pages = {532},
publisher = {Chapman and Hall},
title = {{Generalized Linear Models}},
year = {1989}
}
@article{McCulloch43,
author = {McCulloch, W S and Pitts, W},
journal = {Bulletin of Mathematical Biophysics},
pages = {115--133},
title = {{A logical calculus of the ideas imminent in nervous activity}},
volume = {5},
year = {1943}
}
@book{McCune02,
address = {Gleneden Beach, Oregon},
author = {McCune, B and Grace, J B},
publisher = {MjM Software Design},
title = {{Analysis of Ecological Communities}},
year = {2002}
}
@article{McKenna05,
author = {McKenna, J E},
journal = {Transactions of the American Fisheries Society},
number = {1},
pages = {28--43},
title = {{Application of neural networks to prediction of fish diversity and salmonid production in the {\{}L{\}}ake {\{}O{\}}ntario basin}},
volume = {134},
year = {2005}
}
@manual{McLeod14,
annote = {R package version 0.1-41},
author = {McLeod, A I and Mohammad, Nagham M and Veenstra, Justin and El-Shaarawi, Abdel},
title = {{cents: Censored time series}},
url = {http://cran.r-project.org/package=cents},
year = {2014}
}
@article{Medalie12,
author = {Medalie, L and Hirsch, R M and Archfield, S A},
journal = {Journal of Great Lakes Research},
number = {SI},
pages = {58--67},
title = {{Use of flow-normalization to evaluate nutrient concentration and flux changes in {\{}L{\}}ake {\{}C{\}}hamplain tributaries, 1990-2009}},
volume = {38},
year = {2012}
}
@article{Meinshausen06,
author = {Meinshausen, N},
journal = {Journal of Machine Learning Research},
pages = {983--999},
title = {{Quantile regression forests}},
volume = {7},
year = {2006}
}
@manual{Meinshausen17,
annote = {R package version 1.3-7},
author = {Meinshausen, Nicolai},
title = {{quantregForest: Quantile Regression Forests}},
url = {https://cran.r-project.org/package=quantregForest},
year = {2017}
}
@article{Melzer99,
author = {Melzer, A},
journal = {Hydrobiologia},
pages = {181--190},
title = {{Aquatic macrophytes as tools for lake management}},
volume = {395/396},
year = {1999}
}
@misc{MGDC07,
annote = {$\backslash$url{\{}http://geogateway.state.mn.us/documents/{\}}. (Accessed January, 2009)},
author = {{MGDC (Minnesota Geographic Data Clearinghouse)}},
title = {{Regional ground water recharge estimates for {\{}M{\}}innesota}},
year = {2007}
}
@article{Michener12,
author = {Michener, W K and Jones, M B},
journal = {Trends in Ecology and Evolution},
number = {2},
pages = {85--93},
title = {{Ecoinformatics: supporting ecology as a data-intensive science}},
volume = {27},
year = {2012}
}
@article{Mikulyuk11,
author = {Mikulyuk, A and Sharma, S and {Van Egeren}, S and Erdmann, E and Nault, M E and Hauxwell, J},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {10},
pages = {1778--1789},
title = {{The relative role of environmental, spatial, and land-use patterns in explaining aquatic macrophyte community composition}},
volume = {68},
year = {2011}
}
@techreport{Milburn07,
address = {St. Paul, Minnesota},
author = {Milburn, S A and Bourdaghs, M and Husveth, J J},
institution = {Minnesota Pollution Control Agency},
number = {wq-bwm2-01},
title = {{Floristic quality assessment for {\{}M{\}}innesota wetlands}},
url = {http://www.pca.state.mn.us/index.php/view-document.html?gid=13346},
year = {2007}
}
@book{Millard13,
address = {New York},
author = {Millard, Steven P},
isbn = {978-1-4614-8455-4},
publisher = {Springer},
title = {{EnvStats: An R Package for Environmental Statistics}},
url = {http://www.springer.com},
year = {2013}
}
@article{Miller88,
author = {Miller, D L and Leonard, P M and Hughes, R M and Karr, J R and Moyle, P B and Schrader, L H and Thompson, B A and Daniels, R A and Fausch, K D and Fitzhugh, G A and Gammon, J R and Halliwell, D B and Angermeier, P L and Orth, D J},
journal = {Fisheries},
number = {5},
pages = {12--20},
title = {{Regional applications of an index of biotic integrity for use in water resource management}},
volume = {13},
year = {1988}
}
@article{Miller06,
author = {Miller, S J and Wardrop, D H and Mahaney, W M and Brooks, R R},
journal = {Ecological Indicators},
number = {2},
pages = {290--312},
title = {{A plant-based index of biological integrity ({\{}IBI{\}}) for headwater wetlands in central {\{}P{\}}ennsylvania}},
volume = {6},
year = {2006}
}
@article{Millie13,
author = {Millie, D F and Weckman, G R and Young, W A and Ivey, J E and Fries, D P and Ardjmand, E and Fahnenstiel, G L},
journal = {Estuarine, Coastal and Shelf Science},
pages = {57--67},
title = {{Coastal `big data' and nature-inspired computation: prediction potentials, uncertainties, and knowledge derivation of neural networks for an algal metric}},
volume = {125},
year = {2013}
}
@article{Milligan89,
author = {Milligan, G W},
journal = {Multivariate Behavioral Research},
pages = {163--176},
title = {{A study of the beta-flexible clustering method}},
volume = {24},
year = {1989}
}
@article{Minns94,
author = {Minns, C K and Cairns, V W and Randall, R G and Moore, J E},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {8},
pages = {1804--1822},
title = {{An index of biotic integrity ({\{}IBI{\}}) for fish assemblages in the littoral zone of {\{}G{\}}reat {\{}L{\}}akes' areas of concern}},
volume = {51},
year = {1994}
}
@phdthesis{Mizak2004,
author = {Mizak, C A},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2004{\_}Mizak{\_}Ammonia{\_}Flux.pdf:pdf},
keywords = {atmospheric deposition,estuary,eutrophication,micrometeorology,modeling},
pages = {225},
title = {{Ammonia Flux at the Air/Water Interface of Tampa Bay}},
year = {2004}
}
@unpublished{Mizak2006,
author = {Mizak, Connie and Tate, Paul and Begum, Mubeena and Poor, Noreen},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}AE{\_}Mizak{\_}Poor{\_}2006.pdf:pdf},
keywords = {Ammonium sulfate,Emission density,Emission inventory,Sulfur dioxide},
pages = {23},
title = {{Atmospheric Ammonia (NH3) and Ammonium (NH4+) Concentrations in a Subtropical, Coastal Urban Environment}},
year = {2006}
}
@misc{MNDNR12a,
annote = {$\backslash$url{\{}http://deli.dnr.state.mn.us/{\}}. (Accessed January, 2010)},
author = {{MNDNR (Minnesota Department of Natural Resources)}},
title = {{MNDNR Data Deli}},
year = {2012}
}
@misc{MNDNR12b,
annote = {$\backslash$url{\{}http://www.dnr.state.mn.us/shorelandmgmt/apg/regulations.html{\}}. (Accessed June, 2012)},
author = {{MNDNR (Minnesota Department of Natural Resources)}},
title = {{Shoreland Management: Aquatic Plant Regulations}},
year = {2012}
}
@misc{MNDNR11,
annote = {$\backslash$url{\{}http://files.dnr.state.mn.us/publications/waters/shoreline{\_}alterations{\_}water{\_}access.pdf{\}}. (Accessed June, 2012)},
author = {{MNDNR (Minnesota Department of Natural Resources)}},
title = {{Docks and Access in Public Waters}},
year = {2011}
}
@techreport{MNDOC02,
address = {St. Paul, Minnesota},
author = {{MNDOC (Minnesota Department of Commerce)}},
institution = {Minnesota Department of Commerce},
title = {{14th Wind Resource Analysis Program Report}},
year = {2002}
}
@misc{MNGEO13,
annote = {$\backslash$url{\{}http://www.mngeo.state.mn.us/chouse/{\}}. (Accessed July, 2012)},
author = {{MnGeo (Minnesota Geospatial Information Office)}},
title = {{Minnesota Geographic Data Clearinghouse}},
year = {2013}
}
@misc{MNPCA12,
address = {St. Paul, Minnesota},
annote = {$\backslash$url{\{}http://www.pca.state.mn.us/index.php/water/{\}}. (Accessed January, 2010)},
author = {{MNPCA (Minnesota Pollution Control Agency)}},
title = {{Minnesota Pollution Control Agency, Surface Water Data Submittal, Review, and Reports}},
year = {2012}
}
@article{Molloy09,
author = {Molloy, J C},
journal = {{\{}PLoS{\}} Biology},
number = {12},
pages = {1--4},
title = {{The {\{}O{\}}pen {\{}K{\}}nowledge {\{}F{\}}oundation: open data means better science}},
volume = {9},
year = {2009}
}
@article{Monbet92,
author = {Monbet, Y},
journal = {Estuaries},
number = {4},
pages = {563--571},
title = {{Control of phytoplankton biomass in estuaries: A comparative analysis of microtidal and macrotidal estuaries}},
volume = {15},
year = {1992}
}
@book{Montgomery92,
address = {New York, New York},
author = {Montgomery, D C and Peck, E A},
pages = {504},
publisher = {Wiley},
title = {{Introduction to Linear Regression Analysis}},
year = {1992}
}
@article{Montgomery95,
author = {Montgomery, D R and Grant, G E and Sullivan, K},
journal = {Water Resources Bulletin},
number = {3},
pages = {369--386},
title = {{Watershed analysis as a framework for implementing ecosystem management}},
volume = {31},
year = {1995}
}
@article{Moore12,
author = {Moore, M J C and Langrehr, H A and Angradi, T R},
journal = {Ecological Indicators},
pages = {196--205},
title = {{A submersed macrophyte index of condition for the {\{}U{\}}pper {\{}M{\}}ississippi river}},
volume = {13},
year = {2012}
}
@article{Morandi2017,
abstract = {River restoration is a main emphasis of river management in European countries. Cross-national com-parisons of its implementation are still rare in scientific literature. Based on French and German national censuses, this study compares river restoration practices and mon-itoring by analysing 102 French and 270 German projects. This comparison aims to draw a spatial and temporal fra-mework of restoration practices in both countries to identify potential drivers of cross-national similarities and differ-ences. The results underline four major trends: (1) a lag of almost 15 years in river restoration implementation between France and Germany, with a consequently higher share of projects in Germany than in France, (2) substantial simila-rities in restored reach characteristics, short reach length, small rivers, and in " agricultural " areas, (3) good corre-spondences between stressors identified and restoration measures implemented. Morphological alterations were the most important highlighted stressors. River morphology enhancement, especially instream enhancements, were the most frequently implemented restoration measures. Some differences exist in specific restoration practices, as river continuity restoration were most frequently implemented in French projects, while large wood introduction or channel re-braiding were most frequently implemented in German projects, and (4) some quantitative and qualitative differ-ences in monitoring practices and a significant lack of project monitoring, especially in Germany compared to France. These similarities and differences between Ger-many and France in restoration application and monitoring possibly result from a complex set of drivers that might be difficult to untangle (e.g., environmental, technical, poli-tical, cultural).},
author = {Morandi, Bertrand and Kail, Jochem and Toedter, Anne and Wolter, Christian and Pi{\'{e}}gay, Herv{\'{e}}},
doi = {10.1007/s00267-017-0923-3},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Morandi{\_}etal{\_}Diverse{\_}approaches.pdf:pdf},
isbn = {0026701709233},
issn = {14321009},
journal = {Environmental Management},
keywords = {France,Germany,Hydromorphologic alteration,Mitigation measures,Project monitoring,River restoration},
number = {5},
pages = {931--946},
publisher = {Springer US},
title = {{Diverse Approaches to Implement and Monitor River Restoration: A Comparative Perspective in France and Germany}},
url = {http://dx.doi.org/10.1007/s00267-017-0923-3},
volume = {60},
year = {2017}
}
@article{Morgan05,
author = {Morgan, R P and Cushman, S E},
journal = {Journal of the North American Benthological Society},
number = {3},
pages = {643--655},
title = {{Urbanization effects on stream fish assemblages in {\{}M{\}}aryland, {\{}USA{\}}}},
volume = {24},
year = {2005}
}
@article{Morrison06,
author = {Morrison, G and Sherwood, E T and Boler, R and Barron, J},
doi = {10.1007/BF02798652},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}Morrison{\_}Variations{\_}in{\_}WQ.pdf:pdf},
issn = {1559-2723},
journal = {Estuaries and Coasts},
month = {dec},
number = {6},
pages = {926--931},
title = {{Variations in water clarity and chlorophylla in Tampa Bay, Florida, in response to annual rainfall, 1985–2004}},
url = {http://link.springer.com/10.1007/BF02798652},
volume = {29},
year = {2006}
}
@incollection{Morrison99,
address = {Cambridge University Press, Cambridge},
author = {Morrison, M and Morgan, M S},
booktitle = {Models as Mediators},
editor = {Morgan, M S and Morrison, M},
pages = {401},
title = {{Models as mediating agents}},
year = {1999}
}
@article{Moss03,
author = {Moss, B and Stephen, D and Alvarez, C and Becares, E and de Bund, W Van and Collings, S E and Donk, E Van and Eyto, E De and Feldmann, T and Alaez-Fernandez, C and Alaez-Fernandez, M and Franken, R J M and Garcia-Criado, F and Gross, E M and Gyllstrom, M and Hansson, L A and Irvine, K and Jarvalt, A and Jensen, J P and Jeppesen, E and Kairesalo, T and Kornijow, R and Krause, T and Kunnap, H and Laas, A and Lille, E and Lorens, B and Luup, H and Miracle, M R and Noges, P and Noges, T and Nykanen, M and Ott, I and Peczula, W and Peeters, E T H M and Phillips, G and Romo, S and Russell, V and Salujoe, J and Scheffer, M and Siewertsen, K and Smal, H and Tesch, C and Timm, H and Tuvikene, L and Tonno, I and Virro, T and Vicente, E and Wilson, D},
journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
pages = {507--549},
title = {{A tested system ({\{}ECOFRAME{\}}) for implementation of the {\{}E{\}}uropean {\{}W{\}}ater {\{}F{\}}ramework {\{}D{\}}irective}},
volume = {13},
year = {2003}
}
@techreport{Moyer12,
address = {Reston, Virginia},
author = {Moyer, D L and Hirsch, R M and Hyer, K E},
institution = {US Geological Survey, US Department of the Interior},
number = {Scientific Investigations Report 2012-544},
pages = {118},
title = {{Comparison of two regression-based approaches for determining nutrient and sediment fluxes and trends in the {\{}C{\}}hesapeake {\{}B{\}}ay Watershed}},
year = {2012}
}
@article{Moyle56,
author = {Moyle, J B},
journal = {The Journal of Wildlife Management},
number = {3},
pages = {303--320},
title = {{Relationships between the chemistry of {\{}M{\}}innesota surface waters and wildlife management}},
volume = {20},
year = {1956}
}
@article{Moyle45,
author = {Moyle, J B},
journal = {American Midland Naturalist},
number = {2},
pages = {402--420},
title = {{Some chemical factors influencing the distribution of aquatic plants in {\{}M{\}}innesota}},
volume = {34},
year = {1945}
}
@techreport{Murrell14,
address = {Washington, DC},
author = {Murrell, M C and Beddick, D L and Devereux, R and Greene, R M and {Hagy III}, J D and Jarvis, B M and Kurtz, J C and Lehrter, J C and Yates, D F},
institution = {US Environmental Protection Agency},
number = {EPA/600/R-13/257},
title = {{Gulf of Mexico hypoxia research program data report: 2002-2007}},
year = {2014}
}
@article{Murrell09,
author = {Murrell, M C and Campbell, J G and Hagy, J D and Caffrey, J M},
journal = {Estuarine, Coastal and Shelf Science},
pages = {501--512},
title = {{Effects of irradiance on benthic and water column processes in a {\{}G{\}}ulf of {\{}M{\}}exico estuary: {\{}P{\}}ensacola {\{}B{\}}ay, {\{}F{\}}lorida, {\{}USA{\}}}},
volume = {81},
year = {2009}
}
@article{Murrell07,
author = {Murrell, M C and Hagy, J D and Lores, E M and Greene, R M},
journal = {Estuaries and Coasts},
number = {3},
pages = {390--402},
title = {{Phytoplankton production and nutrient distributions in a subtropical esuary: Importance of freshwater flow}},
volume = {30},
year = {2007}
}
@article{Murrell13,
author = {Murrell, M C and Stanley, R S and Lehrter, J C and Hagy, J D},
journal = {Continental Shelf Research},
pages = {27--38},
title = {{Plankton community respiration, net ecosystem metabolism, and oxygen dynamics on the {\{}L{\}}ouisiana continental shelf: Implications for hypoxia}},
volume = {52},
year = {2013}
}
@article{MurrellIR,
abstract = {Seasonal responses in estuarine metabolism (primary production, respiration, and net metabolism) were examined using two complementary approaches. Total ecosystem metabolism rates were calculated from dissolved oxygen time series using Odum's open water method. Water column rates were calculated from oxygen-based bottle experiments. The study was conducted over a spring-summer season in the Pensacola Bay estuary at a shallow seagrass-dominated site and a deeper bare-bottomed site. Water column integrated gross production rates more than doubled (58.7 to 130.9 mmol O2 m−2 day−1) from spring to summer, coinciding with a sharp increase in water column chlorophyll-a, and a decrease in surface salinity. As expected, ecosystem gross production rates were consistently higher than water column rates but showed a different spring-summer pattern, decreasing at the shoal site from 197 to 168 mmol O2 m−2 day−1 and sharply increasing at the channel site from 93.4 to 197.4 mmol O2 m−2 day−1. The consistency among approaches was evaluated by calculating residual metabolism rates (ecosystem − water column). At the shoal site, residual gross production rates decreased from spring to summer from 176.8 to 99.1 mmol O2 m−2 day−1 but were generally consistent with expectations for seagrass environments, indicating that the open water method captured both water column and benthic processes. However, at the channel site, where benthic production was strongly light-limited, residual gross production varied from 15.7 mmol O2 m−2 day−1 in spring to 86.7 mmol O2 m−2 day−1 in summer. The summer rates were much higher than could be realistically attributed to benthic processes and likely reflected a violation of the open water method due to water column stratification. While the use of sensors for estimating complex ecosystem processes holds promise for coastal monitoring programs, careful attention to the sampling design, and to the underlying assumptions of the methods, is critical for correctly interpreting the results. This study demonstrated how using a combination of approaches yielded a fuller understanding of the ecosystem response to hydrologic and seasonal variability.},
author = {Murrell, Michael C and Caffrey, Jane M. and Marcovich, Dragoslav T and Beck, Marcus W and Jarvis, Brandon M and Hagy, James D.},
doi = {10.1007/s12237-017-0328-9},
issn = {1559-2723},
journal = {Estuaries and Coasts},
keywords = {Dissolved oxygen,Estuary,Net ecosystem metabolism,Plankton community respiration,Primary production},
month = {sep},
number = {3},
pages = {690--707},
title = {{Seasonal Oxygen Dynamics in a Warm Temperate Estuary: Effects of Hydrologic Variability on Measurements of Primary Production, Respiration, and Net Metabolism}},
url = {http://link.springer.com/10.1007/s12237-017-0328-9},
volume = {41},
year = {2017}
}
@book{NRC90,
address = {Washington, DC},
author = {{National Research Council}},
pages = {136},
publisher = {National Academy Press},
title = {{Managing Troubled Waters: The Role of Environmental Monitoring}},
year = {1990}
}
@misc{HADS15,
annote = {$\backslash$url{\{}http://www.nws.noaa.gov/oh/hads/{\}}. (Accessed March, 2015)},
author = {{National Weather Service}, National Oceanic and Administration, Atmospheric},
title = {{Hydrometeorological Automated Data System website}},
year = {2015}
}
@misc{NDBC15,
annote = {$\backslash$url{\{}http://www.ndbc.noaa.gov/{\}}. (Accessed March, 2015)},
author = {{NDBC (National Data Buoy Center)}},
title = {{National Oceanic and Atmospheric Administration's National Data Buoy Center}},
year = {2015}
}
@article{Neckles12,
author = {Neckles, H A and Kopp, B S and Peterson, B J and Pooler, P S},
journal = {Estuaries and Coasts},
number = {1},
pages = {23--46},
title = {{Integrating scales of seagrass monitoring to meet conservation needs}},
volume = {35},
year = {2012}
}
@incollection{Needoba12,
address = {New York},
author = {Needoba, J A and Peterson, T D and Johnson, K S},
booktitle = {Molecular Biological Technologies for Ocean Sensing},
editor = {Tiquia-Arashiro, S M},
pages = {73--101},
publisher = {Springer-Verlag},
title = {{Method for the quantification of aquatic primary production and net ecosystem metabolism using in situ dissolved oxygen sensors}},
year = {2012}
}
@article{Nelder77,
author = {Nelder, J A},
journal = {Journal of the Royal Statistical Society},
number = {1},
pages = {48--77},
title = {{A reformulation of linear models}},
volume = {140},
year = {1977}
}
@article{Nerem2018,
