refs.bib

article{,
	author={},
	year={},
	title={},
	journal={},
	volume={},
	number={},
	pages={}
}

@preamble{ " \newcommand{\noop}[1]{} " } 

@article{Aguiar09,
	author={F. C. Aguiar and M. T. Ferreira and A. Albuquerque and P. Rodriguez-Gonzalez and P. Segurado},
	year={2009},
	title={Structural and functional responses of riparian vegetation to human disturbance: Performance and spatial scale-dependence},
	journal={Fundamental and Applied Limnology},
	volume={175},
	number={3},
	pages={249-267}
}

@incollection{Akaike73,
	author={H. Akaike},
	editor={B. N. Petrov and F. Csaki},
	year={1973},
	title={Information theory and an extension of the maximum likelihood principle},
	booktitle={Second International Symposium on Information Theory},
	address={Akademiai Kiado, Budapest},
	pages={267-281}
}

@article{Alexander08,
	author={M. L. Alexander and M. P. Woodford and S. C. Hotchkiss},
	year={2008},
	title={Freshwater macrophyte communities in lakes of variable landscape position and development in northern {W}isconsin, {U.S.A.}},
	journal={Aquatic Botany},
	volume={88},
	number={1},
	pages={77-86}
}

@article{Alpine88,
	author={A. E. Alpine and J. E. Cloern},
	year={1988},
	title={Phytoplankton growth rates in a light-limited environment, {S}an {F}rancisco {B}ay},
	journal={Marine Ecology Progress Series},
	volume={44},
	number={2},
	pages={167-173}
}

@article{Alpine92,
	author={A. E. Alpine and J. E. Cloern},
	year={1992},
	title={Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary},
	journal={Limnology and Oceanography},
	volume={37},
	number={5},
	pages={946-955}
}

@techreport{Anderson01,
	author={J. L. Anderson and J. C. Bell and T. H. Cooper and D. F. Grigal},
	year={2001},
	title={Soils and landscapes of {M}innesota},
	institution={University of Minnesota Extension},
	address={St. Paul, Minnesota},
	url={http://www.extension.umn.edu/distribution/cropsystems/dc2331.html}
}

@techreport{Anderson99,
	author={K. A. Anderson and T. J. Kelly and R. M. Sushak and C. A. Hagley and D. A. Jensen and G. M. Kreag},
	year={1999},
	title={Summary report on public perceptions of the impacts, use, and future of {M}innesota lakes: Results of the 1998 {M}innesota lake survey},
	institution={University of Minnesota Sea Grant Program, Minnesota Department of Natural Resources, Office of Management and Budget Services},
	address={Duluth, Minnesota}
}

@techreport{Anon93,
	author={{Anonymous}},
	year={1993},
	title={Manual of Instructions for Lake Survey},
	institution={Division of Fish and Wildlife, Section of Fisheries, Minnesota Department of Natural Resources},
	number={No. 147},
	address={St. Paul, Minnesota},
	url={http://files.dnr.state.mn.us/publications/fisheries/special_reports/147.pdf}
}

@article{Ansola95,
	author={G. Ansola and C. Fernandez and E. Deluis},
	year={1995},
	title={Removal of organic-matter and nutrients from urban waste-water by using an experimental emergent aquatic macrophyte system},
	journal={Ecological Engineering},
	volume={5},
	number={1},
	pages={13-19}
}

@misc{APHA05,
  author={{APHA (American Public Health Association)}},
	year={2005},
	title={Standard methods for the examination of water and wastewater},
	note={Washington, DC}
}

@article{Arhonditsis08,
	author={G. B. Arhonditsis and G. Perhar and W. Zhang and E. Massos and M. Shi and A. Das},
	year={2008},
	title={Addressing equifinality and uncertainty in eutrophication models},
	journal={Water Resources Research},
	volume={44},
	number={1},
	pages={W01420}
}

@article{Arlot10,
	author={S. Arlot and A. Celisse},
	year={2010},
	title={A survey of cross-validation procedures for model selection},
	journal={Statistics Surveys},
	volume={4},
	number={},
	pages={40-79}
}