abstract = {Using a 25-y time series of precision satellite altimeter data from TOPEX/Poseidon, Jason-1, Jason-2, and Jason-3, we estimate the climate-change-driven acceleration of global mean sea level over the last 25 y to be 0.084 ± 0.025 mm/y2Coupled with the average climate-change-driven rate of sea level rise over these same 25 y of 2.9 mm/y, simple extrapolation of the quadratic implies global mean sea level could rise 65 ± 12 cm by 2100 compared with 2005, roughly in agreement with the Intergovernmental Panel on Climate Change (IPCC) 5th Assessment Report (AR5) model projections.},
author = {Nerem, R. S. and Beckley, B. D. and Fasullo, J. T. and Hamlington, B. D. and Masters, D. and Mitchum, G. T.},
doi = {10.1073/pnas.1717312115},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2018{\_}Mitchum{\_}SLR{\_}Satellite{\_}Acceleration.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
pages = {201717312},
pmid = {29440401},
title = {{Climate-change–driven accelerated sea-level rise detected in the altimeter era}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1717312115},
volume = {0},
year = {2018}
}
@article{Newall00,
author = {Newall, P and Wells, F},
journal = {Journal of the North American Benthological Society},
number = {3},
pages = {557--571},
title = {{Potential for delineating indicator-defined regions for streams in {\{}V{\}}ictoria, {\{}A{\}}ustralia}},
volume = {19},
year = {2000}
}
@article{Nichols85,
author = {Nichols, F H},
journal = {Estuarine, Coastal and Shelf Science},
number = {3},
pages = {379--388},
title = {{Increased benthic grazing: An alternative explanation for low phytoplankton biomass in northern {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay during the 1976-1977 drought}},
volume = {21},
year = {1985}
}
@article{Nichols90,
author = {Nichols, F H and Thompson, J K and Schemel, L E},
journal = {Marine Ecology Progress Series},
number = {1-2},
pages = {95--101},
title = {{Remarkable invasion of {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay ({\{}C{\}}alifornia, {\{}USA{\}}) by the {\{}A{\}}sian claim $\backslash$textit{\{}Potamocorbula amurensis{\}}. {\{}II.{\}} {\{}D{\}}isplacement of a former community}},
volume = {66},
year = {1990}
}
@article{Nichols99,
author = {Nichols, S},
journal = {Journal of Lake and Reservoir Management},
number = {2},
pages = {133--141},
title = {{Floristic quality assessment of {\{}W{\}}isconsin lake plant communities with example applications}},
volume = {15},
year = {1999}
}
@article{Nichols00,
author = {Nichols, S and Weber, S and Shaw, B},
journal = {Environmental Management},
number = {5},
pages = {491--502},
title = {{A proposed aquatic plant community biotic index for {\{}W{\}}isconsin lakes}},
volume = {26},
year = {2000}
}
@article{Nidzieko14,
author = {Nidzieko, N J and Needoba, J A and Monismith, S G and Johnson, K S},
journal = {Estuaries and Coasts},
number = {1},
pages = {91--110},
title = {{Fortnightly tidal modulations affect net community production in a mesotidal estuary}},
volume = {37},
year = {2014}
}
@techreport{Niemela02,
address = {St. Paul, Minnesota},
author = {Niemela, S and Feist, M},
institution = {Biological Monitoring Program, Minnesota Pollution Control Agency},
pages = {56},
title = {{{\{}I{\}}ndex of {\{}B{\}}iotic {\{}I{\}}ntegrity ({\{}IBI{\}}) guidance for coolwater rivers and streams of the {\{}U{\}}pper {\{}M{\}}ississippi river basin in {\{}M{\}}innesota}},
year = {2002}
}
@techreport{Niemela00,
address = {St. Paul, Minnesota},
author = {Niemela, S and Feist, M},
institution = {Biological Monitoring Program, Minnesota Pollution Control Agency},
pages = {47},
title = {{{\{}I{\}}ndex of {\{}B{\}}iotic {\{}I{\}}ntegrity ({\{}IBI{\}}) guidance for coolwater rivers and streams of the {\{}S{\}}t. {\{}C{\}}roix river basin in {\{}M{\}}innesota}},
year = {2000}
}
@article{Niemi04,
author = {Niemi, G J and McDonald, M E},
journal = {Annual Review of Ecology, Evolution, and Systematics},
pages = {89--111},
title = {{Application of ecological indicators}},
volume = {35},
year = {2004}
}
@article{Nisbet14,
author = {Nisbet, E G and Dlugokencky, E J and Bousquet, P},
journal = {Science},
number = {6170},
pages = {493--495},
title = {{Methane on the rise -- again}},
volume = {343},
year = {2014}
}
@article{Nixon95,
author = {Nixon, S W},
journal = {Ophelia},
pages = {199--219},
title = {{Coastal marine eutrophication: A definition, social causes, and future concerns}},
volume = {41},
year = {1995}
}
@book{Nocedal06,
address = {New York, New York},
author = {Nocedal, J and Wright, S J},
edition = {2nd},
pages = {664},
publisher = {Springer-Verlag},
title = {{Numerical Optimization}},
year = {2006}
}
@article{Norton00,
author = {Norton, S B and Cormier, S M and Smith, M and Jones, R C},
journal = {Environmental Toxicology and Chemistry},
number = {4},
pages = {1113--1119},
title = {{Can biological assessments discriminate among types of stress? {\{}A{\}} case study from the {\{}E{\}}astern {\{}C{\}}orn {\{}B{\}}elt {\{}P{\}}lains ecoregion}},
volume = {19},
year = {2000}
}
@article{Nossent12,
author = {Nossent, J and Bauwens, W},
journal = {Water Science {\&} Technology},
number = {3},
pages = {539--549},
title = {{Multi-variable sensitivity and identifiability analysis for a complex environmental model in view of integrated water quantity and water quality modeling}},
volume = {65},
year = {2012}
}
@techreport{Novick15,
address = {Richmond, CA},
author = {Novick, E and Holleman, R and Jabusch, T and Sun, J and Trowbridge, P and Senn, D and Guerin, M and Kendall, C and Young, M and Peek, S},
institution = {San Francisco Estuary Institute},
number = {Contribution Number 785},
title = {{Characterizing and quantifying nutrient sources, sinks and transformations in the {\{}D{\}}elta: synthesis, modeling, and recommendations for monitoring}},
url = {http://www.sfei.org/documents/characterizing-and-quantifying-nutrient-sources-sinks-and-transformations-delta-synthesis},
year = {2015}
}
@techreport{Novick14,
address = {Richmond, CA},
author = {Novick, E and Senn, D},
institution = {San Francisco Estuary Institute},
number = {Contribution Number 704},
title = {{External nutrient loads to {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
url = {http://www.sfei.org/sites/default/files/biblio{\_}files/NutrientLoadsFINAL{\_}FINAL{\_}Jan232014{\_}0.pdf},
year = {2014}
}
@article{Novotny05,
author = {Novotny, V and Barto$\backslash$usov{\'{a}}, A and O'Reilly, N and Ehlinger, T},
doi = {10.1016/j.watres.2004.09.002},
journal = {Water Research},
number = {1},
pages = {184--198},
title = {{Unlocking the relationship of biotic integrity of impaired waters to anthropogenic stresses}},
volume = {39},
year = {2005}
}
@article{Novotny09,
author = {Novotny, V and Bedoya, D and Virani, H and Manolakos, E},
journal = {Water Science and Technology},
number = {1},
pages = {1--8},
title = {{Linking indices of biotic integrity to environmental and land use variables: Multimetric clustering and predictive models}},
volume = {59},
year = {2009}
}
@book{NRC00,
address = {Washington, DC},
author = {{NRC (National Research Council}},
pages = {405},
publisher = {National Academy Press},
title = {{Clean Coastal Waters: Understanding and Reducing the Effects of Nutrient Pollution}},
year = {2000}
}
@misc{NRCS10,
annote = {Soil Survey Staff, Natural Resource Conservation Service, US Department of Agriculture. $\backslash$url{\{}http://soildatamart.nrcs.usda.gov/{\}}. (Accessed January, 2010)},
author = {{NRCS (Natural Resource Conservation Service)}},
title = {{Soil {\{}S{\}}urvey {\{}G{\}}eographic ({\{}SSURGO{\}}) {\{}D{\}}atabase for {\{}M{\}}innesota}},
year = {2010}
}
@misc{NRCS06,
annote = {Soil Survey Staff, Natural Resource Conservation Service, US Department of Agriculture. $\backslash$url{\{}http://soildatamart.nrcs.usda.gov/{\}}. (Accessed January, 2010)},
author = {{NRCS (Natural Resource Conservation Service)}},
title = {{U{\{}S{\}} {\{}G{\}}eneral {\{}S{\}}oil {\{}M{\}}ap ({\{}STATSGO2{\}})}},
year = {2006}
}
@article{Oneill89,
author = {O`Neill, R V and Johnson, A R and King, A W},
journal = {Landscape Ecology},
number = {3-4},
pages = {193--205},
title = {{A hierarchical framework for the analysis of scale}},
volume = {3},
year = {1989}
}
@article{Obenour15,
author = {Obenour, D R and Michalak, A M and Scavia, D},
journal = {Ecological Applications},
number = {2},
pages = {492--505},
title = {{Assessing biophysical controls on {\{}G{\}}ulf of {\{}M{\}}exico hypoxia through probabilistic modeling}},
volume = {25},
year = {2015}
}
@misc{Ode07,
address = {Surface Water Ambient Monitoring Program. Sacramento, CA},
author = {Ode, P R},
title = {{Standard operating procedures for collecting benthic macroinvertebrate samples and associated physical and chemical data for ambient bioassessment in {\{}C{\}}alifornia}},
year = {2007}
}
@article{Ode16,
author = {Ode, P R and Rehn, A C and Mazor, R D and Schiff, K C and Stein, E D and May, J T and Brown, L R and Herbst, D B and Gillett, D and Lunde, K and Hawkins, C P},
journal = {Freshwater Science},
number = {1},
pages = {237--248},
title = {{Evaluating the adequacy of a reference-site pool for ecological assessments in environmentally complex regions}},
volume = {35},
year = {2016}
}
@article{Odum56,
author = {Odum, H T},
journal = {Limnology and Oceanography},
number = {2},
pages = {102--117},
title = {{Primary production in flowing waters}},
volume = {1},
year = {1956}
}
@book{Ojakangas82,
address = {Minneapolis, Minnesota},
author = {Ojakangas, R W and Matsch, C L},
publisher = {The University of Minnesota Press},
title = {{Minnesota's Geology}},
year = {1982}
}
@article{Okimoto2013,
abstract = {Mangrove trees act important roles in the coastal ecosystems, protecting community against high-tide and storms, controlling land erosion and providing fish breeding ground. In the last few decades, the massive area has devastated due to commercial shrimp and fish ponds development. To rehabilitate the coastal ecosystems, some mangrove has been planted with spacing distances of 1x1 m with minimal forest management. Those dense-spaced stands enhanced light competitions and inhibit growth. These poor quality and immature stands that reach an early climax in 10-15 years were observed in two adjacent sites near Nam Dinh and Thanh Hoa in northern Vietnam, where Kandelia candel were planted. To cultivate the resurgent stands and increase their growth, thinning mangrove is essential. Stand densities of the mangrove trees with and without the thinning practice were 17,800 and 5,200 trees ha-1, respectively. Their potential of the maximum above-ground biomass were 303 and 239 Mg ha-1, respectively. However, quality of the single tree was largely different whether or not thinning practice is conducted, as the thinned one of 46 kg tree-1 was about three times higher than the non-thinned of 17 kg tree-1. The thinning practice enhances stand biomass growth with improved growth condition in the forest, which advances carbon sequestration for the climate change mitigation. The cultivated trees also ensure the climate change adaptation of coastal protection, fishery products and bio-diversity. Synergizing mitigation and adaptation strategies with the mangrove thinning would enhance the benefits for coastal communities most vulnerable to climate change},
author = {Okimoto, Y and Nose, A and Murdiyarso, D and Purbopuspito, J and Sasmito, S D},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Okimoto{\_}thinning{\_}practices.pdf:pdf},
journal = {Proceedings of the 7th International Conference on Asian and Pacific Coasts (APAC 2013) Bali, Indonesia, September 24-26, 2013},
keywords = {biomass and coastal ecosystem,mangrove plantation,rehabilitation},
number = {Apac},
pages = {964--968},
title = {{Thinning practices in rehabilitated mangroves: Opportunity to synergize climate change mitigation and adaptation}},
url = {http://repository.unhas.ac.id/bitstream/handle/123456789/7667/154.CC 16.pdf?sequence=1},
year = {2013}
}
@misc{Oksanen10,
annote = {$\backslash$url{\{}http://CRAN.R-project.org/package=vegan{\}}},
author = {Oksanen, J and Blanchet, F Guillaume and Kindt, R and Legendre, P and 0'Hara, R B and Simpson, G L and Solymos, P and Henry, M and Stevens, H and Wagener, H},
title = {{Vegan: community ecology package, {\{}R{\}} package version 1.17-2}},
year = {2010}
}
@article{Olander2015,
abstract = {The online Federal Resource Management and Ecosystem Services Guidebook (FRMES Guidebook, https://nespguidebook.com), published in December 2014, is designed to increase understanding of ecosystem services within federal agencies and to increase consistency of ecosystem services approaches to management across agencies. Although the guidebook presents methods for implementing these approaches, it is not focused on best practices recommendations. This paper, “Best Practices for Integrating Ecosystem Services into Federal Decision Making,” was developed by acknowledged academic experts in the field to provide such recommendations. It refines and clarifies the methods presented in the FRMES Guidebook. The recommendations herein will be incorporated into the guidebook in the second half of 2015.},
author = {Olander, Lydia and Johnston, Robert J and Tallis, Heather and Kagan, Jimmy and Maguire, Lynn and Polasky, Steve and Urban, Dean and Boyd, James and Wainger, Lisa and Palmer, Margaret},
doi = {10.13016/M2CH07},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2015{\_}Olander{\_}Best{\_}Practices.pdf:pdf},
journal = {Durham: National Ecosystem Services Partnership, Duke University},
pages = {48},
title = {{Best Practices for Integrating Ecosystem Services into Federal Decision Making}},
year = {2015}
}
@article{Olden02,
author = {Olden, J D and Jackson, D A},
journal = {Ecological Modelling},
number = {1-2},
pages = {135--150},
title = {{Illuminating the ``black box'': A randomization approach for understanding variable contributions in artifical neural networks}},
volume = {154},
year = {2002}
}
@article{Olden01,
author = {Olden, J D and Jackson, D A},
journal = {Transactions of the American Fisheries Society},
number = {5},
pages = {878--897},
title = {{Fish-habitat relationships in lakes: Gaining perspective and explanatory insight by using artificial neural networks}},
volume = {130},
year = {2001}
}
@article{Olden04,
author = {Olden, J D and Joy, M K and Death, R G},
journal = {Ecological Modelling},
number = {3-4},
pages = {389--397},
title = {{An accurate comparison of methods for quantifying variable importance in artificial neural networks using simulated data}},
volume = {178},
year = {2004}
}
@article{Olmanson08,
author = {Olmanson, L G and Bauer, M E and Brezonik, P L},
journal = {Remote Sensing of Environment},
number = {11},
pages = {4086--4097},
title = {{A 20-year {\{}L{\}}andsat water clarity census of {\{}M{\}}innesota's 10,000 lakes}},
volume = {112},
year = {2008}
}
@article{Olmanson11,
author = {Olmanson, L G and Brezonik, P L and Bauer, M E},
journal = {Water Resources Research},
number = {W09515},
pages = {1--14},
title = {{Evaluation of medium to low resolution satellite imagery for regional lake water quality assessments}},
volume = {47},
year = {2011}
}
@article{Omernik87,
author = {Omernik, J M},
journal = {Annals of the Association of American Geographers},
number = {1},
pages = {118--125},
title = {{Ecoregions of the Conterminous {\{}U{\}}nited-{\{}S{\}}tates}},
volume = {77},
year = {1987}
}
@article{Omlin01,
author = {Omlin, M and Brun, R and Reichert, P},
journal = {Ecological Modelling},
number = {1-3},
pages = {105--123},
title = {{Biogeochemical model of {\{}L{\}}ake {\{}Z{\}}{\"{u}}rich: sensitivity, identifiability and uncertainty analysis}},
volume = {141},
year = {2001}
}
@article{Omlin01b,
author = {Omlin, M and Reichert, P and Forster, R},
journal = {Ecological Modelling},
number = {1-3},
pages = {77--103},
title = {{Biogeochemical model of {\{}L{\}}ake {\{}Z{\}}{\"{u}}rich: model equations and results}},
volume = {141},
year = {2001}
}
@book{Ong2013,
abstract = {This book Structure, Function and Management of Mangrove Ecosystems is the second in a trilogy to be published simultaneously. The others are Continuing the Journey Amongst Mangroves by Barry Clough, and Useful Products from Mangrove and other Coastal Plants by Shigeyuki Baba, Hung Tuck Chan and Sanit Aksornkoae. This book is about mangrove plants and animals that colonise the main part of the intertidal zone in the tropics and subtropics. It highlights the structure, function, state of health, and as importantly, the sustainable economic and ecological management of mangrove forests. This book is not written for the professionals but aimed more at semi-professionals, students and those who need an introduction to mangroves at a higher than just a superficial treatment. The confusion with rehabilitation of mangroves after the 2004 Indian Ocean tsunami strongly suggests that such a book would fulfil a need. The authors also wish to share their considerable experience working (mainly in the field in hands-on situations) in some of the most biologically diverse and luxuriant mangroves in the world. It is not the intention of this book to provide a highly technical review of the subject. As such, the references are not extensive but enough to point the way for further reading. This makes for easier reading. This book is also structured in such a way that the photographs, with their own captions, can be read independently from the text. The boxes provide further details and need not be read with the text or photographs.},
author = {Ong, J E and Gong, W K},
edition = {ISME Mangr},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Ong{\_}structure{\_}function.pdf:pdf},
isbn = {9784906584178},
pages = {81},
publisher = {International Society for Mangrove Ecosystems},
title = {{Structure, Function and Management of Mangrove Ecosystems}},
year = {2013}
}
@article{Orth10,
author = {Orth, R J and Williams, M R and Marion, S R and Wilcox, D J and Carruthers, T J B and Moore, K A and Kemp, W M and Dennison, W C and Rybicki, N and Bergstrom, P and Batiuk, R A},
journal = {Estuaries and Coasts},
number = {5},
pages = {1144--1163},
title = {{Long-term trends in submersed aquatic vegetation (SAV) in {\{}C{\}}hesapeake {\{}B{\}}ay, {\{}USA{\}}, related to water quality}},
volume = {33},
year = {2010}
}
@article{Osland2013,
abstract = {We live in an era of unprecedented ecological change in which ecologists and natural resource managers are increasingly challenged to anticipate and prepare for the ecological effects of future global change. In this study, we investigated the potential effect of winter climate change upon salt marsh and mangrove forest foundation species in the southeastern United States. Our research addresses the following three questions: (1) What is the relationship between winter climate and the presence and abundance of mangrove forests relative to salt marshes; (2) How vulnerable are salt marshes to winter climate change-induced mangrove forest range expansion; and (3) What is the potential future distribution and relative abundance of mangrove forests under alternative winter climate change scenarios? We developed simple winter climate-based models to predict mangrove forest distribution and relative abundance using observed winter temperature data (1970-2000) and mangrove forest and salt marsh habitat data. Our results identify winter climate thresholds for salt marsh-mangrove forest interactions and highlight coastal areas in the southeastern United States (e.g., Texas, Louisiana, and parts of Florida) where relatively small changes in the intensity and frequency of extreme winter events could cause relatively dramatic landscape-scale ecosystem structural and functional change in the form of poleward mangrove forest migration and salt marsh displacement. The ecological implications of these marsh-to-mangrove forest conversions are poorly understood, but would likely include changes for associated fish and wildlife populations and for the supply of some ecosystem goods and services.},
author = {Osland, Michael J and Enwright, Nicholas and Day, Richard H and Doyle, Thomas W},
doi = {10.1111/gcb.12126},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Osland{\_}winter{\_}climate.pdf:pdf},
journal = {Global Change Biology},
keywords = {Avicennia germinans,Coastal wetlands,Ecological thresholds,Extreme events,Foundation species,Mangrove forest,Range expansion,Salt marsh,Vulnerability assessment,Winter climate change},
number = {5},
pages = {1482--1494},
title = {{Winter climate change and coastal wetland foundation species: Salt marshes vs. mangrove forests in the southeastern United States}},
volume = {19},
year = {2013}
}
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author = {{\"{O}}zesmi, S L and {\"{O}}zesmi, U},
journal = {Ecological Modelling},
number = {1},
pages = {15--31},
title = {{An artificial neural network approach to spatial habitat modelling with interspecific interaction}},
volume = {116},
year = {1999}
}
@article{Ozesmi06,
author = {{\"{O}}zesmi, S L and Tan, C O and {\"{O}}zesmi, U},
journal = {Ecological Modelling},
number = {1-2},
pages = {83--93},
title = {{Methodological issues in building, training, and testing artificial neural networks in ecological applications}},
volume = {195},
year = {2006}
}
@article{Paerl06,
author = {Paerl, H W},
journal = {Ecological Engineering},
number = {1},
pages = {40--54},
title = {{Assessing and managing nutrient-enhanced eutrophication in estuarine and coastal waters: Interacive effects of human and climatic perturbations}},
volume = {26},
year = {2006}
}
@article{Paerl2002,
author = {Paerl, H W},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2002{\_}paerl{\_}Connecting{\_}Atmospheric.pdf:pdf},
journal = {Environmental Science {\&} Technology},
pages = {323--326},
title = {{Connecting atmospheric nitrogen deposition to coastal eutrophication}},
volume = {August 1, },
year = {2002}
}
@article{Paerl14,
author = {Paerl, H W and Hall, N S and Peierls, B L and Rossignol, K L},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2014{\_}Paerl{\_}Coastal{\_}Ecosystem.pdf:pdf},
journal = {Estuaries and Coasts},
number = {2},
pages = {243--258},
title = {{Evolving paradigms and challenges in estuarine and coastal eutrophication dynamics in a culturally and climatically stressed world}},
volume = {37},
year = {2014}
}
@article{Paerl98,
author = {Paerl, H W and Pinckney, J L and Fear, J M and Peierls, B L},
journal = {Marine Ecology Progress Series},
pages = {17--25},
title = {{Ecosystem responses to internal and watershed organic matter loading: consequences for hypoxia in the eutrophying {\{}N{\}}euse {\{}R{\}}iver {\{}E{\}}stuary, {\{}N{\}}orth {\{}C{\}}arolina, {\{}USA{\}}}},
volume = {166},
year = {1998}
}
@article{Paerl1990,
author = {Paerl, Hans W and Rudek, J and Mallin, M A},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1990{\_}Paerl{\_}Stimulation{\_}of.pdf:pdf},
journal = {Marine Biology},
pages = {247--254},
title = {{Stimulation of phytoplankton production in coastal waters by natural rainfall inputs: nutritional and trophic implications}},
volume = {107},
year = {1990}
}
@article{Pamatmat97,
author = {Pamatmat, M M},
journal = {Marine Biology},
number = {4},
pages = {735--746},
title = {{Non-photosynthetic oxygen production and non-respiratory oxygen uptake in the dark: A theory of oxygen dynamics in plankton communities}},
volume = {129},
year = {1997}
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author = {Parchaso, F and Thompson, J K},
journal = {Pacific Science},
number = {3},
pages = {329--345},
title = {{Influence of hydrologic processes on reproduction of the introduced bivalve $\backslash$textit{\{}{\{}P{\}}otamocorbula amurensis{\}} in northern {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay, {\{}C{\}}alifornia}},
volume = {56},
year = {2002}
}
@article{Parker12,
author = {Parker, A E and Hogue, V E and Wilkerson, F P and Dugdale, R C},
journal = {Estuarine, Coastal, and Shelf Science},
pages = {91--101},
title = {{The effect of inorganic nitrogen speciation on primary production in the {\{}S{\}}an {\{}F{\}}rancisco {\{}E{\}}stuary}},
volume = {104},
year = {2012}
}
@book{Parsons85,
address = {New York},
author = {Parsons, T R and Maita, Y and Lalli, C M},
pages = {188},
publisher = {Pergamon Press},
title = {{A manual of chemical methods for seawater analysis}},
year = {1985}
}
@article{Paruelo97,
author = {Paruelo, J M and Tomasel, F},
journal = {Ecological Modelling},
number = {2-3},
pages = {173--186},
title = {{Prediction of functional characteristics of ecosystems: A comparison of artificial neural networks and regression models}},
volume = {98},
year = {1997}
}
@article{Pauer16,
author = {Pauer, J J and Feist, T J and Anstead, A M and DePetro, P A and Melendez, W and Lehrter, J C and Murrell, M C and Zhang, X and Ko, D S},
journal = {Ecological Modelling},
pages = {136--147},
title = {{A modeling study examining the impact of nutrient boundaries on primary production on the {\{}L{\}}ouisiana continental shelf}},
volume = {328},
year = {2016}
}
@article{Pebesma04,
author = {Pebesma, E J},
journal = {Computers and Geosciences},
number = {7},
pages = {683--691},
title = {{Multivariable geostatistics in {\{}S{\}}: the gstat package}},
volume = {30},
year = {2004}
}
@article{Pellerin14,
author = {Pellerin, B A and Bergamaschi, B A and Gilliom, R J and Crawford, C G and Saraceno, J F and Frederick, C P and Downing, B D and Murphy, J C},
journal = {Environmental Science and Technology},
pages = {12612--12619},
title = {{{\{}M{\}}ississippi {\{}R{\}}iver nitrate loads from high frequency sensor measurements and regression-based load estimation}},
volume = {48},
year = {2014}
}
@article{Penning08,
author = {Penning, W E and Dudley, B and Mjelde, M and Hellsten, S and Hanganu, J and Kolada, A and van den Berg, M and Poikane, S and Phillips, G and Willby, N and Ecke, F},
journal = {Aquatic Ecology},
pages = {253--264},
title = {{Using aquatic macrophyte community indices to define the ecological status of {\{}E{\}}uropean lakes}},
volume = {42},
year = {2008}
}
@article{Penta09,
author = {Penta, B and Lee, Z and Kudela, R M and Palacios, S L and Gray, D J and Jolliff, J K and Shulman, I G},
journal = {Optical Express},
number = {25},
pages = {23351},
title = {{An underwater light attenuation scheme for marine ecosystem models: errata}},
volume = {17},
year = {2009}
}
@article{Penta08,
author = {Penta, B and Lee, Z and Kudela, R M and Palacios, S L and Gray, D J and Jolliff, J K and Shulman, I G},
journal = {Optical Express},
number = {21},
pages = {16581--16591},
title = {{An underwater light attenuation scheme for marine ecosystem models}},
volume = {16},
year = {2008}
}
@article{Peres-Neto06,
author = {Peres-Neto, P R and Legendre, P and Dray, S and Borcard, D},
journal = {Ecology},
number = {10},
pages = {2614--2625},
title = {{Variation partitioning of species data matrices: {\{}E{\}}stimation and comparison of fractions}},
volume = {87},
year = {2006}
}
@techreport{Perleberg12,
address = {St. Paul, Minnesota},
author = {Perleberg, D and Radomski, P and Simon, S},
institution = {Division of Ecological and Water Resources, Minnesota Department of Natural Resources},
number = {version 2, January 2012},
pages = {48},
title = {{Score your shore, citizen shoreline description survey}},
year = {2012}
}
@article{Perry02,
author = {Perry, J N and Liebhold, A M and Rosenberg, M S and Dungan, J and Miriti, M and Jakomulska, A and Citron-Pousty, S},
journal = {Ecography},
number = {5},
pages = {578--600},
title = {{Illustrations and guidelines for selecting statistical methods for quantifying spatial pattern in ecological data}},
volume = {25},
year = {2002}
}
@article{Petrucci14,
author = {Petrucci, G and Bonhomme, C},
journal = {Journal of Hydrology},
pages = {997--1007},
title = {{The dilemma of spatial representation for urban hydrology semi-distributed modelling: trade-offs among complexity, calibration and geographical data}},
volume = {517},
year = {2014}
}
@article{Pierce86,
author = {Pierce, D A and Schafer, D W},
journal = {Journal of the American Statistical Association},
number = {396},
pages = {977--986},
title = {{Residuals in generalized linear models}},
volume = {81},
year = {1986}
}
@article{Pitts47,
author = {Pitts, W and McCulloch, W S},
journal = {Bulletin of Mathematical Biophysics},
number = {3},
pages = {127--147},
title = {{How we know universals: The perception of auditory and visual forms}},
volume = {9},
year = {1947}
}
@techreport{Plafkin89,
address = {Washington, DC},
author = {Plafkin, J L and Barbour, M T and Porter, K D and Gross, S K and Hughes, R M},
institution = {U.S. Environmental Protection Agency},
number = {EPA 841-B-99-002},
title = {{Rapid bioassessment protocols for use in streams and rivers. Benthic macroinvertebrates and fish}},
year = {1989}
}
@article{Platt80,
author = {Platt, T and Gallegos, C L and Harrison, W G},
journal = {Journal of Marine Research},
pages = {687--701},
title = {{Photoinhibition of photosynthesis in natural assemblages of marine phytoplankton}},
volume = {38},
year = {1980}
}
@techreport{Poe05,
address = {St. Petersburg, Florida, USA},
author = {Poe, A and Hackett, K and Janicki, S and Pribble, R and Janicki, A},
institution = {Tampa Bay Estuary Program},
number = {{\#}02-05},
title = {{Estimates of total nitrogen, total phosphorus, total suspended solids, and biochemical oxygen demand loadings to {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida: 1999-2003}},
year = {2005}
}
@article{Poff97,
author = {Poff, N L},
journal = {Journal of the North American Benthological Society},
number = {2},
pages = {391--409},
title = {{Landscape filters and species traits: Towards mechanistic understanding and prediction in stream ecology}},
volume = {16},
year = {1997}
}
@article{Pollard98,
author = {Pollard, P and Huxham, M},
journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
number = {6},
pages = {773--792},
title = {{The {\{}E{\}}uropean {\{}W{\}}ater {\{}F{\}}ramework {\{}D{\}}irective: A new era in the management of aquatic ecosystem health?}},
volume = {8},
year = {1998}
}
@article{Poole29,
author = {Poole, H H and Atkins, W R G},
journal = {Journal of the Marine Biological Association of the United Kingdom},
pages = {297--324},
title = {{Photo-electric measurements of submarine illumination throughout the year}},
volume = {16},
year = {1929}
}
@article{Poor2013,
abstract = {The U.S. Environmental Protection Agency (EPA) has developed the Watershed Deposition Tool (WDT) to calculate from the Community Multiscale Air Quality (CMAQ) model output the nitrogen, sulfur, and mercury deposition rates to watersheds and their sub-basins. The CMAQ model simulates from first principles the transport, transformation, and removal of atmospheric pollutants. We applied WDT to estimate the atmospheric deposition of reactive nitrogen (N) to Tampa Bay and its watershed. For 2002 and within the boundaries of Tampa Bay's watershed, modeled atmospheric deposition rates averaged 13.3 kg N ha-1 yr-1 and ranged from 6.24 kg N ha-1 yr-1 at the bay's boundary with Gulf of Mexico to 21.4 kg N ha-1 yr-1 near Tampa's urban core, based on a 12-km × 12-km grid cell size. CMAQ-predicted loading rates were 1,080 metric tons N yr-1 to Tampa Bay and 8,280 metric tons N yr-1 to the land portion of its watershed. If we assume a watershed-to-bay transfer rate of 18{\%} for indirect loading, our estimates of the 2002 direct and indirect loading rates to Tampa Bay were 1,080 metric tons N and 1,490 metric tons N, respectively, for an atmospheric loading of 2,570 metric tons N or 71{\%} of the total N loading to Tampa Bay. To evaluate the potential impact of the U.S. EPA Clean Air Interstate Rule (CAIR, replaced with Cross-State Air Pollution Rule), Tier 2 Vehicle and Gasoline Sulfur Rules, Heavy Duty Highway Rule, and Non-Road Diesel Rule, we compared CMAQ outputs between 2020 and 2002 simulations, with only the emissions inventories changed. The CMAQ-projected change in atmospheric loading rates between these emissions inventories was 857 metric tons N to Tampa Bay, or about 24{\%} of the 2002 loading of 3,640 metric tons N to Tampa Bay from all sources.Air quality modeling reveals that atmospheric deposition of reactive nitrogen (N) contributes a significant fraction to Tampa Bay's total N loading from external sources. Regulatory drivers that lower nitrogen oxide emissions from power plants and motor vehicles are important to bay management strategies, which seek to improve water quality through N load reduction. {\textcopyright} 2013 Copyright 2013 A{\&}WMA.},
author = {Poor, Noreen D and Pribble, J Raymond and Schwede, Donna B},
doi = {10.1080/10962247.2012.739109},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2013{\_}Poor{\_}Application{\_}of.pdf:pdf},
issn = {1096-2247},
journal = {Journal of the Air and Waste Management Association},
number = {1},
pages = {100--114},
title = {{Application of watershed deposition tool to estimate from CMAQ simulations the atmospheric deposition of nitrogen to Tampa Bay and its watershed}},
volume = {63},
year = {2013}
}
@article{Poor2004,
author = {Poor, Noreen and Tremblay, Raphael and Kay, Heidi and Bhethanabotla, Venkat and Swartz, Erick and Luther, Mark and Campbell, Scott},
doi = {10.1016/j.atmosenv.2004.06.037},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/200x{\_}Kay{\_}Atmospheric{\_}deposition{\_}AWMA{\_}70464.pdf:pdf},
issn = {13522310},
journal = {Atmospheric Environment},
month = {nov},
number = {35},
pages = {6005--6015},
title = {{Atmospheric concentrations and dry deposition rates of polycyclic aromatic hydrocarbons (PAHs) for Tampa Bay, Florida, USA}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1352231004006478},
volume = {38},
year = {2004}
}
@article{Poor01,
author = {Poor, P J and Boyle, K J and Taylor, L O and Bouchard, R},
journal = {Land Economics},
number = {4},
pages = {482--493},
title = {{Objective versus subjective measures of water clarity in hedonic property value models}},
volume = {77},
year = {2001}
}
@article{Poor2007,
abstract = {Non-point source water pollution of local watersheds can result from various sources but is tied most closely to runoff from impervious surfaces associated with development activities such as roadways, parking lots and large commercial structures. This research investigates the value of ambient water quality as measured by data from twenty-two monitoring stations located throughout a local watershed in Maryland; the St. Mary's River watershed. A hedonic property value model is used to investigate the marginal implicit values of the following water quality variables: total suspended solids and dissolved inorganic nitrogen. The econometric results indicate the marginal implicit prices associated with a one milligram per liter change in total suspended solids and dissolved inorganic nitrogen, are {\$}- 1086 and {\$}- 17,642, respectively. {\textcopyright} 2006 Elsevier B.V. All rights reserved.},
author = {Poor, P. Joan and Pessagno, Keri L. and Paul, Robert W.},
doi = {10.1016/j.ecolecon.2006.02.013},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}Poor{\_}Exploring{\_}the{\_}hedonic.pdf:pdf},
isbn = {0921-8009},
issn = {09218009},
journal = {Ecological Economics},
keywords = {Hedonic model,Water quality implicit prices},
number = {4},
pages = {797--806},
title = {{Exploring the hedonic value of ambient water quality: A local watershed-based study}},
volume = {60},
year = {2007}
}
@article{Portnoy03,
author = {Portnoy, S},
journal = {Journal of the American Statistical Association},
number = {464},
pages = {1001--1012},
title = {{Censored regression quantiles}},
volume = {98},
year = {2003}
}
@article{Post02,
author = {Post, J R and Sullivan, M and Cox, S and Lester, N P and Walters, C J and Parkinson, E A and Paul, A J and Jackson, L and Shuter, B J},
journal = {Fisheries},
number = {1},
pages = {6--17},
title = {{{\{}C{\}}anada's recreational fisheries: The invisible collapse?}},
volume = {27},
year = {2002}
}
@article{Powers05,
author = {Powers, S P and Peterson, C H and Christian, R R and Sullivan, E and Powers, M J and Bishop, M J and Buzzelli, C P},
journal = {Marine Ecology Progress Series},
pages = {233--243},
title = {{Effects of eutrophication on bottom habitat and prey resources of demersal fishes}},
volume = {302},
year = {2005}
}
@techreport{Pribble01,
address = {St. Petersburg, Florida, USA},
author = {Pribble, R and Janicki, A and Zarbock, H and Janicki, S and Winowitch, M},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2001 Tech Pubs/TBEP{\_}05{\_}01-95-98{\_}LOADS.pdf:pdf},
institution = {Tampa Bay Estuary Program},
number = {{\#}05-01},
title = {{Estimates of total nitrogen, total phosphorus, total suspended solids, and biochemical oxygen demand loadings to {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida: 1995-1998}},
year = {2001}
}
@article{Proffitt2005,
abstract = {We assessed the sensitivity of a viviparous estuarine tree species, Rhizophora mangle, to historic sublethal mutagenic stress across a fine spatial scale by comparing the frequency of trees producing albino propagules in historically contaminated (n4) and uncontaminated (n11) forests in Tampa Bay, Florida, USA. Data from uncontaminated forests were used to provide estimates of background mutation rates. We also determined whether other fitness parameters were negatively correlated with mutagenic stress (e.g., degree of outcrossing and numbers of reproducing trees km1 ). Contaminated sites in Tampa Bay had sig- nificantly higher frequencies of trees that were heterozygous for albinism per 1000 total reproducing trees (FHT) than uncontaminated forests (mean  SE: 11.4  4.3 vs 4.3  0.73, P0.022). Two sites that were contaminated by oil failed to show elevated FHT, although in the first instance, the mutagenic effects of the oil may have been reduced by several weeks of weathering in open water before coming ashore, and in the second  25 yrs of subsequent recruitment and tree replacement may have allowed an initial elevation in the FHT to decay. Patterns of FHT were not explained by distance from the bay mouth or the degree of urbanization. However, there was a significant positive relationship between tree size and FHT (r0.83, P0.018), which suggests that forests with older or larger trees provide a more lasting record of cumulative mutagenic stress. No other fitness parameters correlated with FHT. There was a difference in FHT between two latitudes, as determined by comparing Tampa Bay with literature values for Puerto Rico. The sensitivity of this bioassay for the effects of mutagens will facilitate future monitoring of contamination events and comparisons of bay-wide recovery in future decades. Development of a database of FHT values for a range of subtropical and tropical estuaries is underway that will provide a baseline against which to compare mutational consequences of global change.},
author = {Proffitt, C E and Travis, S E},
doi = {10.1672/9},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2005{\_}proffittalbino{\_}mutation.pdf:pdf},
journal = {Wetlands},
keywords = {albino mutation,breeding system,contamination bioassay,rhizophora mangle},
number = {2},
pages = {326--334},
title = {{Albino mutation rates in red mangroves (Rhizophora mangle L.) as a bioassay of contamination history in Tampa Bay, Florida, USA}},
url = {http://www.springerlink.com/index/G68211W4365K9G6R.pdf},
volume = {25},
year = {2005}
}
@article{Publishing2011,
author = {Publishing, Blackwell and Ecology, Global},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1999{\_}Saintilan{\_}Mangrove{\_}Transgression.pdf:pdf},
number = {2},
pages = {117--124},
title = {{Mangrove Transgression into Saltmarsh Environments in South-East Australia Author ( s ): Neil Saintilan and Robert J . Williams Source : Global Ecology and Biogeography , Vol . 8 , No . 2 ( Mar ., 1999 ), pp . 117-124 Published by : Blackwell Publishing S}},
volume = {8},
year = {2011}
}
@article{Rabalais02,
author = {Rabalais, N N and Turner, R E and Scavia, D},
journal = {BioScience},
number = {2},
pages = {129--142},
title = {{Beyond science into policy: {\{}G{\}}ulf of {\{}M{\}}exico hypoxia and the {\{}M{\}}ississippi river}},
volume = {52},
year = {2002}
}
@article{Rabotyagov2014,
abstract = {water quality},
author = {Rabotyagov, S. S. and Kling, C. L. and Gassman, P. W. and Rabalais, N. N. and Turner, R. E.},
doi = {10.1093/reep/ret024},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2014{\_}Rabotyagov{\_}The{\_}Economics{\_}dead{\_}zones.pdf:pdf},
isbn = {1750-6816$\backslash$r1750-6824},
issn = {1750-6816},
journal = {Review of Environmental Economics and Policy},
month = {jan},
number = {1},
pages = {58--79},
title = {{The Economics of Dead Zones: Causes, Impacts, Policy Challenges, and a Model of the Gulf of Mexico Hypoxic Zone}},