@misc{ASC17,
  author = {ASC},
  year = {2017},
  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 Monitoring Program}}, 
  note = {Report v1.2}
}

@article{Aulenbach06,
	author={B. T. Aulenbach and R. P. Hooper},
	year={2006},
	title={The composite-method: An improved method for stream-water solute load estimation},
	journal={Hydrological Processes},
	volume={20},
	number={14},
	pages={3029-3047}
}

@incollection{Baatz00,
	author={M. Baatz and A. Sch\"{a}pe},
	editor={J. Strobl and T. Blaschke and G. Griesebner},
	year={2000},
	title={Multiresolution segmentation: An optimization approach for high quality multi-scale image segmentation},
	booktitle={Angewandte Geographische Informationsverarbeitung XII. Beitr\"{a}ge zum AGIT-Symposium Salzburg 2000},
	publisher={Herbert Wichmann Verlag},
	address={Berlin},
	pages={12-23}
}

@article{Bajer18,
	author={P. G. Bajer and M. W. Beck and P. J. Hundt},
	year={2018},
	title={Effect of non-native versus native invaders on macrophyte richness: are carp and bullheads ecological proxies?},
	journal={Hydrobiologia},
	volume={},
	number={},
	pages={}, 
	doi={10.1007/s10750-018-3592-1}
}

@article{Bajer16,
	author={P. G. Bajer and M. W. Beck and T. K. Cross and J. Koch and B. Bartodziej and P. W. Sorensen},
	year={2016},
	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},
	journal={Global Change Biology},
	volume={22},
	number={12},
	pages={3937-3947}, 
	doi={10.1111/gcb.13377}
}

@incollection{Ball00,
	author={G. R. Ball and D. Palmer-Brown and G. E. Mills},
	editor={S. Lek and J. F. Gu\'{e}gan},
	year={2000},
	title={A comparison of artificial neuronal network and conventional statistical techniques for analysing environmental data},
	booktitle={{Artificial Neuronal Networks: Application to Ecology and Evolution}},
	publisher={Springer-Verlag},
	address={Berlin, Germany},
	pages={165-183}
}

@article{Barbour00,
	author={M. T. Barbour and W. F. Swietlik and S. K. Jackson and D. L. Courtemanch and S. P. Davies and C. O. Yoder},
	year={2000},
	title={Measuring the attainment of biological integrity in the {USA}: A critical element of ecological integrity},
	journal={Hydrobiologia},
	volume={422-423},
	number={0},
	pages={453-464}
}

@article{Barbour96,
	author={M. T. Barbour and J. Gerritsen and G. E. Griffith and R. Frydenborg and E. McCarron and J. S. White and M. L. Bastian},
	year={1996},
	title={A framework for biological criteria for {F}lorida streams using benthic macroinvertebrates},
	journal={Journal of the North American Benthological Society},
	volume={15},
	number={2},
	pages={185-211}
}

@article{Barko82,
	author={J. W. Barko and D. G. Hardin and M. S. Matthews},
	year={1982},
	title={Growth and morphology of submersed freshwater macrophytes in relation to light and temperature},
	journal={Canadian Journal of Botany},
	volume={60},
	number={6},
	pages={877-887}
}

@article{Barko91,
	author={J. W. Barko and D. Gunnison and S. R. Carpenter},
	year={1991},
	title={Sediment interactions with submersed macrophyte growth and community dynamics},
	journal={Aquatic Botany},
	volume={41},
	pages={41-65}
}

@incollection{Bates92,
  author={D. M. Bates and J. M. Chambers},
  editor={J. M. Chambers and T. J. Hastie},
	year={1992},
	title={Nonlinear models},
	booktitle={Statistical Models in S},
	publisher={Wadsworth and Brooks/Cole},
	address={Pacific Grove, California},
	pages={421-454}
}

@article{Batt12,
  author={R. D. Batt and S. R. Carpenter},
	year={2012},
	title={Free-water lake metabolism: Addressing noisy time series with a {K}alman filter},
	journal={Limnology and Oceanography: Methods},
	volume={10},
	number={},
	pages={20-30}
}