url = {https://academic.oup.com/reep/article-lookup/doi/10.1093/reep/ret024},
volume = {8},
year = {2014}
}
@article{Radomski06,
author = {Radomski, P},
journal = {North American Journal of Fisheries Management},
number = {4},
pages = {932--940},
title = {{Historical changes in abundance of floating-leaf and emergent vegetation in {\{}M{\}}innesota lakes}},
volume = {26},
year = {2006}
}
@article{Radomski10,
author = {Radomski, P and Bergquist, L A and Duval, M and Williquett, A},
journal = {Fisheries},
number = {10},
pages = {489--495},
title = {{Potential impacts of docks on littoral habitats in {\{}M{\}}innesota lakes}},
volume = {35},
year = {2010}
}
@article{Radomski01,
author = {Radomski, P and Goeman, T J},
journal = {North American Journal of Fisheries Management},
number = {1},
pages = {46--61},
title = {{Consequences of human lakeshore development on emergent and floating-leaf vegetation abundance}},
volume = {21},
year = {2001}
}
@article{Radomski12,
author = {Radomski, P and Perleberg, D},
journal = {Ecological Indicators},
pages = {252--268},
title = {{Application of a versatile aquatic macrophyte integrity index for {\{}M{\}}innesota lakes}},
volume = {20},
year = {2012}
}
@article{Ramstack04,
author = {Ramstack, J M and Fritz, S C and Engstrom, D R},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
pages = {561--576},
title = {{Twentieth century water quality trends in Minnesota lakes compared to presettlment variability}},
volume = {61},
year = {2004}
}
@article{Rasmussen05,
author = {Rasmussen, P and Anderson, N J},
journal = {Journal of Biogeography},
number = {11},
pages = {1993--2005},
title = {{Natural and anthropogenic forcing of aquatic macrophyte development in a shallow {\{}D{\}}anish lake during the last 7000 years}},
volume = {32},
year = {2005}
}
@article{Razi05,
author = {Razi, M A and Athappilly, K},
journal = {Expert Systems and Applications},
number = {1},
pages = {65--74},
title = {{A comparative predictive analysis of neural networks ({\{}NN{\}}s), nonlinear regression and classification and regression tree ({\{}CART{\}}) models}},
volume = {29},
year = {2005}
}
@misc{RDCT17,
annote = {$\backslash$url{\{}http://www.R-project.org{\}}},
author = {{RDCT (R Development Core Team)}},
title = {{R: A language and environment for statistical computing, v3.3.2. R Foundation for Statistical Computing, Vienna, Austria}},
year = {2017}
}
@article{Reckhow90,
author = {Reckhow, K H and Clements, J T and Dodd, R C},
journal = {Journal of Environmental Engineering},
number = {2},
pages = {250--268},
title = {{Statistical evaluation of mechanistic water-quality models}},
volume = {116},
year = {1990}
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@book{Recknagel06,
address = {Berlin, Germany},
author = {Recknagel, F},
edition = {2nd},
pages = {496},
publisher = {Springer-Verlag},
title = {{Ecological Informatics: Scope, Techniques and Applications}},
year = {2006}
}
@incollection{Recknagel00,
address = {Berlin, Germany},
author = {Recknagel, F and Wilson, H},
booktitle = {Artificial Neuronal Networks: Application to Ecology and Evolution},
editor = {Lek, S and Gu{\'{e}}gan, J F},
pages = {143--155},
publisher = {Springer-Verlag},
title = {{Elucidation and prediction of aquatic ecosystems by artificial neuronal networks}},
year = {2000}
}
@article{Reed09,
author = {Reed, J R and Pereira, D L},
journal = {North American Journal of Fisheries Management},
number = {4},
pages = {943--948},
title = {{Relationships between shoreline development and nest site selection by black crappie and largemouth bass}},
volume = {29},
year = {2009}
}
@incollection{Reed10,
address = {Denver, Colorado},
author = {Reed, R E and Burkholder, J M and Allen, E H},
booktitle = {American Water Works Association Manual M57, Algae},
pages = {1--24},
publisher = {American Water Works Association},
title = {{Current online monitoring technology for surveillance of algal blooms, potential toxicity, and physicalechemical structure in rivers, reservoirs, and lakes}},
year = {2010}
}
@article{Refsgaard07,
author = {Refsgaard, J C and van der Sluijs, J P and H{\o}jberg, A L and Vanrolleghem, P A},
journal = {Environmental Modelling {\&} Software},
number = {11},
pages = {1543--1556},
title = {{Uncertainty in the environmental modelling process - A framework and guidance}},
volume = {22},
year = {2007}
}
@article{Reichert97,
author = {Reichert, P and Omlin, M},
journal = {Ecological Modelling},
number = {2},
pages = {289--299},
title = {{On the usefulness of over parameterized ecological models}},
volume = {95},
year = {1997}
}
@article{Reichert01,
author = {Reichert, P and Vanrolleghem, P},
journal = {Water Science and Technology},
number = {7},
pages = {329--338},
title = {{Identifiability and uncertainty analysis of the {\{}R{\}}iver {\{}W{\}}ater {\{}Q{\}}uality {\{}M{\}}odel {\{}N{\}}o. 1 {\{}RWQM1{\}}}},
volume = {43},
year = {2001}
}
@article{Reichert2015,
abstract = {Environmental decision support intends to use the best available scientific knowledge to help decision makers find and evaluate management alternatives. The goal of this process is to achieve the best fulfillment of societal objectives. This requires a careful analysis of (i) how scientific knowledge can be represented and quantified, (ii) how societal preferences can be described and elicited, and (iii) how these concepts can best be used to support communication with authorities, politicians, and the public in environmental management. The goal of this paper is to discuss key requirements for a conceptual framework to address these issues and to suggest how these can best be met. We argue that a combination of probability theory and scenario planning with multi-attribute utility theory fulfills these requirements, and discuss adaptations and extensions of these theories to improve their application for supporting environmental decision making. With respect to (i) we suggest the use of intersubjective probabilities, if required extended to imprecise probabilities, to describe the current state of scientific knowledge. To address (ii), we emphasize the importance of value functions, in addition to utilities, to support decisions under risk. We discuss the need for testing "non-standard" value aggregation techniques, the usefulness of flexibility of value functions regarding attribute data availability, the elicitation of value functions for sub-objectives from experts, and the consideration of uncertainty in value and utility elicitation. With respect to (iii), we outline a well-structured procedure for transparent environmental decision support that is based on a clear separation of scientific prediction and societal valuation. We illustrate aspects of the suggested methodology by its application to river management in general and with a small, didactical case study on spatial river rehabilitation prioritization.},
author = {Reichert, Peter and Langhans, Simone D. and Lienert, Judit and Schuwirth, Nele},
doi = {10.1016/j.jenvman.2015.01.053},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2015{\_}Reichert{\_}The{\_}conceptual{\_}foundation.pdf:pdf},
issn = {10958630},
journal = {Journal of Environmental Management},
keywords = {Environmental management,Intersubjective probabilities,Multi-attribute utility theory,Multi-attribute value theory,Multi-criteria decision analysis,River management,Societal decision support,Stakeholder involvement,Uncertainty},
pages = {316--332},
pmid = {25748599},
publisher = {Elsevier Ltd},
title = {{The conceptual foundation of environmental decision support}},
url = {http://dx.doi.org/10.1016/j.jenvman.2015.01.053},
volume = {154},
year = {2015}
}
@techreport{Reschke06,
address = {Duluth, Minnesota},
author = {Reschke, C and Host, G E and Johnson, L B},
institution = {Natural Resources Research Institute, University of Minnesota, Minnesota Department of Natural Resources, CFMS Contract {\#}A61156},
title = {{Evaluation of {\{}DNR{\}} aquatic vegetation surveys: data summaries and comparative analysis}},
year = {2006}
}
@article{Reynoldson97,
author = {Reynoldson, T B and Norris, R H and Resh, V H and Day, K E and Rosenberg, D M},
journal = {Journal of the North American Benthological Society},
number = {4},
pages = {833--852},
title = {{The reference condition: a comparison of multimetric and multivariate approaches to assess water-quality impairment using benthic macroinvertebrates}},
volume = {16},
year = {1997}
}
@book{Richards06b,
address = {Berlin},
author = {Richards, J A and Jia, X},
edition = {fourth},
publisher = {Springer-Verlag, (Chapter 8)},
title = {{Remote Sensing Digital Image Analysis}},
year = {2006}
}
@book{Richards06a,
address = {Berlin},
author = {Richards, J A and Jia, X},
edition = {fourth},
publisher = {Springer-Verlag, (Chapter 9)},
title = {{Remote Sensing Digital Image Analysis}},
year = {2006}
}
@article{Riis03,
author = {Riis, T and Hawes, I},
journal = {Freshwater Biology},
number = {1},
pages = {75--87},
title = {{Effect of wave exposure on vegetation abundance, richness, and depth distribution of shallow water plants in a {\{}N{\}}ew {\{}Z{\}}ealand lake}},
volume = {48},
year = {2003}
}
@book{Ripley96,
address = {Cambridge, United Kingdom},
author = {Ripley, B D},
pages = {403},
publisher = {Cambridge University Press},
title = {{Pattern Recognition and Neural Networks}},
year = {1996}
}
@book{Rivera-Monroy2017,
abstract = {{\textcopyright} Springer International Publishing AG 2017. This book presents a comprehensive overview and analysis of mangrove ecological processes, structure, and function at the local, biogeographic, and global scales and how these properties interact to provide key ecosystem services to society. The analysis is based on an international collaborative effort that focuses on regions and countries holding the largest mangrove resources and encompasses the major biogeographic and socio-economic settings of mangrove distribution. Given the economic and ecological importance of mangrove wetlands at the global scale, the chapters aim to integrate ecological and socio-economic perspectives on mangrove function and management using a system-level hierarchical analysis framework. The book explores the nexus between mangrove ecology and the capacity for ecosystem services, with an emphasis on thresholds, multiple stressors, and local conditions that determine this capacity. The interdisciplinary approach and illustrative study cases included in the book will provide valuable resources in data, information, and knowledge about the current status of one of the most productive coastal ecosystem in the world.},
author = {Rivera-Monroy, Victor H. and Kristensen, Erik and Lee, Shing Yip and Twilley, Robert R.},
booktitle = {Mangrove Ecosystems: A Global Biogeographic Perspective: Structure, Function, and Services},
doi = {10.1007/978-3-319-62206-4},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}LopezPortillo{\_}Mangrove{\_}Forest.pdf:pdf},
isbn = {9783319622064},
keywords = {Biogeochemistry,Biogeography,Ecosystem services,Fisheries,Mangrove and climate change,Mangrove ecosystem services,Mangrove ecosystems,Mangrove forest,Mangrove forest ecosystem,Mangrove management,Mangrove remote sensing,Wetland},
number = {January 2018},
pages = {1--399},
title = {{Mangrove ecosystems: A global biogeographic perspective: Structure, function, and services}},
year = {2017}
}
@article{Ro06,
author = {Ro, K S and Hunt, P G},
journal = {Transactions of the American Society of Agricultural and Biological Engineers},
number = {5},
pages = {1615--1622},
title = {{A new unified equation for wind-driven surficial oxygen transfer into stationary water bodies}},
volume = {49},
year = {2006}
}
@article{Roadman2003,
abstract = {The Ogawa passive sampler (Ogawa USA, Pompano Beach, Florida) is a useful tool for monitoring atmospheric ammonia (NH3(g)) concentrations and assessing the effects of agricultural waste management practices on NH3(g) emissions. The Ogawa sampler, with filter-discs impregnated with citric acid, was used to trap and determine NH3(g) concentrations in a variety of agricultural settings. A wide range of NH3(g) concentrations can be monitored by varying the sampler exposure time, provided that no more than ∼10$\mu$g of NH3-N are adsorbed on the acid-coated filters. Concentrations less than 1$\mu$g NH3-Nm-3can be detected using long deployments (≤14 days), while concentrations as great as 10mg NH3-Nm-3may be determined in very short (e.g. 5min) deployments. Reproducibility ranged from 5{\%} to 10{\%} over the range of concentrations studied and passive determinations of NH3(g) were similar to those determined using dilute-acid gas scrubbers. Background levels of NH3(g) at a non-agricultural site in southern Delaware were typically {\textless}1$\mu$g NH3-Nm-3. The air entering a chicken house was 10$\mu$g NH3-Nm-3, reflecting the background levels in agricultural settings in this region. Within the house, concentrations ≤8.5mg NH3-Nm-3were observed, reflecting the high rates of NH3(g) emission from chicken excreta. Using measured NH3(g) concentrations and poultry house ventilation rates, we estimate that each broiler grown to production size over 6 weeks contributes approximately 19±3g of NH3-N to the atmosphere, a value consistent with other published results. {\textcopyright} 2003 Elsevier Science Ltd. All rights reserved.},
author = {Roadman, M J and Scudlark, J R and Meisinger, J J and Ullman, W J},
doi = {10.1016/S1352-2310(03)00163-8},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2003{\_}Roadman{\_}Validation{\_}of.pdf:pdf},
issn = {1352-2310},
journal = {Atmospheric Environment},
keywords = {Agricultural emissions,Atmospheric nitrogen,Gas sampling,Nitrogen budget},
number = {17},
pages = {2317--2325},
title = {{Validation of Ogawa passive samplers for the determination of gaseous ammonia concentrations in agricultural settings}},
volume = {37},
year = {2003}
}
@article{Robertson04,
author = {Robertson, W V and Whitman, D and Zhang, K Q and Leatherman, S P},
journal = {Journal of Coastal Research},
number = {3},
pages = {884--892},
title = {{Mapping shoreline position using airborne laser altimetry}},
volume = {20},
year = {2004}
}
@article{Roelke00,
author = {Roelke, D L},
journal = {Ecological Modelling},
pages = {245--274},
title = {{Copepod food-quality threshold as a mechanism influencing phytoplankton succession and accumulation of biomass, and secondary productivity: a modeling study with management implications}},
volume = {134},
year = {2000}
}
@article{Roelke99,
author = {Roelke, D L and Eldridge, P M and Cifuentes, L A},
journal = {Estuaries},
pages = {92--104},
title = {{A model of phytoplankton competition for limiting and non-limiting nutrients: implications for management of dynamic environments}},
volume = {22},
year = {1999}
}
@incollection{Rohlich69,
address = {Washington DC, USA},
author = {Rohlich, G A},
booktitle = {Eutrophication: Causes, Consequences, and Correctives},
editor = {Rohlich, G A},
pages = {3--16},
publisher = {National Academy of Sciences},
title = {{Introduction, summary, and recommendations}},
year = {1969}
}
@article{Rooney00,
author = {Rooney, N and Kalff, J},
journal = {Aquatic Botany},
number = {4},
pages = {321--335},
title = {{Inter-annual variation in submerged macrophyte community biomass and distribution: the influence of temperature and lake morphometry}},
volume = {68},
year = {2000}
}
@article{Rorslett91,
author = {Rorslett, B},
journal = {Aquatic Botany},
number = {1-2},
pages = {173--193},
title = {{Principal determinants of aquatic macrophyte richness in northern {\{}E{\}}uropean lakes}},
volume = {39},
year = {1991}
}
@article{Rosenberg85,
author = {Rosenberg, R},
journal = {Marine Pollution Bulletin},
number = {6},
pages = {227--231},
title = {{Eutrophication -- the future marine coastal nuisance?}},
volume = {16},
year = {1985}
}
@article{Ruaro13,
author = {Ruaro, R and Gubiani, E Andr{\'{e}}},
journal = {Ecological Indicators},
pages = {105--110},
title = {{A scientometric assessment of 30 years of the {\{}I{\}}ndex of {\{}B{\}}iotic {\{}I{\}}ntegrity in aquatic systems: Applications and main flaws}},
volume = {29},
year = {2013}
}
@article{Rumelhart86,
author = {Rumelhart, D E and Hinton, G E and Williams, R J},
journal = {Nature},
number = {6088},
pages = {533--536},
title = {{Learning representations by back-propagating errors}},
volume = {323},
year = {1986}
}
@article{Rumson2017,
abstract = {Increasing numbers of people are living in and using coastal areas. Combined with the presence of pervasive coastal threats, such as flooding and erosion, this is having widespread impacts on coastal populations, infrastructure and ecosystems. For the right adaptive strategies to be adopted, and planning decisions to be made, rigorous evaluation of the available options is required. This evaluation hinges on the availability and use of suitable datasets. For knowledge to be derived from coastal datasets, such data needs to be combined and analysed in an effective manner. This paper reviews a wide range of literature relating to data-driven approaches to coastal risk evaluation, revealing how limitations have been imposed on many of these methods, due to restrictions in computing power and access to data. The rapidly emerging field of ‘Big Data' can help overcome many of these hurdles. ‘Big Data' involves powerful computer infrastructures, enabling storage, processing and real-time analysis of large volumes and varieties of data, in a fast and reliable manner. Through consideration of examples of how ‘Big Data' technologies are being applied to fields related to coastal risk, it becomes apparent that geospatial Big Data solutions hold clear potential to improve the process of risk based decision making on the coast. ‘Big Data' does not provide a stand-alone solution to the issues and gaps outlined in this paper, yet these technological methods hold the potential to optimise data-driven approaches, enabling robust risk profiles to be generated for coastal regions.},
author = {Rumson, Alexander G. and Hallett, Stephen H. and Brewer, Timothy R.},
doi = {10.1016/j.marpol.2017.05.032},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Rumson{\_}Coastal{\_}risk{\_}adaptation.pdf:pdf},
isbn = {0308-597X},
issn = {0308597X},
journal = {Marine Policy},
keywords = {Big Data,Coastal management,Environmental risk,Geospatial data},
number = {March},
pages = {100--110},
publisher = {Elsevier Ltd},
title = {{Coastal risk adaptation: the potential role of accessible geospatial Big Data}},
url = {http://dx.doi.org/10.1016/j.marpol.2017.05.032},
volume = {83},
year = {2017}
}
@article{Russell07,
author = {Russell, M J and Montagna, P A},
journal = {Estuaries and Coasts},
number = {1},
pages = {137--153},
title = {{Spatial and tepmoral variability and drivers of net ecosystem metabolism in western {\{}G{\}}ulf of {\{}M{\}}exico estuaries}},
volume = {30},
year = {2007}
}
@article{Saeys07,
author = {Saeys, Y and Inza, I and Larra{\~{n}}aga, P},
journal = {Bioinformatics},
number = {19},
pages = {2507--2517},
title = {{A review of feature selection techniques in bioinformatics}},
volume = {23},
year = {2007}
}
@article{Sakamoto89,
author = {Sakamoto, M and Tanaka, T},
journal = {Marine Biology},
number = {2},
pages = {265--271},
title = {{Phosphorus dynamics associated with phytoplankton blooms in eutrophic {\{}M{\}}ikawa {\{}B{\}}ay, {\{}J{\}}apan}},
volume = {101},
year = {1989}
}
@article{Sanders01,
author = {Sanders, C A and Rodriguez, M and Greenbaum, E},
journal = {Biosensors and Bioelectronics},
number = {7-8},
pages = {439--446},
title = {{Stand-off tissue-based biosensors for the detection of chemical warfare agents using photosynthetic fluorescence induction}},
volume = {16},
year = {2008}
}
@techreport{Sanger02,
address = {Charleston, South Carolina},
author = {Sanger, D M and Arendt, M D and Chen, Y and Wenner, E L and Holland, A F and Edwards, D and Caffrey, J},
institution = {National Estuarine Research Reserve Technical Report Series 2002:3. South Carolina Department of Natural Resources, Marine Resources Division Contribution No. 500},
pages = {135},
title = {{A synthesis of water quality data: National Estuarine Research Reserve System-wide Monitoring Program (1995-2000)}},
year = {2002}
}
@article{Santos09,
author = {Santos, M J and Khanna, S and Hestir, E L and Andrew, M E},
journal = {Invasive Plant Science and Management},
number = {3},