@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={M. B. Beck},
	year={1987},
	title={Water quality modeling: A  review of the analysis of uncertainty},
	journal={Water Resources Research},
	volume={23},
	number={8},
	pages={1393-1442}
}

@phdthesis{Beckdiss,
	author={M. W. Beck},
	year={2013},
	title={{M}innesota macrophytes: Linking aquatic plants, lake health, and human activities},
	school={University of Minnesota},
	address={St. Paul, Minnesota}
}

@article{BeckIR,
  author={M. W. Beck and T. W. Jabusch and P. R. Trowbridge and D. B. Senn},
	year={\noop{3002}in review},
	title={Four decades of water quality change in the upper {S}an {F}rancisco {E}stuary},
	journal={Environmental Science \& Technology},
	volume={},
	number={},
	pages={},
	doi={}
}

@article{BeckIP,
  author={M. W. Beck},
	year={\noop{3001}in press},
	title={{NeuralNetTools}: Visualization and analysis tools for neural networks},
	journal={Journal of Statistical Software},
	volume={},
	number={},
	pages={},
	doi={}
}

@article{Beck18,
  author={M. W. Beck and K. Cressman and C. Griffin and J. Caffrey},
	year={2018},
	title={Water quality trends following anomalous phosphorus inputs to Grand Bay},
	journal={Gulf and Caribbean Research},
	volume={29},
	number={1},
	pages={1-14},
	doi={10.18785/gcr.2901.02}
}

@article{Beck17,
  author={M. W. Beck and R. R. Murphy},
	year={2017},
	title={Numerical and qualitative contrasts of two statistical models for water quality change in tidal waters},
	journal={Journal of the American Water Resources Association},
	volume={53},
	number={1},
	pages={197-219},
	doi={10.1111/1752-1688.12489}
}

@manual{Beck17b, 
  author={M. W. Beck},
  year={2017},
  title={{WRTDStidal: Weighted Regression for Water Quality Evaluation in Tidal Waters}},
  note={R package version 1.1.0},
  url={\url{http://CRAN.R-project.org/package=WRTDStidal}}
}

@article{Beck17c,
	author={M. W. Beck and J. D. {Hagy III} and C. Le},
	year={2017},
	title={Quantifying seagrass light requirements using an algorithm to spatially resolve depth of colonization},
	journal={Estuaries and Coasts},
	volume={},
	number={},
	pages={1-17}
}

@article{Beck16c,
  author={M. W. Beck and J. Alahuhta},
	year={2016},
	title={Ecological determinants of {P}otamogetontaxa in glacial lakes: assemblage composition, species richness, and species-level approach},
	journal={Aquatic Sciences},
	volume={},
	number={},
	pages={1-15},
	doi={10.1007/s00027-016-0508-x}
}

@article{Beck16,
  author={M. W. Beck},
	year={2016},
	title={{SWMPr}: An {R} package for retrieving, organizing, and analyzing environmental data for estuaries},
	journal={The R Journal},
	volume={8},
	number={1},
	pages={219-232}
}

@article{Beck15b,
  author={M. W. Beck and J. D. {Hagy III} and M. C. Murrell},
	year={2015},
	title={Improving estimates of ecosystem metabolism by reducing effects of tidal advection on dissolved oxygen time series},
	journal={Limnology and Oceanography: Methods},
	volume={13},
	number={12},
	pages={731-745},
	doi={10.1002/lom3.10062}
}

@article{Beck15,
	author={M. W. Beck and J. D. {Hagy III}},
	year={2015},
	title={Adaptation of a weighted regression approach to evaluate water quality trends in an estuary},
	journal={Environmental Modelling and Assessment},
	volume={20},
	number={6},
	pages={637-655},
	doi={10.1007/s10666-015-9452-8}
}