pages = {216--229},
title = {{Use of hyperspectral remote sensing to evaluate efficacy of aquatic plant management}},
volume = {2},
year = {2009}
}
@article{Santos80,
author = {Santos, S L and Simon, J L},
journal = {Marine Ecology - Progress Series},
number = {3},
pages = {235--241},
title = {{Marine soft-bottom community establishment following annual defaunation: Larval or adult recruitment}},
volume = {2},
year = {1980}
}
@article{Santos1980,
abstract = {ABSTRACT: A portion of Hillsborough Bay (Tampa, Florida, USA), part of the Tampa Bay estuary, undergoes annual summer defaunation, presumably due to hypoxia. Dissolved oxygen levels are very low ({\textless} 1.0 mg 1-l) at the times of the defaunations. In the ensuing period between defaunations, recolonization occurs. Monthly samples for 42 consecutive months were collected by SCUBA-diver-operated, hand-held PVC cores and screened through a 0.5 mm sieve. Eight species, Mysella planulata, Arnpelisca abdita, Streblospio benedicti, Grandjdierella bonnieroides, Mulinia lateralis, Mediomastus californiensis, Cyclaspls sp. and Nereissuccinea were numerically dominant, accounting for more than 95 {\%} of the total density during the entire penod. These 8 species are all classified as r-strategists and utilize several dispersal mechanisms to attain large populations rapidly. Circumstantial evidence is present},
author = {Santos, Sl and Simon, Jl},
doi = {10.3354/meps003347},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1980{\_}Santos{\_}response{\_}of.pdf:pdf},
journal = {Marine Ecology Progress Series},
pages = {347--355},
title = {{Response of Soft-Bottom Benthos to Annual Catastrophic Disturbance in a South Florida Estuary }},
volume = {3},
year = {1980}
}
@article{Sasaki09,
author = {Sasaki, A and Hagimori, Y and Nakatsubo, T and Hoshika, A},
journal = {Ecological Research},
number = {4},
pages = {723--729},
title = {{Tidal effects on the organic carbon mineralization rate under aerobic conditions in sediments of an intertidal estuary}},
volume = {24},
year = {2009}
}
@article{Sass10,
author = {Sass, L L and Bozek, M A and Hauxwell, J A and Wagner, K and Knight, S},
journal = {Aquatic Botany},
pages = {1--8},
title = {{Response of aquatic macrophytes to human land use perturbations in the watersheds of {\{}W{\}}isconsin lakes, {\{}U.S.A.{\}}}},
volume = {93},
year = {2010}
}
@article{Saunders2017,
abstract = {Many coastal marine ecosystems are threatened by anthropogenic activities, but often, the best way to restore and protect these important ecosystems is unclear. Conventional wisdom suggests that the 2 most effective conservation actions to benefit coastal marine ecosystems are implementation of marine protected areas or, alternatively, reduction of land-based threats. Active marine restoration is typically considered a low-priority option, in part due to high costs and low success rates. But does this conventional wisdom hold up to closer scrutiny? We developed a model to ask: should we restore or protect, on either the land or in the ocean, to maximise the extent of coastal marine ecosystems? We based the model on seagrass meadows and adjacent catchments in Queensland, Australia. Surprisingly, we found that direct, active marine restoration can be the most cost-effective approach to maximising extent of marine ecosystems over longer (decades-long) timescales. There is, however, substantial uncertainty in our understanding of the dynamics of complex linked land–sea ecosystems. Further, geomorphological and ecological conditions vary geographically. Therefore, we also used the model to investigate how uncertainty in key parameters affects decision-making outcomes. Our results can be used to guide investment into coastal marine conservation in the absence of complex, region-specific modelling.},
author = {Saunders, Megan I. and Bode, Michael and Atkinson, Scott and Klein, Carissa J. and Metaxas, Anna and Beher, Jutta and Beger, Maria and Mills, Morena and Giakoumi, Sylvaine and Tulloch, Vivitskaia and Possingham, Hugh P.},
doi = {10.1371/journal.pbio.2001886},
editor = {Mace, Georgina},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Saunders{\_}Simple{\_}rules.pdf:pdf},
isbn = {1111111111},
issn = {1545-7885},
journal = {PLOS Biology},
month = {sep},
number = {9},
pages = {e2001886},
title = {{Simple rules can guide whether land- or ocean-based conservation will best benefit marine ecosystems}},
url = {http://dx.plos.org/10.1371/journal.pbio.2001886},
volume = {15},
year = {2017}
}
@article{Sawaya03,
author = {Sawaya, K E and Olmanson, L G and Heinert, N J and Brezonik, P L and Bauer, M E},
journal = {Remote Sensing of Environment},
number = {1-2},
pages = {144--156},
title = {{Extending satellite remote sensing to local scales: Land and water resource monitoring using high-resolution imagery}},
volume = {88},
year = {2003}
}
@article{Scardi01,
author = {Scardi, M},
journal = {Ecological Modelling},
number = {1-3},
pages = {33--45},
title = {{Advances in neural network modeling of phytoplankton primary production}},
volume = {146},
year = {2001}
}
@article{Scavia04,
author = {Scavia, D and Justic, D and Bierman, V J},
journal = {Estuaries},
number = {3},
pages = {419--425},
title = {{Reducing hypoxia in the {\{}G{\}}ulf of {\{}M{\}}exico: Advice from three models}},
volume = {27},
year = {2004}
}
@misc{Schad11,
annote = {Minnesota Department of Natural Resources Roundtable Meeting, January 7-8, 2011, Brooklyn Center, MN},
author = {Schad, D},
title = {{Game and fish fund: {\{}T{\}}he big picture.}},
year = {2011}
}
@article{Schaeffer13,
author = {Schaeffer, B A and {Hagy III}, J D and Stumpf, R P},
journal = {Journal of Applied Remote Sensing},
number = {1},
pages = {73544},
title = {{Approach to developing numeric water quality criteria for coastal waters: transition from {\{}SeaWiFS{\}} to {\{}MODIS{\}} and {\{}MERIS{\}} satellites}},
volume = {7},
year = {2013}
}
@article{Schaeffer12,
author = {Schaeffer, B A and Hagy, J D and Conmy, R N and Lehrter, J C and Stumpf, R P},
journal = {Environmental Science and Technology},
number = {2},
pages = {916--922},
title = {{An approach to developing numeric water quality criteria for coastal waters using the {\{}SeaWiFS{\}} satellite data record}},
volume = {46},
year = {2012}
}
@article{Scheffer98,
author = {Scheffer, M and Carpenter, S and Foley, J A and Folkes, C and Walker, B},
journal = {Nature},
pages = {591--596},
title = {{Catastrophic shifts in ecosystems}},
volume = {413},
year = {1998}
}
@article{Scheffer93,
author = {Scheffer, M and Hosper, S H and Meijer, M L and Moss, B and Jeppesen, E},
journal = {Trends in Ecology and Evolution},
number = {8},
pages = {275--279},
title = {{Alternative equilibria in shallow lakes}},
volume = {8},
year = {1993}
}
@article{Scheuerell04,
author = {Scheuerell, M D and Schindler, D E},
journal = {Ecosystems},
number = {1},
pages = {98--106},
title = {{Changes in the spatial distribution of fishes in lakes along a residential development gradient}},
volume = {7},
year = {2004}
}
@article{Schiff16,
abstract = {Water quality monitoring is a cornerstone of environmental protection and ambient monitoring provides managers with the critical data they need to take informed action. Unlike site-specific monitoring that is at the heart of regulatory permit compliance, regional monitoring can provide an integrated, holistic view of the environment, allowing managers to obtain a more complete picture of natural variability and cumulative impacts, and more effectively prioritize management actions. By reviewing four long-standing regional monitoring programs that cover portions of all three coasts in the United States–Chesapeake Bay, Tampa Bay, Southern California Bight, and San Francisco Bay–important insights can be gleaned about the benefits that regional monitoring provides to managers. These insights include the underlying reasons that make regional monitoring programs successful, the challenges to maintain relevance and viability in the face of ever-changing technology, competing demands and shifting management priorities. The lessons learned can help other managers achieve similar successes as they seek to establish and reinvigorate their own monitoring programs.},
author = {Schiff, K. and Trowbridge, P. R. and Sherwood, E. T. and Tango, P. and Batiuk, R. A.},
doi = {10.1016/j.rsma.2015.11.007},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2015 Tech Pubs/TBEP{\_}08{\_}15{\_}Schiff{\_}et{\_}al-2015-RSMS.pdf:pdf},
issn = {23524855},
journal = {Regional Studies in Marine Science},
month = {mar},
pages = {A1--A7},
publisher = {Elsevier B.V.},
title = {{Regional monitoring programs in the United States: Synthesis of four case studies from Pacific, Atlantic, and Gulf Coasts}},
url = {http://dx.doi.org/10.1016/j.rsma.2015.11.007 http://linkinghub.elsevier.com/retrieve/pii/S2352485515000742},
volume = {4},
year = {2016}
}
@article{Schindler00,
author = {Schindler, D E and Geib, S I and Williams, M R},
journal = {Ecosystems},
number = {3},
pages = {229--237},
title = {{Patterns of fish growth along a residential development gradient in north temperate lakes}},
volume = {3},
year = {2000}
}
@article{Schmidt02,
author = {Schmidt, N and Luther, M E},
journal = {Estuaries and Coasts},
number = {5},
pages = {976--984},
title = {{{\{}ENSO{\}} impacts on salinity in {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida}},
volume = {25},
year = {2002}
}
@article{Schmitt2012,
abstract = {Trees compared to other organisms have a very high level of genetic diversity (Hamrick and Godt 1990). As sessile long-living plants, they need this high level of genetic variation for adaptation to highly variable environmental conditions. A set of population genetic processes such as the mating system, gene flow, selection, and migration determine the genetic composition of a tree population. First we will give an introduction and overview on the most important processes and their impact on the genetic diversity of tropical trees, and then we will go in more details for some of the processes. The genetic diversity is of fundamental function for the stability of forest ecosystems. Thus adequate measures on gene conservation are very important. We will cover this topic with a specific chapter. More recently with the advance of genomics and molecular genetics, we have a broad set of molecular markers in hand for diagnostic purposes. We highlight as one important application the use of gene markers and DNA bar coding for tree species identification and as a tool to fight against illegal logging. Finally we will give an introduction to tree breeding programs and provenance tests in the tropics.},
author = {Schmitt, Klaus and Duke, Norman C},
doi = {10.1111/btp.12004},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2015{\_}schmitt{\_}Mangrove{\_}management.pdf:pdf},
journal = {Biotropica},
keywords = {climate change,co-management,coastal dynamic and protection,economic,ecosystem services,hydrology,mangrove management,ment,monitoring,planting,rehabilitation,restoration,site assess-},
pages = {1--29},
title = {{Tropical Forestry}},
year = {2012}
}
@article{Schoellhamer11,
author = {Schoellhamer, David H},
journal = {Estuaries and Coasts},
pages = {885--899},
title = {{Sudden clearing of estuarine waters upon crossing the threshold from transport to supply regulation of sediment transport as an erodible sediment pool is depleted: San Francisco Bay, 1999}},
volume = {34},
year = {2011}
}
@incollection{Schopfer08,
address = {Heidelberg, Berlin, New York},
author = {Sch{\"{o}}pfer, E and Lang, S and Strobl, J},
booktitle = {Object-Based Image Analysis: Spatial Concepts for Knowledge-Driven Remote Sensing Applications},
editor = {Blaschke, T and Lang, S and Hay, G J},
pages = {181--192},
publisher = {Springer-Verlag},
title = {{Segmentation and object-based image analysis}},
year = {2008}
}
@article{Schultz08,
author = {Schultz, P and Urban, N R},
journal = {Ecological Modelling},
number = {1-2},
pages = {1--14},
title = {{Effects of bacterial dynamics on organic matter decomposition and nutrient release from sediments: A modeling study}},
volume = {210},
year = {2008}
}
@techreport{Schupp92,
address = {St. Paul, Minnesota},
author = {Schupp, D H},
institution = {Section of Fisheries, Minnesota Department of Natural Resources},
number = {41},
title = {{An ecological classification of {\{}M{\}}innesota lakes with associated fish communities}},
year = {1992}
}
@book{Sculthorpe67,
address = {New York, New York},
author = {Sculthorpe, C D},
pages = {610},
publisher = {St. Martin's Press},
title = {{The Biology of Aquatic Vascular Plants}},
year = {1967}
}
@misc{SFWMD13,
annote = {$\backslash$url{\{}http://www.swfwmd.state.fl.us/data/gis/layer{\_}library/category/swim{\}}. (Accessed October, 2013)},
author = {{SFWMD (Southwest Florida Water Management District)}},
title = {{GIS, Maps and Survey Shapefile Library for Support of Surface Water Improvement and Management Projects}},
year = {2013}
}
@article{Shanley05,
author = {Shanley, J B and Kamman, N C and Clair, T A and Chalmers, A},
journal = {Ecotoxicology},
pages = {125--134},
title = {{Physical controls on total methylmercury concentrations in streams and lakes of the northeastern {\{}USA{\}}}},
volume = {14},
year = {2005}
}
@techreport{Shellenbarger08,
address = {Reston, Virginia},
author = {Shellenbarger, G G and Schoellhamer, D H and Morgan, T L and Takekawa, J Y and Athearn, N D and Henderson, K D},
institution = {US Geological Survey},
number = {Open-File Report 2008-1097},
pages = {26},
title = {{Dissolved oxygen in {\{}G{\}}uadalupe {\{}S{\}}lough and {\{}P{\}}ond {\{}A3W{\}}, {\{}S{\}}outh {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay, {\{}C{\}}alifornia, {\{}A{\}}ugust and {\{}S{\}}eptember 2007}},
year = {2008}
}
@article{Sherwood2014,
abstract = {The Tampa Bay estuary is a unique and valued ecosystem that currently thrives between subtropical and temperate climates along Florida's west-central coast. The watershed is considered urbanized (42 {\{}{\{}{\}}{\{}{\%}{\}}{\{}{\}}{\}} lands developed); however, a suite of critical coastal habitats still persists. Current management efforts are focused toward restoring the historic balance of these habitat types to a benchmark 1950s period. We have modeled the anticipated changes to a suite of habitats within the Tampa Bay estuary using the sea level affecting marshes model under various sea level rise (SLR) scenarios. Modeled changes to the distribution and coverage of mangrove habitats within the estuary are expected to dominate the overall proportions of future critical coastal habitats. Modeled losses in salt marsh, salt barren, and coastal freshwater wetlands by 2100 will significantly affect the progress achieved in "Restoring the Balance" of these habitat types over recent periods. Future land management and acquisition priorities within the Tampa Bay estuary should consider the impending effects of both continued urbanization within the watershed and climate change. This requires the recognition that: (1) the Tampa Bay estuary is trending towards a mangrove-dominated system; (2) the current management paradigm of "Restoring the Balance" may no longer provide realistic, attainable goals; (3) restoration that creates habitat mosaics will prove more resilient in the future; and (4) establishing subtidal and upslope "refugia" may be a future strategy in this urbanized estuary to allow sensitive habitat types (e.g., seagrass and salt barren) to persist under anticipated climate change and SLR impacts. {\{}{\{}{\}}{\{}{\textcopyright}{\}}{\{}{\}}{\}} 2013 Springer Science+Business Media New York.},
author = {Sherwood, E T and Greening, H S},
doi = {10.1007/s00267-013-0179-5},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2014 Tech Pubs/TBEP{\_}07{\_}14{\_}Sherwood{\_}Greening{\_}2013{\_}SLR{\_}Impacts{\_}on{\_}TB{\_}10.1007{\_}s00267-013-0179-5.pdf:pdf},
issn = {0364152X},
journal = {Environmental Management},
keywords = {Climate Change,Climate change,Conservation of Natural Resources,Ecosystems,Estuaries,Florida [United States],Freshwater wetlands,Managemen,Management efforts,Ocean habitats,Sea le,Tampa Bay,United States,article,climate change,climate effect,coastal waters,coastal wetland,environm,fresh water},
number = {2},
pages = {401--415},
pmid = {24122098},
title = {{Potential impacts and management implications of climate change on tampa bay estuary critical coastal habitats}},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893498479{\%}7B{\%}7B{\%}7D{\%}7B{\&}{\%}7D{\%}7B{\%}7D{\%}7DpartnerID=40{\%}7B{\%}7B{\%}7D{\%}7B{\&}{\%}7D{\%}7B{\%}7D{\%}7Dmd5=2238e2d2ce447d1b4746064b3ea71cc5},
volume = {53},
year = {2014}
}
@inproceedings{Sherwood2016,
author = {Sherwood, E T and Greening, H S and Garcia, L and Kaufman, K and Janicki, A and Pribble, R and Cunningham, B and Peene, S and Fitzpatrick, J and Dixon, L K and Wessel, M},
booktitle = {Headwaters to estuaries: advances in watershed science and management—Proceedings of the Fifth Interagency Conference on Research in the Watersheds},
editor = {Stringer, C E and Kraus, K W and Latimer, J S},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2015 Tech Pubs/TBEP{\_}10{\_}15{\_}OTB{\_}IM{\_}Summary{\_}5thICRW.pdf:pdf},
pages = {156--163},
publisher = {U.S. Department of Agriculture Forest Service, Southern Research Station},
title = {{Development of an Integrated Ecosystem Model to Determine Effectiveness of Potential Watershed Management Projects on Improving Old Tampa Bay}},
url = {https://www.srs.fs.usda.gov/pubs/gtr/gtr{\_}srs211.pdf},
year = {2016}
}
@article{Sherwood2016a,
abstract = {Historically, significant impacts to Tampa Bay's water quality (e.g. chlorophyll-a concentrations) and ecosystem (e.g. seagrass coverage) have been documented as a result of early coastal development and urban expansion that occurred between the 1950s and 1980s. Since this time, Tampa Bay's estuarine water quality and ecosystems have significantly recovered. A long-term water quality monitoring program, first established by the Environmental Protection Commission of Hillsborough County (EPCHC) in 1972, was instrumental in the development of water quality management targets and regulatory thresholds related to the recovery of seagrass that helped guide restoration activities in the Bay from the 1980s to present. The EPCHC monitoring program has provided over 40 years of consistent and quality assured data that have been used to document Tampa Bay's ecosystem recovery, as well as, guide future research, monitoring, and management actions. Forecasted future pressures of continuing coastal population growth and climate change impacts further necessitate the need to maintain long-term water quality monitoring efforts in the Tampa Bay estuary. Maintenance of a robust estuarine monitoring program will not only help to identify future risks to the important environmental assets represented in the Tampa Bay estuary, but also help to identify potential risks to Tampa Bay's economic vitality that are garnered from maintaining a “healthy” Tampa Bay.},
author = {Sherwood, E T and Greening, H S and Janicki, A and Karlen, D J},
doi = {10.1016/j.rsma.2015.05.005},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2015 Tech Pubs/TBEP{\_}05{\_}15{\_}TBEP{\_}Monitoring{\_}long-term{\_}recovery{\_}through{\_}regional{\_}partnerships.pdf:pdf},
issn = {23524855},
journal = {Regional Studies in Marine Science},
keywords = {Estuarine,Tampa Bay,Water quality monitoring},
month = {mar},
pages = {1--11},
title = {{Tampa Bay estuary: Monitoring long-term recovery through regional partnerships}},
url = {http://www.sciencedirect.com/science/article/pii/S2352485515000183 http://linkinghub.elsevier.com/retrieve/pii/S2352485515000183},
volume = {4},
year = {2016}
}
@article{Sherwood17,
author = {Sherwood, E T and Greening, H S and Johansson, J O R and Kaufman, K and Raulerson, G E},
doi = {10.1353/sgo.2017.0026},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/2017 Tech Pubs/TBEP{\_}09{\_}17{\_}Sherwood{\_}et{\_}al{\_}TB{\_}Seagrass{\_}SE{\_}Geographer{\_}project{\_}muse{\_}667989.pdf:pdf},
issn = {1549-6929},
journal = {Southeastern Geographer},
number = {3},
pages = {294--319},
title = {{Tampa Bay (Florida, USA): Documenting Seagrass Recovery since the 1980's and Reviewing the Benefits}},
url = {https://muse.jhu.edu/article/667989},
volume = {57},
year = {2017}
}
@article{Shoredits13,
author = {Shoredits, A S and Clayton, J A},
doi = {10.1111/gec3.12039},
journal = {Geography Compass},
number = {5},
pages = {358--372},
title = {{Assessing the practice and challenges of stream restoration in urbanized environments of the {\{}USA{\}}}},
volume = {7},
year = {2013}
}
@book{Short2017,
address = {Dordrecht},
author = {Short, F T and Short, C A and Novak, A B},
booktitle = {The Wetland Book},
doi = {10.1007/978-94-007-6173-5},
editor = {Finlayson, C Max and Milton, G. Randy and Prentice, R. Crawford and Davidson, Nick C},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Short{\_}Seagrasses.pdf:pdf},
isbn = {978-94-007-6173-5},
keywords = {angiosperm,carbon storage,coastal habitat,estuarine vegetation,fl owering plants,seagrass,submerged marine,vascular plants,zostera},
publisher = {Springer Netherlands},
title = {{The Wetland Book}},
url = {http://link.springer.com/10.1007/978-94-007-6173-5},
year = {2017}
}
@article{Short96,
author = {Short, F T and Wyllie-Echeverria, S},
journal = {Environmental Conservation},
number = {1},
pages = {17--27},
title = {{Natural and human-induced disturbance of seagrasses}},
volume = {23},
year = {1996}
}
@book{Shumway11,
address = {New York, New York},
author = {Shumway, R H and Stoffer, D S},
edition = {3rd},
pages = {596},
publisher = {Springer-Verlag},
title = {{Time Series Analysis and its Applications: With R Examples}},
year = {2011}
}
@article{Sleeter11,
author = {Sleeter, B M and Wilson, T S and Soulard, C E and Liu, J},
doi = {10.1007/s10661-010-1385-8},
journal = {Environmental Monitoring and Assessment},
number = {1-4},
pages = {251--266},
title = {{Estimation of the late twentieth century land-cover change in {\{}C{\}}alifornia}},
volume = {173},
year = {2011}
}
@article{Smetacek08,
author = {Smetacek, V and Cloern, J E},
journal = {Science},
number = {5868},
pages = {1346--1348},
title = {{On phytoplankton trends}},
volume = {319},
year = {2008}
}
@phdthesis{Smith2003,
author = {Smith, R D},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2003{\_}Smith{\_}The{\_}Influence.pdf:pdf},
keywords = {Estuary,NH4,NO3,NOx,Sulfate},
pages = {105},
title = {{The Influence of Air Mass Origin on the Wet Deposition of Nitrogen to Tampa Bay, Florida}},
year = {2003}
}
@article{Smith2007,
abstract = {The wetlands surrounding Tampa Bay, Florida were extensively ditched for mosquito control in the 1950s. Spoil from ditch construction was placed adjacent to the wetlands ditches creating mound-like features (spoil-mounds). These mounds represent a loss of 14{\{}{\{}{\}}{\{}{\%}{\}}{\{}{\}}{\}} of the wetland area in Tampa Bay. Spoil mounds interfere with tidal flow and are locations for non-native plants to colonize (e.g., Schinus terebinthifolius). Removal of the spoil mounds to eliminate exotic plants, restore native vegetation, and re-establish natural hydrology is a restoration priority for environmental managers. Hydro-leveling, a new technique, was tested in a mangrove forest restoration project in 2004. Hydro-leveling uses a high pressure stream of water to wash sediment from the spoil mound into the adjacent wetland and ditch. To assess the effectiveness of this technique, we conducted vegetation surveys in areas that were hydro-leveled and in non-hydro-leveled areas 3 years post-project. Adult Schinus were reduced but not eliminated from hydro-leveled mounds. Schinus seedlings however were absent from hydro-leveled sites. Colonization by native species was sparse. Mangrove seedlings were essentially absent (≈2 m-2) from the centers of hydro-leveled mounds and were in low density on their edges (17 m-2) in comparison to surrounding mangrove forests (105 m-2). Hydro-leveling resulted in mortality of mangroves adjacent to the mounds being leveled. This was probably caused by burial of pneumatophores during the hydro-leveling process. For hydro-leveling to be a useful and successful restoration technique several requirements must be met. Spoil mounds must be lowered to the level of the surrounding wetlands. Spoil must be distributed further into the adjacent wetland to prevent burial of nearby native vegetation. Finally, native species may need to be planted on hydro-leveled areas to speed up the re-vegetation process. {\{}{\{}{\}}{\{}{\textcopyright}{\}}{\{}{\}}{\}} Springer Science+Business Media B.V. 2007.},
author = {Smith, Thomas J and Tiling, Ginger and Leasure, Pamela S},
doi = {10.1007/s11852-007-0007-2},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}Smith{\_}Restoring{\_}Coastal.pdf:pdf},
journal = {Journal of Coastal Conservation},
keywords = {Avicennia germinans,Florida,Laguncularia racemosa,Mangroves,Salt marshes,Schinus terebinthifolius,Tampa Bay,Wetlands loss},
number = {1},
pages = {67--74},
title = {{Restoring coastal wetlands that were ditched for mosquito control: A preliminary assessment of hydro-leveling as a restoration technique}},
volume = {11},
year = {2007}
}
@book{Snedaker1984,
author = {Snedaker, Samuel C and Snedaker, J G},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1984{\_}Snedaker{\_}the{\_}mangrove.pdf:pdf},
isbn = {9231021818},
keywords = {ecological research,ecosystems,mangrove areas,scientific methods},
title = {{The mangrove ecosystem : research methods}},
year = {1984}
}
@article{Snowling01,
author = {Snowling, S D and Kramer, J R},
journal = {Ecological Modelling},
pages = {17--30},
title = {{Evaluating modelling uncertainty for model selection}},
volume = {138},
year = {2001}
}
@article{Soetaert10,
author = {Soetaert, K and Petzoldt, T},
journal = {Journal of Statistical Software},
number = {3},
pages = {1--28},
title = {{Inverse modelling, sensitivity, and {\{}M{\}}onte {\{}C{\}}arlo analysis in {\{}R{\}} using package {\{}FME{\}}}},
volume = {33},
year = {2010}
}
@book{Soille03,
address = {Secaucus, New Jersey, USA},
author = {Soille, P},
edition = {2nd},
publisher = {Springer-Verlag},
title = {{Morphological Image Analysis: Principles and Applications}},
year = {2003}
}
@book{Sokal94,
address = {San Francisco, California, USA},
author = {Sokal, R and Rohlf, F J},
edition = {3rd},
pages = {880},
publisher = {W. H. Freeman},
title = {{Biometry}},
year = {1994}
}
@article{Sondergaard13,
author = {S{\o}ndergaard, M and Phillips, G and Hellsten, S and Kolada, A and Ecke, F and M{\"{a}}emets, H and Mjelde, M and Azzella, M M and Oggioni, A},
journal = {Hydrobiologia},
number = {1},
pages = {165--177},
title = {{Maximum growing depth of submerged macrophytes in {\{}E{\}}uropean lakes}},
volume = {704},
year = {2013}
}
@article{Soranno08,
author = {Soranno, P A and Cheruvelil, K S and Stevenson, R J and Rollins, S L and Holden, S W and Heaton, S and Torng, E},
journal = {Limnology and Oceanography},
number = {2},
pages = {773--787},
title = {{A framework for developing ecosystem-specific nutrient criteria: Integrating biological thresholds with predictive modeling}},
volume = {53},
year = {2008}
}
@article{Sousa2007,
author = {Sousa, W P and Kennedy, P G and Mitchell, B J and Ordonez, B M},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}Sousa{\_}Supply-side{\_}ecology.pdf:pdf},
journal = {Ecological Monographs},
number = {1},
pages = {53--76},
title = {{Supply-side ecology in mangroves: do propagule dispersal and seedling establishment explain forest structur?}},
volume = {77},
year = {2007}
}
@article{Southerland07,
author = {Southerland, M T and Rogers, G M and Kline, M J and Morgan, R P and Boward, D M and Kazyak, R and Klauda, R J and Stranko, S A},
journal = {Ecological Indicators},
number = {4},
pages = {751--767},
title = {{Improving biological indicators to better assess the condition of streams}},
volume = {7},
year = {2007}
}
@article{Spears09,
author = {Spears, B M and Gunn, I D M and Carvalho, L and Winfield, I J and Dudley, B and Murphy, K and May, L},
journal = {Aquatic Botany},
number = {2},
pages = {75--81},
title = {{An evaluation of methods for sampling macrophyte maximum colonisation depth in {\{}L{\}}och {\{}L{\}}even, {\{}S{\}}cotland}},
volume = {91},
year = {2009}
}
@article{Sponseller01,
author = {Sponseller, R A and Benfield, E F and Valett, H M},
doi = {10.1046/j.1365-2427.2001.00758.x},
journal = {Freshwater Biology},
number = {10},
pages = {1409--1424},
title = {{Relationships between land use, spatial scale and stream macroinvertebrate communities}},
volume = {46},
year = {2001}
}
@article{Sprague11,
author = {Sprague, L A and Hirsch, R M and Aulenbach, B T},
journal = {Environmental Science and Technology},
number = {17},
pages = {7209--7216},
title = {{Nitrate in the {\{}M{\}}ississippi {\{}R{\}}iver and its tributaries, 1980 to 2008: Are we making progress?}},
volume = {45},
year = {2011}
}
@article{Staehr10,
author = {Staehr, P A and Bade, D and de Bogert, M C Van and Koch, G R and Williamson, C and Hanson, P and Cole, J J and Kratz, T},
journal = {Limnology and Oceanography: Methods},
pages = {628--644},
title = {{Lake metabolism and the diel oxygen technique: State of the science}},
volume = {8},
year = {2010}
}
@article{Stein17,
author = {Stein, E D and Sengupta, A and Mazor, R D and McCune, K and Bledsoe, B P and Adams, S},
journal = {Ecohydrology},
title = {{Application of regional flow-ecology relationships to inform watershed management decisions: Applications of the {\{}ELOHA{\}} framework in the {\{}S{\}}an {\{}D{\}}iego {\{}R{\}}iver watershed, {\{}C{\}}alifornia, {\{}USA{\}}}},
year = {2017}
}
@article{Stelzer05,
author = {Stelzer, D and Schneider, S and Melzer, A},
journal = {International Review of Hydrobiology},
number = {2},
pages = {223--237},
title = {{Macrophyte-based assessment of lakes - a contribution to the implementation of the {\{}E{\}}uropean {\{}W{\}}ater {\{}F{\}}ramework {\{}D{\}}irective in {\{}G{\}}ermany}},
volume = {90},
year = {2005}
}
@article{Steward07,
author = {Steward, J S and Green, W C},
journal = {Estuaries and Coasts},
number = {4},
pages = {657--670},
title = {{Setting load limits for nutrients and suspended solids based upon seagrass depth-limit targets}},
volume = {30},
year = {2007}
}
@article{Steward10,
author = {Steward, J S and Lowe, E F},
journal = {Limnology and Oceanography},
number = {1},
pages = {433--445},
title = {{General empirical models for estimating nutrient load limits for {\{}F{\}}lorida's estuaries and inland waters}},
volume = {55},
year = {2010}
}
@article{Steward05,
author = {Steward, J S and Virnstein, R W and Morris, L J and Lowe, E F},
journal = {Estuaries},
number = {6},
pages = {923--935},
title = {{Setting seagrass depth, coverage, and light targets for the {\{}I{\}}ndian {\{}R{\}}iver {\{}L{\}}agoon System, {\{}F{\}}lorida}},
volume = {28},
year = {2005}
}
@article{Stoddard06,
author = {Stoddard, J L and Larsen, D P and Hawkins, C P and Johnson, R K and Norris, R H},
journal = {Ecological Applications},
number = {4},
pages = {1267--1276},
title = {{Setting expectations for the ecological condition of streams: The concept of reference condition}},
volume = {16},
year = {2006}
}
@article{Stow05,
author = {Stow, C A and Qian, S S and Craig, J K},
journal = {Environmental Science and Technology},
number = {3},
pages = {716--723},
title = {{Declining threshold for hypoxia in the {\{}G{\}}ulf of {\{}M{\}}exico}},
volume = {39},
year = {2005}
}
@article{Suter93,
author = {Suter, G W},
journal = {Environmental Toxicology and Chemistry},
number = {9},
pages = {1533--1539},
title = {{A critique of ecosystem health concepts and indexes}},
volume = {12},
year = {1993}
}
@article{Sutula17,
author = {Sutula, M and Kudela, R and {Hagy III}, J D and Jr., L W Harding and Senn, D and Cloern, J E and Bricker, S and Berg, G M and Beck, M W},
journal = {Estuarine, Coastal and Shelf Science},
pages = {107--118},
title = {{Novel analyses of long-term data provide a scientific basis for chlorophyll-a thresholds in {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {197},
year = {2017}
}
@article{Swackhamer2004,
abstract = {Considerable progress has been made in reducing the discharge of atmospheric pollutants from point sources such as effluent pipes. A more difficult challenge involves identifying and controlling environmental contaminants generated by dispersed or nonpoint sources such as automobile exhaust, pesticide applications, and myriad commercial and industrial processes. Nonpoint pollutants can travel far from their sources when they are discharged into rivers or enter the atmosphere. While waterborne contaminantshavereceivedgrowingattention, littlerecognitionhassofarbeengiventothefar-rangingenvironmentalconsequences of toxic substances and nutrients that are transported via the air. This report reviews three categories of airborne pollutants that we consider of greatest concern, both for their ecological effects and their impacts on the health of fish, wildlife, and humans: {\textperiodcentered} Organic compounds: These include long-recognized persistent organic pollutants and a vastly larger group of chemicals such as brominated flame retardants, water-repellent coatings, and synthetic fragrances that remain largely unmonitored andunregulated. {\textperiodcentered} Mercury: Oxidized forms of mercury readily rain from the air onto terrestrial and aquatic ecosystems. In sediments, they can be transformed into monomethyl mercury, the form most toxic to fish and the wildlife and humans that consume fish. {\textperiodcentered} Nutrients: Atmospheric transport is a significant and increasing source of plant nutrients to freshwater and marine ecosystems and can accelerate eutrophication of these waters. A review of the available scientific information indicates that: {\textperiodcentered} The pollutants that are most likely to present ecological risks are those that are (1) highly bioaccumulative, building up to high levels in animal tissues even when concentrations in the water remain relatively low, and (2) highly toxic, so that they cause harm at comparatively low doses. {\textperiodcentered} Atmosphere-water interactions that control the input and outgassing of persistent organic pollutants in aquatic systems arecriticallyimportantindeterminingthecyclingandresidencetimesofthesecompoundsandtheextentofcontamination of food webs. {\textperiodcentered} Although the effects of various types of pollutants are usually evaluated independently, many regions are subject to multiple pollutants, and their fate and impacts are intertwined. The effects of nutrient deposition on coastal waters, for instance, can alter how various organic contaminants and mercury are processed and bioaccumulated, and ultimately, how they affect aquatic organisms. {\textperiodcentered} For many organic pollutants, even long-banned chemicals such as PCBs and other organochlorines, non-atmospheric sources have been well controlled while atmospheric sources have either been neglected or ignored. {\textperiodcentered} Ecological effects of airborne organochlorines are a particular concern at high latitudes and altitudes. Even though concentrations of organochlorines in air masses and snow from northern and alpine regions are generally low, the food web dynamics, physiologies, and life cycles of cold region animals allow these contaminants to be biomagnified to extraordinary degrees in food chains. Atmospherically deposited contaminants are generated largely by human activities, and reducing the extent and impacts of this increasingly significant source of environmental pollution will require greater recognition, monitoring, and ultimately, regulation.},
author = {Swackhamer, Deborah L and Paerl, Hans W and Eisenreich, Steven J and Hurley, James and Hornbuckle, Keri C and McLachlan, Michael and Mount, David and Muir, Derek and Schindler, David},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2004{\_}Swackhamer{\_}Impacts{\_}of.pdf:pdf},
issn = {ISSN 1092-8987},
journal = {Issues in Ecology},
pages = {1--24},
title = {{Impacts of Atmospheric Pollutants on Aquatic Ecosystems}},
volume = {12},
year = {2004}
}
@article{Swanson15,
author = {Swanson, A and Kosmala, M and Lintott, C and Simpson, R and Smith, A and Packer, C},
journal = {Scientific Data},
pages = {150026},
title = {{{\{}S{\}}napshot {\{}S{\}}erengeti: High-frequency annotated camera trap images of 40 mammalian species in {\{}A{\}}frican savanna}},
volume = {2},
year = {2015}
}
@article{Swanson88,
author = {Swanson, F J and Kratz, T K and Caine, N and Woodmansee, R G},
journal = {Bioscience},
number = {2},
pages = {92--98},
title = {{Landform effects on ecosystem patterns and processes}},
volume = {38},
year = {1988}
}
@book{Swink94,
address = {Indianapolis, Indiana},
author = {Swink, F and Wilhelm, G},
edition = {fourth},
pages = {921},
publisher = {Indiana Academy of Science},
title = {{Plants of the {\{}C{\}}hicago Region}},
year = {1994}
}
@misc{SWMP14,
annote = {$\backslash$url{\{}http://copepod.org/nerrs-swmp-workshop/{\}}},
author = {{System-Wide Monitoring Program Data Analysis Training}},
title = {{SWMP Data Analysis Training Workshop provided at the 2014 NERRS/NERRA Annual Meeting, November 17, 2014}},
year = {2014}
}
@inproceedings{Tate2003,
author = {Tate, Paul and Begum, Mubeena and Mizak, Connie and Poor, Noreen and Hartsell, Ben and Edgerton, Eric and Way, Midenhall and Luther, Mark and Subramanian, Vembu and Gilbert, Sherryl and Batten, Jeff and Merchant, Chris and Atkeson, Thomas and Stevens, Robert},
booktitle = {Proceedings of the AWMA 96th Annual Meeting {\&} Exhibition},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/200x{\_}Tate{\_}A{\_}Comparison{\_}AWMA.pdf:pdf},
title = {{A Comparison of Continuous and Integrated Nitric Acid Ambient Air Concentrations and Atmospheric Deposition Rates}},
year = {2003}
}
@misc{TBEP17,
annote = {$\backslash$url{\{}http://www.tampabay.wateratlas.usf.edu/{\}}. (Accessed July, 2017)},
author = {{TBEP (Tampa Bay Estuary Program)}},
title = {{Tampa Bay Water Atlas}},
year = {2017}
}
@techreport{TBRPC86,
address = {St. Petersburg, Florida},
author = {{TBRPC (Tampa Bay Regional Planning Council)}},
institution = {Tampa Bay Regional Planning Council, Agency on Bay Management},
number = {Final},
title = {{Documenting the Economic Importance of {\{}T{\}}ampa {\{}B{\}}ay}},
year = {1986}
}
@article{Terrell96,
author = {Terrell, J W and Cade, B S and Carpenter, J and Thompson, J M},
journal = {Transactions of the American Fisheries Society},
number = {1},
pages = {104--117},
title = {{Modeling stream fish habitat limitations from wedge-shaped patterns of variation in standing stock}},
volume = {125},
year = {1996}
}
@article{Testa08b,
author = {Testa, J M and Kemp, W M},
journal = {Marine Ecology Progres Series},
pages = {63--79},
title = {{Variability of biogeochemical processes and physical transport in a partially stratified estuary: a box-modeling analysis}},
volume = {356},
year = {2008}
}
@article{Testa08a,
author = {Testa, J M and Kemp, W M and Boynton, W R and Hagy, J D},
journal = {Estuaries and Coasts},
number = {6},
pages = {1021--1037},
title = {{Long-term changes in water quality and productivity in the {\{}P{\}}atuxent {\{}R{\}}iver {\{}E{\}}stuary: 1985 to 2003}},
volume = {31},
year = {2008}
}
@article{Tewfik07,
author = {Tewfik, A and Rasmussen, J B and McCann, K S},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {7},
pages = {956--967},
title = {{Simplification of seagrass food webs across a gradient of nutrient enrichment}},
volume = {64},
year = {2007}
}
@article{Thebault08,
author = {Th{\'{e}}bault, J and Schraga, T S and Cloern, J E and Dunlavey, E G},
journal = {Wetlands},
number = {3},
pages = {841--851},
title = {{Primary production and carrying capacity of former salt ponds after reconnection to {\{}S{\}}an {\{}F{\}}rancisco {\{}B{\}}ay}},
volume = {28},
year = {2008}
}
@article{Thompson08,
author = {Thompson, J K and Koseff, J R and Monismith, S G and Lucas, L V},
journal = {Journal of Marine Systems},
number = {1-2},
pages = {153--166},
title = {{Shallow water processes govern system-wide phytoplankton bloom dynamics: A field study}},
volume = {74},
year = {2008}
}
@article{Thompson11,
author = {Thompson, S E and Basu, N B and Jr., J Lascurain and Aubeneau, A and Rao, P S C},
journal = {Water Resources Research},
number = {10},
pages = {W00J05},
title = {{Relative dominance of hydrologic versus biogeochemical factors on solute export across impact gradients}},
volume = {47},
year = {2011}
}
@book{Tiner2017,
address = {Dordrecht},
author = {Tiner, R W and Milton, G R},