@article{Beck14b,
  author={M. W. Beck and C. M. Tomcko and R. D. Valley and D. F. Staples},
	year={2014},
	title={Analysis of macrophyte indicator variation as a function of sampling, temporal, and stressor effects},
	journal={Ecological Indicators},
	volume={46},
	number={},
	pages={323-335},
	doi={10.1016/j.ecolind.2014.07.002}
}

@article{Beck14a,
  author={M. W. Beck and B. N. Wilson and B. Vondracek and L. K. Hatch},
	year={2014},
	title={Application of neural networks to quantify the utility of indices of biotic integrity for biological monitoring},
	journal={Ecological Indicators},
	volume={45},
	number={},
	pages={195-208},
	doi={10.1016/j.ecolind.2014.04.002}
}

@article{Beck13c,
	author={M. W. Beck and B. Voncracek and L. K. Hatch},
	year={2013},
	title={Between- and within-lake responses of macrophyte richness metrics to shoreline development},
	journal={Lake and Reservoir Managmenet},
	volume={29},
	number={3},
	pages={179-193},
	doi={10.1080/10402381.2013.828806}
}
	
@article{Beck13b,
	author={M. W. Beck and B. Vondracek and L. K. Hatch and J. Vinje},
	year={2013},
	title={Semi-automated analysis of high-resolution aerial images to quantify docks in glacial lakes},
	journal={ISPRS Journal of Photogrammetry and Remote Sensing},
	volume={81},
	pages={60-69},
	doi={10.1016/j.isprsjprs.2013.04.006}
	}

@article{Beck13,
	author={M. W. Beck and B. Vondracek and L. K. Hatch},
	year={2013},
	title={Environmental clustering of lakes to evaluate performance of a macrophyte index of biotic integrity},
	journal={Aquatic Botany},
	volume={108},
	pages={16-25},
	doi={10.1016/j.aquabot.2013.02.003}
}

@article{Beck12,
	author={M. W. Beck and A. H. Claassen and P. Hundt},
	year={2012},
	title={Environmental and livelihood impacts of dams: Common lessons across development gradients that challenge sustainability},
	journal={International Journal of River Basin Management},
	volume={10},
	number={1},
	pages={73-92},
	doi={10.1080/15715124.2012.656133}
}

@article{Beck10,
	author={M. W. Beck and L. K. Hatch and B. Vondracek and R. D. Valley},
	year={2010},
	title={Development of a macrophyte-based index of biotic integrity for {M}innesota lakes},
	journal={Ecological Indicators},
	volume={10},
	number={5},
	pages={968-979},
	doi={10.1016/j.ecolind.2010.02.006}
}

@article{Beck09,
	author={M. W. Beck and L. K. Hatch},
	year={2009},
	title={A review of research on the development of lake indices of biotic integrity},
	journal={Environmental Reviews},
	volume={17},
	pages={21-44},
	doi={10.1139/A09-001}
}

@article{Bedoya11,
	author={D. Bedoya and E. S. Manolakos and V. Novotny},
	year={2011},
	title={Prediction of biological integrity based on environmental similarity - Revealing the scale-dependent link between study area and top environmental predictors},
	journal={Water Research},
	volume={45},
	number={7},
	pages={2359-2374}
}

@article{Beisner06,
	author={B. E. Beisner and P. R. Peres-Neto and E. S. Lindstrom and A. Barnett and M. L. Longhi},
	year={2006},
	title={The role of environmental and spatial processes in structuring lake communities from bacteria to fish},
	journal={Ecology},
	volume={87},
	number={12},
	pages={2985-2991}
}

@article{Bell09,
	author={G. Bell and T. Hey and A. Szalay},
	year={2009},
	title={Beyond the data deluge},
	journal={Science},
	volume={323},
	number={5919},
	pages={1297-1298}
}

@article{Benitez97,
  author={J. M. Benitez and J. L. Castro and I. Requena},
	year={1997},
	title={Are artificial neuronal networks black boxes?},
	journal={IEEE Transactions on Neuronal Networks},
	volume={8},
	number={5},
	pages={1156-1164}
}