booktitle = {The Wetland Book},
doi = {10.1007/978-94-007-6173-5},
editor = {Finlayson, C Max and Milton, G. Randy and Prentice, R. Crawford and Davidson, Nick C},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Tiner{\_}Estuarine Marsh.pdf:pdf;:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2016{\_}Tiner{\_}Estuarine Marsh.pdf:pdf},
isbn = {978-94-007-6173-5},
pages = {1--12},
publisher = {Springer Netherlands},
title = {{The Wetland Book}},
url = {http://link.springer.com/10.1007/978-94-007-6173-5},
year = {2017}
}
@article{Tobin58,
author = {Tobin, J},
journal = {Econometrica},
number = {1},
pages = {24--36},
title = {{Estimation of relationships for limited dependent variables}},
volume = {26},
year = {1958}
}
@article{Tolonen01,
author = {Tolonen, K T and Hamalainen, H and Holopainen, I J and Karjalainen, J},
journal = {Hydrobiologia},
number = {1},
pages = {39--67},
title = {{Influences of habitat type and environmental variables on littoral macroinvertebrate communities in a large lake system}},
volume = {152},
year = {2001}
}
@article{Tomasko05,
abstract = {The estuaries of Tampa Bay, Sarasota Bay, Lemon Bay, and Upper Charlotte Harbor are contiguous waterbodies located within the subtropical environment of Southwest Florida. Based on an examination of rainfall data over the period of record (1916-2001) within the watersheds of these estuaries, there is no evidence for spatial differences (at the watershed level) or monotonic trends in annual rainfall. During the 1980s, nitrogen loads into Tampa Bay and Sarasota Bay (generated primarily by domestic wastewater treatment facilities) were reduced by 57{\%} and 46{\%}, respectively. In response, both Tampa Bay and Sarasota Bay have lower phytoplankton concentrations, greater water clarity and more extensive seagrass coverage in 2002 than in the early 1980s. As there is no evidence of a concurrent trend in rainfall during the period of 1982-2001, it is unlikely that variation in rainfall can account for the observed increase in seagrass coverage in these two bays. In contrast, seagrass coverage has remained relatively constant since the mid 1980s in Lemon Bay and Charlotte Harbor. Domestic wastewater treatment facilities are minor sources of nitrogen to Lemon Bay, and water clarity in Charlotte Harbor varies mostly as a function of dissolved organic matter and non-chlorophyll associated turbidity, not phytoplankton levels. Even in estuaries that share boundaries and are within 100 km of each other, varied responses to anthropogenic changes and natural phenomena were observed in water quality and associated seagrass extent. Resource management strategies must take into account system-specific factors-not all strategies will result in similar results in different systems. {\textcopyright} 2005 Elsevier Ltd. All rights reserved.},
author = {Tomasko, D.A. and Corbett, C.A. and Greening, H.S. and Raulerson, G.E.},
doi = {10.1016/j.marpolbul.2005.02.010},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2005{\_}Tomasko{\_}SWFL{\_}Seagrass.pdf:pdf},
issn = {0025326X},
journal = {Marine Pollution Bulletin},
keywords = {Estuaries,Eutrophication,Florida,Seagrass,Water quality},
month = {aug},
number = {8},
pages = {797--805},
pmid = {16115497},
title = {{Spatial and temporal variation in seagrass coverage in Southwest Florida: assessing the relative effects of anthropogenic nutrient load reductions and rainfall in four contiguous estuaries}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0025326X05000615},
volume = {50},
year = {2005}
}
@unpublished{Tonneijck2016,
abstract = {Mangrove planting has become hugely popular. The majority of planting efforts are however failing. A more effective approach is to create the right conditions for mangroves to grow back naturally. Mangroves restored in this way generally survive and function better. This leaflet aims to contribute to best practice by exploring the question that everyone involved in mangrove restoration should ask: ‘To plant or not to plant?'},
author = {Tonneijck, F and International, Wetlands},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2017{\_}Tonneijck{\_}mangrove{\_}restoration.pdf:pdf},
pages = {12},
title = {{Mangrove restoration: to plant or not to plant?}},
year = {2016}
}
@article{Townsend08,
author = {Townsend, C R and Uhlmann, S S and Matthaei, C D},
doi = {10.1111/j.1365-2664.2008.01548.x},
journal = {Journal of Applied Ecology},
number = {6},
pages = {1810--1819},
title = {{Individual and combined responses of stream ecosystems to multiple stressors}},
volume = {45},
year = {2008}
}
@article{Townshend00,
author = {Townshend, J R G and Huang, C and Kalluri, S N V and Defries, R S and Liang, S},
journal = {International Journal of Remote Sensing},
number = {4},
pages = {839--843},
title = {{Beware of per-pixel characterization of land cover}},
volume = {21},
year = {2000}
}
@article{Tuerlinckx06,
author = {Tuerlinckx, F and Rijmen, F and Verbeke, G and DeBoeck, P},
journal = {British Journal of Mathematical and Statistical Psychology},
pages = {225--255},
title = {{Statistical inference in generalized linear mixed models: A review}},
volume = {59},
year = {2006}
}
@book{Tukey77,
address = {Reading, Massachusetts},
author = {Tukey, J W},
pages = {688},
publisher = {Addison-Wesley},
title = {{Exploratory Data Analysis}},
year = {1977}
}
@techreport{Tyler07,
address = {St. Petersburg, Florida},
author = {Tyler, D and Zawada, D G and Nayegandhi, A and Brock, J C and Crane, M P and Yates, K K and Smith, K E L},
institution = {US Geological Survey, US Department of the Interior},
number = {Open-File Report 2007-1051 (revised)},
title = {{Topobathymetric data for {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida}},
year = {2007}
}
@misc{USDA11,
annote = {{\{}Aerial Photography Field Office, Farm Service Agency, United States Department of Agriculture{\}}, Salt Lake City, Utah. $\backslash$url{\{}http://www.fsa.usda.gov/FSA/apfoapp?area=apfohome{\&}subject=landing{\&}topic=landing{\}}. (Accessed January, 2010)},
author = {{USDA (US Department of Agriculture)}},
title = {{2008 National Agricultural Imagery Program}},
year = {2011}
}
@misc{USDOC11,
annote = {$\backslash$url{\{}http://www.ncdc.noaa.gov/oa/ncdc.html{\}}. (Accessed January, 2010)},
author = {{USDOC (US Department of Commerce)}},
title = {{National Climatic Data Center}},
year = {2011}
}
@techreport{USEPA10,
address = {Annapolis, MD},
author = {{USEPA (US Environmental Protection Agency)}},
institution = {US Environmental Protection Agency, Chesapeake Bay Program Office},
number = {EPA903S10002 - CBP/TRS-303-10},
title = {{{\{}C{\}}hesapeake {\{}B{\}}ay phase 5.3 community watershed model}},
year = {2010}
}
@techreport{USEPA06,
address = {Washington, DC},
author = {{USEPA (US Environmental Protection Agency)}},
number = {EPA-842-B-06-003},
title = {{Volunteer estuary monitoring: A methods manual, second edition}},
year = {2006}
}
@techreport{USEPA02,
address = {Washington, DC},
author = {{USEPA (US Environmental Protection Agency)}},
institution = {Office of Environmental Information, Office of Water, US Environmental Protection Agency},
number = {EPA-822-R-02-048},
title = {{Summary of biological assessment programs and biocriteria development for states, tribes, and interstate commissions: Streams and wadeable rivers}},
year = {2002}
}
@techreport{USEPA00,
address = {Washington, DC},
author = {{USEPA (US Environmental Protection Agency)}},
institution = {Office of Water, Office of Research and Development, US Environmental Protection Agency},
number = {EPA-822-B-00-025},
title = {{Stressor identification guidance document}},
year = {2000}
}
@techreport{USEPA98,
address = {Washington, DC},
author = {{USEPA (US Environmental Protection Agency)}},
institution = {Office of Water, Office of Research and Development, US Environmental Protection Agency},
number = {EPA-822-R-98-002},
title = {{National strategy for the development of regional nutrient criteria}},
year = {1998}
}
@techreport{USEPA98,
address = {Washington, DC},
author = {{USEPA (US Environmental Protection Agency)}},
institution = {Office of Water, Office of Research and Development, US Environmental Protection Agency},
number = {EPA-822-R-98-002},
title = {{National strategy for the development of regional nutrient criteria}},
year = {1998}
}
@misc{USGS15,
annote = {$\backslash$url{\{}http://cbrim.er.usgs.gov/{\}}. (Accessed November, 2015)},
author = {{USGS (US Geological Survey)}},
title = {{Water Quality Loads and Trends at Nontidal Monitoring Stations in the Chesapeake Bay Watershed}},
year = {2015}
}
@misc{USGS14,
annote = {$\backslash$url{\{}https://nhd.usgs.gov{\}}. (Accessed August, 2017)},
author = {{USGS (US Geological Survey)}},
title = {{National Hydrography Dataset available on the World Wide Web}},
year = {2014}
}
@book{Usinger56,
address = {Berkeley, California},
author = {Usinger, J L},
doi = {10.5962/bhl.title.61952},
pages = {508},
publisher = {University of California Press},
title = {{Aquatic Insects of California: With Keys to North American Genera and California Species}},
year = {1956}
}
@article{Vadeboncoeur03,
author = {Vadeboncoeur, Y and Jeppesen, E and Zanden, M J Vander and Schierup, H H and Christoffersen, K and Lodge, D M},
journal = {Limnology and Oceanography},
number = {4},
pages = {1408--1418},
title = {{From {\{}G{\}}reenland to green lakes: Cultural eutrophication and the loss of benthic pathways in lakes}},
year = {2003}
}
@article{Valiela2007,
abstract = {The abundance of birds recorded in the North American Breeding Bird Survey decreased by tip to 18 percent between 1966 and 2005. The abundance of US and Canadian resident species decreased by 30 percent, and that of migrants within the United States and Canada decreased by 19 percent. By contrast, Neotropical migrants increased by up to 20 percent. Land-cover changes in northern latitudes therefore seem more consequential for bird populations than those occurring in Neotropical habitats. Lower abundances were most marked for resident breeding birds that used open, edge, and wetland habitats, the environments most affected by human disturbances-particularly urban sprawl-in northern latitudes. The abundance of resident and migrant forest-dwelling birds increased (although trends varied from species to species), with the increases seeming to follow the 20th-century expansion of forest area in northern latitudes, rather than the loss of Neotropical forests. The geographic footprint of changes in bird abundance linked to habitat changes in North America may thus be extending southward, with negative effects on birds that use open habitats and positive effects on forest birds.},
author = {Valiela, Ivan and Martinetto, Paulina},
doi = {10.1641/B570410},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}Valiela{\_}Changes{\_}in.pdf:pdf},
issn = {0006-3568},
journal = {BioScience},
keywords = {habitat losses,loss of birds,temperate avifauna,tropical avifauna},
number = {4},
pages = {360--370},
title = {{Changes in Bird Abundance in Eastern North America: Urban Sprawl and Global Footprint?}},
url = {http://academic.oup.com/bioscience/article/57/4/360/220630/Changes-in-Bird-Abundance-in-Eastern-North-America},
volume = {57},
year = {2007}
}
@unpublished{Valigura1996,
address = {Silver Spring, MD},
author = {Valigura, R A and Luke, W T and Artz, R S and Hicks, B B},
booktitle = {Decision Analysis Series},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1996{\_}Valigura{\_}Atmospheric{\_}nutrient.pdf:pdf},
number = {9},
pages = {78},
title = {{Atmospheric nutrient input to coastal areas: Reducing the uncertainties}},
year = {1996}
}
@techreport{Valley04,
address = {St. Paul, Minnesota},
author = {Valley, R D and Cross, T K and Radomski, P},
institution = {Division of Fish and Wildlife, Minnesota Department of Natural Resources},
number = {Special Publication 160},
title = {{The role of submersed aquatic vegetation as habitat for fish in {\{}M{\}}innesota lakes, including the implications of non-native plant invasions and their management}},
year = {2004}
}
@article{Valley10,
author = {Valley, R D and Habrat, M D and Dibble, E D and Drake, M T},
journal = {Hydrobiologia},
number = {1},
pages = {385--389},
title = {{Movement patterns and habitat use of three declining littoral fish species in a north-temperate mesotrophic lake}},
year = {2010}
}
@article{Valley12,
author = {Valley, R D and Heiskary, S},
journal = {Lake and Reservoir Management},
number = {4},
pages = {338--345},
title = {{Short-term declines in curlyleaf pondweed in {\{}M{\}}innesota: Potential influences of snowfall}},
volume = {28},
year = {2012}
}
@unpublished{VanDolah2007,
abstract = {Recently, the Chesapeake Bay Program convened a workshop in Binghamton, NY to discuss the current understanding of nitrogen that enters the Chesapeake Bay from the air. Surprisingly, the group concluded that at least one third of all the nitrogen reaching the Bay — and likely significantly more — comes from atmospheric deposition.},
author = {{Van Dolah}, E},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2007{\_}CBSTAC{\_}Air{\_}nitrogen.pdf:pdf},
pages = {3},
title = {{Workshop on Atmospheric Depostion of Nitrogen}},
year = {2007}
}
@techreport{Vaughn09,
address = {St. Paul, Minnesota},
author = {Vaughn, S R},
institution = {Division of Waters, Minnesota Department of Natural Resources},
number = {{\{}D{\}}raft},
title = {{{\{}DNR{\}} watershed delineation: Project history, methodology, terminology, and data attribution}},
year = {2009}
}
@book{Venables02,
address = {New York, New York},
author = {Venables, W N and Ripley, B D},
edition = {Fourth},
publisher = {Springer-Verlag},
title = {{Modern Applied Statistics with {\{}S{\}}}},
url = {http://www.stats.ox.ac.uk/pub/MASS4},
year = {2002}
}
@article{Vestergaard00,
author = {Vestergaard, O and Sand-Jensen, K},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {10},
pages = {2022--2031},
title = {{Aquatic macrophyte richness in {\{}D{\}}anish lakes in relation to alkalinity, transparency, and lake area}},
volume = {57},
year = {2000}
}
@article{Vondracek14,
author = {Vondracek, B and Koch, J D and Beck, M W},
doi = {10.1016/j.ecolind.2013.07.002},
journal = {Ecological Indicators},
pages = {178--185},
title = {{A comparison of survey methods to evaluate macrophyte index of biotic integrity performance in {\{}M{\}}innesota lakes}},
volume = {36},
year = {2014}
}
@article{Wade08,
author = {Wade, A J and Jackson, B M and Butterfield, D},
journal = {Science of the Total Environment},
number = {1-3},
pages = {52--74},
title = {{Over-parameterised, uncertain `mathematical marionettes' - how can we best use catchment water quality models? {\{}A{\}}n example of an 80-year catchment-scale nutrient balance}},
volume = {400},
year = {2008}
}
@article{Wagener01,
author = {Wagener, T and Boyle, D P and Lees, M J and Wheater, H S and Gupta, H V and Sorooshian, S},
journal = {Hydrology and Earth System Sciences},
number = {1},
pages = {13--26},
title = {{A framework for development and application of hydrological models}},
volume = {5},
year = {2001}
}
@incollection{Wagener01b,
address = {USA},
author = {Wagener, T and Lees, M J and Wheater, H S},
booktitle = {Mathematical Models of Small Watershed Hydrology and Applications - Volume 2},
editor = {Singh, V P and Meyer, D K Frevert S P},
pages = {91--140},
publisher = {Water Resources Publications LLC},
title = {{A toolkit for the development and application of parsimonious hydrological models}},
year = {2001}
}
@article{Wagner06,
author = {Wagner, T and Jubar, A K and Bremigan, M T},
journal = {Transactions of the American Fisheries Society},
number = {4},
pages = {843--852},
title = {{Can habitat alteration and spring angling explain largemouth bass nest success?}},
volume = {135},
year = {2006}
}
@article{Wagner08,
author = {Wagner, T and Soranno, P A and Cheruvelil, K S and Renwick, W H and Webster, K E and Vaux, P and Abbitt, R J},
journal = {Environmental Monitoring and Assessment},
number = {1-3},
pages = {131--147},
title = {{Quantifying sample biases of inland lake sampling programs in relation to lake surface area and land use/cover}},
volume = {141},
year = {2008}
}
@article{Wainger2011,
abstract = {Increasingly government agencies are seeking to quantify the outcomes of proposed policy options in terms of ecosystem service benefits, yet conflicting definitions and ad hoc approaches to measuring ecosystem services have created confusion regarding how to rigorously link ecological change to changes in human well-being. Here, we describe a step-by-step framework for producing ecological models and metrics that can effectively serve an economic-benefits assessment of a proposed change in policy or management. A focus of the framework is developing comparable units of ecosystem goods and services to support decision-making, even if outcomes cannot be monetized. Because the challenges to translating ecological changes to outcomes appropriate for economic analyses are many, we discuss examples that demonstrate practical methods and approaches to overcoming data limitations. The numerous difficult decisions that government agencies must make to fairly use and allocate natural resources provides ample opportunity for interdisciplinary teams of natural and social scientists to improve methods for quantifying changes in ecosystem services and their effects on human well-being. This framework is offered with the intent of promoting the success of such teams as they support managers in evaluating the equivalency of ecosystem service offsets and trades, establishing restoration and preservation priorities, and more generally, in developing environmental policy that effectively balances multiple perspectives.},
archivePrefix = {arXiv},
arxivId = {arXiv:physics/0608246v3},
author = {Wainger, Lisa and Mazzotta, Marisa},
doi = {10.1007/s00267-011-9726-0},
eprint = {0608246v3},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2011{\_}Wainger{\_}Realizing{\_}Potential{\_}Ecosystem.pdf:pdf},
isbn = {0026701197},
issn = {0364152X},
journal = {Environmental Management},
keywords = {Benefit transfer,Cost-benefit analysis,Ecological indicators,Ecological-economic modeling,Ecosystem services,Ecosystem valuation,Environmental economics,Environmental policy and management,Spatial analysis},
number = {4},
pages = {710--733},
pmid = {21786182},
primaryClass = {arXiv:physics},
title = {{Realizing the potential of ecosystem services: A framework for relating ecological changes to economic benefits}},
volume = {48},
year = {2011}
}
@article{Wan10,
author = {Wan, H and Chizinski, C J and Dolph, C L and Vondracek, B and Wilson, B N},
journal = {Ecological Indicators},
number = {4},
pages = {781--788},
title = {{The impact of rare taxa on a fish index of biotic integrity}},
volume = {10},
year = {2010}
}
@article{Wan17,
author = {Wan, Y and Wan, L and Li, Y and Doering, P},
journal = {Water Research},
pages = {180--194},
title = {{Decadal and seasonal trends of nutrient concentration and export from highly managed coastal catchments}},
volume = {115},
year = {2017}
}
@article{Wang10,
author = {Wang, L Z and Wehrly, K and Breck, J E and Kraft, L S},
journal = {Environmental Management},
number = {3},
pages = {471--483},
title = {{Landscape-based assessment of human disturbance for {\{}M{\}}ichigan lakes}},
volume = {46},
year = {2010}
}
@article{Wang99,
author = {Wang, P F and Martin, J and Morrison, G},
journal = {Estuarine, Coastal and Shelf Science},
number = {1},
pages = {1--20},
title = {{Water quality and eutrophication in {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida}},
volume = {49},
year = {1999}
}
@article{Ward13,
author = {Ward, B A and Schartau, M and Oschlies, A and Martin, A P and Follows, M J and Anderson, T R},
journal = {Progress in Oceanography},
pages = {49--65},
title = {{When is a biogeochemical model too complex? Objective model reduction and selection for {\{}N{\}}orth {\{}A{\}}tlantic time-series sites}},
volume = {116},
year = {2013}
}
@article{Warner05,
author = {Warner, J C and Geyer, W R and Lerczak, J A},
journal = {Journal of Geophysical Research: Oceans},
number = {C5},
pages = {13},
title = {{Numerical modeling of an estuary: a comprehensive skill assessment}},
volume = {110},
year = {2005}
}
@book{Warner09,
address = {Thousand Oaks, California},
author = {Warner, T A and Nellis, M D and Foody, G M},
publisher = {SAGE Publications},
title = {{The {\{}SAGE{\}} Handbook of Remote Sensing}},
year = {2009}
}
@techreport{Warren79,
address = {Corvallis, Oregon},
author = {Warren, C E},
institution = {Corvallis Environmental Research Laboratory, U.S Environmental Protection Agency},
number = {EPA 600/3-79-059},
title = {{Toward classification and rationale for watershed management and stream protection}},
year = {1979}
}
@article{Wehrly12,
author = {Wehrly, K E and Breck, J E and Wang, L and Szabo-Kraft, L},
journal = {Lake and Reservoir Management},
number = {2},
pages = {158--169},
title = {{Assessing local and landscape patterns of residential shoreline development in {\{}M{\}}ichigan lakes}},
volume = {28},
year = {2012}
}
@unpublished{Welsh1994,
address = {Tallahassee, FL},
author = {Welsh, S and Pichard, E},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/1994{\_}Welsh{\_}Pollution{\_}effects.pdf:pdf},
pages = {15},
title = {{Pollution effects of outboard marine engines}},
year = {1994}
}
@techreport{Wenner01,
address = {Charleston, South Carolina},
author = {Wenner, E L and Holland, A F and Arendt, M D and Chen, Y and Edwards, D and Miller, C and Meece, M and Caffrey, J},
institution = {MRD Contribution No. 459. The Cooperative Institute for Coastal and Estuarine Environmental Technology. NOAA Grant Number: NA97OR0209.},
pages = {276},
title = {{A synthesis of water quality data from the National Estuarine Research Reserve's System-Wide Monitoring Program}},
year = {2001}
}
@article{Wenner04,
author = {Wenner, E and Sanger, D and Arendt, M and Holland, A F and Chen, Y},
journal = {Journal of Coastal Research},
number = {SI},
pages = {17--38},
title = {{Variability in dissolved oxygen and other water-quality variables within the {\{}N{\}}ational {\{}E{\}}stuarine {\{}R{\}}esearch {\{}R{\}}eserve {\{}S{\}}ystem}},
volume = {45},
year = {2004}
}
@article{Werner93,
author = {Werner, I and Hollibaugh, J T},
journal = {Limnology and Oceanography},
number = {5},
pages = {949--964},
title = {{$\backslash$textit{\{}{\{}P{\}}otamocorbula amurensis{\}} - comparison of clearance rates and assimilation efficiencies for phytoplankton and bacterioplankton}},
volume = {38},
year = {1993}
}
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address = {San Diego, California},
author = {Wetzel, R G},
pages = {1006},
publisher = {Academic Press},
title = {{Limnology: Lake and River Ecosystems}},
year = {2001}
}
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author = {Wheater, H S and Bishop, K H and Beck, M B},
journal = {Hydrological Processes},
number = {1},
pages = {89--109},
title = {{The identification of conceptual hydrological models for surface water acidification}},
volume = {1},
year = {1986}
}
@incollection{Whittier99,
address = {Boca Raton, Florida},
author = {Whittier, T R},
booktitle = {Assessing the Sustainability and Biological Integrity of Water Resources Using Fish Communities},
editor = {Simon, T P},
pages = {563--582},
publisher = {CRC Press},
title = {{Development of {\{}IBI{\}} metrics for lakes in southern {\{}N{\}}ew {\{}E{\}}ngland}},
year = {1999}
}
@article{Whittier88,
author = {Whittier, T R and Hughes, R M and Larsen, D P},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
number = {7},
pages = {1264--1278},
title = {{Correspondence between ecoregions and spatial patterns in stream ecosystems in {\{}O{\}}regon}},
volume = {45},
year = {1988}
}
@article{Whittier07,
author = {Whittier, T R and Hughes, R M and Stoddard, J L and Lomnicky, G A and Peck, D V and Herlihy, A T},
journal = {Transactions of the American Fisheries Society},
number = {3},
pages = {718--735},
title = {{A structured approach for developing indices of biotic integrity: {\{}T{\}}hree examples from streams and rivers in the {\{}W{\}}estern {\{}USA{\}}}},
volume = {136},
year = {2007}
}
@book{Wickham14,
address = {Boca Raton, Florida},
author = {Wickham, H},
pages = {476},
publisher = {Chapman and Hall, CRC Press},
title = {{Advanced R}},
year = {2014}
}
@manual{Wickham14b,
annote = {R package version 0.1},
author = {Wickham, H},
title = {{nycflights13: Data about flights departing NYC in 2013.}},
url = {http://cran.r-project.org/package=nycflights13},
year = {2014}
}
@book{Wickham09,
author = {Wickham, Hadley},
isbn = {978-0-387-98140-6},
publisher = {Springer-Verlag. New York},
title = {{ggplot2: Elegant Graphics for Data Analysis}},
url = {http://had.co.nz/ggplot2/book},
year = {2009}
}
@article{Wilcox92,
author = {Wilcox, D A and Meeker, J E},
journal = {Wetlands},
number = {3},
pages = {192--203},
title = {{Implications for Faunal Habitat Related to Altered Macrophyte Structure in Regulated Lakes in Northern {\{}M{\}}innesota}},
volume = {12},
year = {1992}
}
@incollection{Williams01,
address = {Sunderland, Massachusetts},
author = {Williams, S L and Heck, K L},
booktitle = {Marine Community Ecology},
editor = {Bertness, M D and Gaines, S D and Hay, M E},
publisher = {Sinauer Associates},
title = {{Seagrass community ecology}},
year = {2001}
}
@article{Wilson13,
author = {Wilson, M and Meyers, S D and Luther, M E},
journal = {Climate Dynamics},
title = {{Synoptic volumetric variations and flushing of the {\{}T{\}}ampa {\{}B{\}}ay estuary}},
year = {2013}
}
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author = {Winder, M and Cloern, J E},
journal = {Philosophical Transactions of the Royal Society B-Biological Sciences},
number = {1555},
pages = {3215--3226},
title = {{The annual cycles of phytoplankton biomass}},
volume = {365},
year = {2010}
}
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author = {Winter, T C},
journal = {Journal of the American Water Resources Association},
number = {2},
pages = {335--349},
title = {{The concept of hydrologic landscapes}},
volume = {37},
year = {2001}
}
@article{Wiseman97,
author = {Wiseman, W J and Rabalais, N N and Turner, R E and Dinnel, S P and MacNaughton, A},
journal = {Journal of Marine Systems},
number = {1-4},
pages = {237--248},
title = {{Seasonal and interannual variability within the {\{}L{\}}ouisiana coastal current: stratification and hypoxia}},
volume = {12},
year = {1997}
}
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author = {Wofsy, S C},
journal = {Limnology and Oceanography},
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pages = {1144--1155},
title = {{A simple model to predict extinction coefficients and phytoplankton biomass in eutrophic waters}},
volume = {28},
year = {1983}
}
@book{Wood06,
address = {London, United Kingdom},
author = {Wood, S N},
pages = {410},
publisher = {Chapman and Hall, CRC Press},
title = {{Generalized Additive Models: An Introduction with R}},
year = {2006}
}
@article{Wood06b,
author = {Wood, S N},
journal = {Biometrics},
number = {4},
pages = {1025--1036},
title = {{Low-rank scale-invariant tensor product smooths for generalized additive mixed models}},
volume = {62},
year = {2006}
}
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author = {Woodruff, D L and Stumpf, R P and Scope, J A and Paerl, H W},
journal = {Remote Sensing of Environment},
number = {1},
pages = {41--52},
title = {{Remote estimation of water clarity in optically complex estuarine waters}},
volume = {68},
year = {1999}
}
@incollection{Wooten85,
address = {Tampa, Florida, USA},
author = {Wooten, G R},
booktitle = {Proceedings of the Tampa Bay Area Scientific Information Symposium},
editor = {Treat, S F and Simon, J L and Lewis, R R and Whitman, R L},
pages = {19--26},
publisher = {Florida Sea Grant Report No. 65, Bellwether Press},
title = {{The meteorology of {\{}T{\}}ampa {\{}B{\}}ay}},
year = {1985}
}
@article{Wright04,
author = {Wright, S A and Schoellhamer, D H},
journal = {San Francisco Estuary and Watershed Science},
number = {2},
pages = {1--14},
title = {{Trends in the sediment yield of the {\{}S{\}}acramento {\{}R{\}}iver, {\{}C{\}}alifornia, 1957-2001}},
volume = {2},
year = {2004}
}
@article{Wu12,
author = {Wu, N and Schmalz, B and Fohrer, N},
journal = {Ecological Indicators},
number = {1},
pages = {158--167},
title = {{Development and testing of a phytoplankton index of biotic integrity ({\{}P-IBI{\}}) for a {\{}G{\}}erman lowland river}},
volume = {13},
year = {2012}
}
@article{Xian07,
author = {Xian, G and Crane, M and Su, J},
journal = {Environmental Management},
number = {4},
pages = {965--976},
title = {{An analysis of urban development and its environmental impact on the {\{}T{\}}ampa {\{}B{\}}ay watershed}},
volume = {85},
year = {2007}
}
@book{Yates2011,
abstract = {Tampa Bay is recognized internationally for its remarkable progress towards recovery since it was pronounced “dead” in the late 1970s. Due to significant efforts by local governments, industries and private citizens throughout the watershed, water clarity in Tampa Bay is now equal to what it was in 1950, when population in the watershed was less than one-quarter of what it is today. Seagrass extent has increased by more than 8,000 acres since the mid-1980s, and fish and wildlife populations are increasing. Central to this successful turn-around has been the Tampa Bay resource management community's long-term commitment to development and implementation of strong science-based management strategies. Research institutions and agencies, including Eckerd College, the Florida Wildlife Commission Fish and Wildlife Research Institute, Mote Marine Laboratory, National Oceanic and Atmospheric Administration, the Southwest Florida Water Management District, University of South Florida, U.S. Environmental Protection Agency, U.S. Geological Survey, local and State governments, and private companies contribute significantly to the scientific basis of our understanding of Tampa Bay's structure and ecological function. Resource management agencies, including the Tampa Bay Regional Planning Council's Agency on Bay Management, the Southwest Florida Water Management District's Surface Water Improvement and Management Program, and the Tampa Bay Estuary Program, depend upon this scientific basis to develop and implement regional adaptive management programs. The importance of integrating science with management has become fully recognized by scientists and managers throughout the region, State and Nation. Scientific studies conducted in Tampa Bay over the past 10–15 years are increasingly diverse and complex, and resource management programs reflect our increased knowledge of geology, hydrology and hydrodynamics, ecology and restoration techniques. However, a synthesis of this research and its integration into resource management has not been prepared for Tampa Bay since the mid-1980s. The need for an up-to-date synthesis of Tampa Bay science and management has resulted in the production of this document. The U.S. Geological Survey recently completed a 5-year Tampa Bay Integrated Science Study, and the Tampa Bay Estuary Program updated the Comprehensive Conservation and Management Plan for Tampa Bay in 2006. These efforts build upon results of the many research and management studies and programs summarized here.},
author = {Yates, K K and Greening, H S and Morrison, G},
isbn = {9781411331600},
pages = {280},
title = {{Integrating Science and Resource Management in Tampa Bay, Florida}},
url = {https://pubs.usgs.gov/circ/1348/},
year = {2011}
}
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author = {Ye, W and Bates, B C and Viney, N R and Sivapalan, M and Jakeman, A J},
journal = {Water Resources Research},
number = {1},
pages = {153--166},
title = {{Performance of conceptual rainfall-runoff models in low yielding ephemeral catchments}},
volume = {33},
year = {1997}
}
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author = {Yin, K D and Lin, Z F and Ke, Z Y},
journal = {Continental Shelf Research},
number = {16},
pages = {1935--1948},
title = {{Temporal and spatial distribution of dissolved oxygen in the {\{}P{\}}earl {\{}R{\}}iver {\{}E{\}}stuary and adjacent coastal waters}},
volume = {24},
year = {2004}
}
@article{Young11,
author = {Young, W A and Millie, D F and Weckman, G R and Anderson, J S and Klarer, D M and Fahnenstiel, G L},
journal = {Environmental Modelling and Software},
number = {10},
pages = {1199--1210},
title = {{Modeling net ecosystem metabolism with an artificial neural network and {\{}B{\}}ayesian belief network}},
volume = {26},
year = {2011}
}
@article{Yvon12,
author = {Yvon-Durocher, G and Caffrey, J M and Cescatti, A and Dossena, M and del Giorgio, P and Gasol, J M and Montoya, J M and Pumpanen, J and Staehr, P A and Trimmer, M and Woodward, G and Allen, A P},
journal = {Nature},
number = {7408},
pages = {472--476},
title = {{Reconciling the temperature dependence of respiration across timescales and ecosystem types}},
volume = {487},
year = {2012}
}
@techreport{Zarbock94,
address = {St. Petersburg, Florida, USA},
author = {Zarbock, H and Janicki, A and Wade, D and Heimbuch, D and Wilson, H},
file = {:T$\backslash$:/06{\_}LIBRARY/02{\_}TBEP{\_}TECH{\_}PUBS/1994 Tech Pubs/TBEP{\_}04{\_}94{\_}TNEstimates.pdf:pdf},
institution = {Prepared for the Tampa Bay National Estuary Program},
number = {No. 04-94},
title = {{Estimates of total nitrogen, total phosphorus, and total suspended solids loadings ot {\{}T{\}}ampa {\{}B{\}}ay, {\{}F{\}}lorida}},
year = {1994}
}
@manual{Zell98,
annote = {University of Stuttgart and WSI, University of T{\"{u}}bingen},
author = {Zell, A and Mamier, G and Vogt, M and Mache, N and H{\"{u}}bner, R and D{\"{o}}ring, S and Herrmann, K U and Soyez, T and Schmalzl, M and Sommer, T and Hatzigeorgiou, A and Posselt, D and Schreiner, T and Kett, B and Clemente, G and Wieland, J and Gatter, J},
title = {{{\{}SNNS{\}}: Stuttgart Neural Network Simulator, User Manual, Version 4.2}},
url = {http://www.ra.cs.uni-tuebingen.de/SNNS/},
year = {1998}
}
@article{Zhang13,
author = {Zhang, Q and Brady, D C and Ball, W P},
journal = {Science of the Total Environment},
pages = {208--221},
title = {{Long-term seasonal trends of nitrogen, phosphorus, and suspended sediment load from the non-tidal {\{}S{\}}usquehanna {\{}R{\}}iver {\{}B{\}}asin to {\{}C{\}}hesapeake {\{}B{\}}ay}},
volume = {452-453},
year = {2013}
}
@article{Zhang15,
author = {Zhang, Q and Brady, D C and Boynton, W R and Ball, W P},
journal = {Journal of the American Water Resources Association},
number = {6},
pages = {1534--1555},
title = {{Long-term trends of nutrients and sediment from the nontidal {\{}C{\}}hesapeake watershed: An assessment of progress by river and season}},
volume = {51},
year = {2015}
}
@article{Zhang16,
author = {Zhang, Q and Harman, C J and Ball, W P},
journal = {Geophysical Research Letters},
number = {10},
pages = {215--224},
title = {{An improved method for interpretation of riverine concentration-discharge relationships indicates long-term shifts in reservoir sediment trapping}},
volume = {43},
year = {2016}
}
@article{Zhao10,
author = {Zhao, L and Chen, C and Vallino, J and Hopkinson, C and Beardsley, R C and Lin, H and Lerczak, J},
journal = {Journal of Geophysical Research},
number = {C10},
pages = {13},
title = {{Wetland-estuarine-shelf interactions on the {\{}P{\}}lum {\{}I{\}}sland {\{}S{\}}ound and {\{}M{\}}errimack {\{}R{\}}iver in the {\{}M{\}}assachusetts coast}},
volume = {115},
year = {2010}
}
@article{Zhao2016,
abstract = {Abstract Coastal wetlands are considered to be amongst the most productive ecosystems and can provide invaluable ecological services. However, coastal wetlands are listed amongst the most threatened ecosystems suffering from anthropogenic activities. The loss or degradation of coastal wetlands has drawn a high level of attention to wetland restoration. Improvement of the structure and function of degraded, damaged and destroyed wetlands may be achieved through ecological restoration. Large numbers of restoration projects have been conducted worldwide based on different restoration goals and different methods. It is undoubtedly important to evaluate whether coastal wetland restoration is successful. However, coastal wetland restoration assessment has become challenging because of current disagreement on definitions and concepts of restoration evaluation. We reviewed the methodology of coastal wetland restoration and criteria for success evaluation, and then summarized the issues for current wetland restoration and success evaluation based on literature review. Moreover, we used an estuarine wetland affected by urbanization as a sample to demonstrate how to establish a success indicator system for guiding wetland restoration and evaluating the success of wetland restoration.},
author = {Zhao, Qingqing and Bai, Junhong and Huang, Laibin and Gu, Binhe and Lu, Qiongqiong and Gao, Zhaoqin},
doi = {10.1016/j.ecolind.2015.07.003},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2015{\_}Zhao{\_}Review{\_}methodologies.pdf:pdf},
isbn = {1470160X},
issn = {1470160X},
journal = {Ecological Indicators},
keywords = {Coastal wetlands,Ecological restoration,Success indicator system,Success indicators},
pages = {442--452},
publisher = {Elsevier Ltd},
title = {{A review of methodologies and success indicators for coastal wetland restoration}},
volume = {60},
year = {2016}
}
@article{Zhu07,
author = {Zhu, B and Fitzgerald, D G and Hoskins, S B and Rudstam, L G and Mayer, C M and Mills, E L},
journal = {Journal of Great Lakes Research},
number = {1},
pages = {122--135},
title = {{Quantification of historical changes of submerged aquatic vegetation cover in two bays of {\{}L{\}}ake {\{}O{\}}ntario with three complementary methods}},
volume = {33},
year = {2007}
}
@article{Ziegler98,
author = {Ziegler, S and Benner, R},
journal = {Marine Ecology Progress Series},
pages = {1--12},
title = {{Ecosystem metabolism in a subtropical, seagrass-dominated lagoon}},
volume = {173},
year = {1998}
}
@book{Zumberge52,
address = {Minneapolis, Minnesota},
author = {Zumberge, J H},
publisher = {Bulletin 35, University of Minnesota Geological Survey, The University of Minnesota Press},
title = {{The Lakes of {\{}M{\}}innesota: Their Origin and Classification}},
year = {1952}
}
@book{Zuur12,
address = {Newburgh, United Kingdom},
author = {Zuur, A F},
pages = {184},
publisher = {Highland Statistics Ltd.},
title = {{A Beginner's Guide to Generalized Additive Models in R}},
year = {2012}
}
@article{Zuur10,
author = {Zuur, A F and Ieno, E N and Elphick, C S},
journal = {Methods in Ecology and Evolution},
number = {1},
pages = {3--14},
title = {{A protocol for data exploration to avoid common statistical problems}},
volume = {1},
year = {2010}
}
@book{Zuur09R,
address = {New York, London},
author = {Zuur, A F and Ieno, E N and Meesters, E},
pages = {236},
publisher = {Springer-Verlag},
title = {{A Beginner's Guide to R (Use R!)}},
year = {2009}
}
@book{Zuur07,
address = {New York, New York},
author = {Zuur, A F and Ieno, E N and Smith, G M},
pages = {672},
publisher = {Springer-Verlag},
title = {{Analysing Ecological Data}},
year = {2007}
}
@book{Zuur09,
address = {New York, New York},
author = {Zuur, A F and Ieno, E N and Walker, N J and Saveliev, A A and Smith, G M},
pages = {574},
publisher = {Springer-Verlag},
title = {{Mixed Effects Models and Extensions in Ecology with R}},
year = {2009}
}
@techreport{,
institution = {NOAA},
title = {{Deepwater Horizon oil spill: Final Programmatic Damage Assessment and Restoration Plan and Final Programmatic Environmental Impact Statement}},
url = {http://www.gulfspillrestoration.noaa.gov/restoration-planning/gulf-plan},
year = {2016}
}
@unpublished{,
address = {Gainesville, FL},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2006{\_}ECT{\_}WQ{\_}Assessment.pdf:pdf},
pages = {130},
title = {{Water Quality Assessment Big Bend Station NPDES Permit Modification (Permit No. FL0000817)}},
year = {2006}
}
@unpublished{,
abstract = {The purpose of this handbook is to provide information about what atmospheric deposition is, how it can be measured, and how the significance of the problem may be determined for a particular area. The handbook may not answer all your questions directly; rather, it is intended to lead you in the right direction and provide enough information to decide how to address the issue in your area.},
file = {:T$\backslash$:/06{\_}LIBRARY/01{\_}SCIENCE{\_}REFERENCES/2001{\_}EPA{\_}Frequently{\_}asked.pdf:pdf},
isbn = {EPA-453/R-01-009},
pages = {89},
title = {{Frequently Asked Questions About Atmospheric Deposition: A Handbook for Watershed Managers}},
year = {2001}
}