@article{Bergmeir12,
  title = {Neural Networks in {R} Using the Stuttgart Neural Network Simulator: {RSNNS}},
  author = {Christoph Bergmeir and  Jos\'e M. Ben\'itez},
  journal = {Journal of Statistical Software},
  year = {2012},
  volume = {46},
  number = {7},
  pages = {1--26},
  url = {http://www.jstatsoft.org/v46/i07/},
}

@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={I. Bhangu and P. H. Whitfield},
	year={1997},
	title={Seasonal and long-term variations in water quality of the {S}keena {R}iver at {U}sk, {B}ritish {C}olumbia},
	journal={Water Research},
	volume={31},
	number={9},
	pages={2187-2194}
}

@article{Bianchi10,
	author={T. S. Bianchi and S. F. DiMarco and J. H. Cowan Jr and R. D. Hetland and P. Chapman and J. W. Day and M. A. Allison},
	year={2010},
	title={The science of hypoxia in the {N}orthern {G}ulf of {M}exico: a review},
	journal={Science of the Total Environment},
	volume={408},
	number={7},
	pages={1471-1484}
}

@article{Bierman94,
	author={V. J. Bierman and S. C. Hinz and D. W. Zhu and W. J. Wiseman and N. N. Rabalais and R. E. Turner},
	year={1994},
	title={A preliminary mass-balance model of primary productivity and dissolved oxygen in the {M}ississippi {R}iver plume/ inner {G}ulf shelf region},
	journal={Estuaries},
	volume={17},
	number={4},
	pages={886-899}
}

@book{Bishop95,
  author={C. M. Bishop},
	year={1995},
	title={Neuronal Networks for Pattern Recognition},
	publisher={Carendon Press},
	address={Oxford, United Kingdom},
	pages={482}
}

@book{Bivand08,
	author={R. S. Bivand and E. J. Pebesma and V. G\'{o}mez-Rubio},
	year={2008},
	title={Applied Spatial Data Analysis with {R}},
	publisher={Springer-Verlag},
	address={New York, New York},
	pages={376}
}

@manual{Bivand14,
  author = {Roger Bivand and Colin Rundel},
  title = {rgeos: Interface to Geometry Engine - Open Source (GEOS)},
  year = {2014},
  note = {R package version 0.3-8},
  url = {http://CRAN.R-project.org/package=rgeos},
}

@article{Blake14,
  author={R. E. Blake and J. E. Duffy and J. P. Richardson},
	year={2014},
	title={Patterns of seagrass community response to local shoreline development},
	journal={Estuaries and Coasts},
	volume={37},
	number={6},
	pages={1549-1561}
}

@techreport{Blann08,
	author={K. Blann and M. Cornett},
	year={2008},
	title={{Identifying lake conservation priorities for The Nature Conservancy in Minnesota, North Dakota, and South Dakota}},
	institution={The Nature Conservancy}, 
	address={Minneapolis, Minnesota}
}

@article{Blaschke10,
	author={T. Blaschke},
	year={2010},
	title={Object based image analysis for remote sensing},
	journal={ISPRS Journal of Photogrammetry and Remote Sensing},
	volume={65},
	number={1},
	pages={2-16}
}

@article{Blaschke01,
	author={T. Blaschke and J. Strobl},
	year={2001},
	title={What's wrong with pixels? {S}ome recent development interfacing remote sensing and {GIS}},
	journal={Interfacing Remote Sensing and GIS},
	volume={14},
	number={6},
	pages={12-17}
}

@article{Blindow93,
	author={I. Blindow and G. Andersson and A. Hargeby and S. Johansson},
	year={1993},
	title={Long-term pattern of alternative stable states in two shallow eutrophic lakes},
	journal={Freshwater Biology},
	volume={30},
	number={1},
	pages={159-167}
}

@incollection{Boet00,
	author={P. Bo\"{e}t and T. Fuhs},
	editor={S. Lek and J. F. Gu\'{e}gan},
	year={2000},
	title={Predicting presence of fish species in the {S}eine river basin using artifical neuronal networks},
	booktitle={{Artificial Neuronal Networks: Application to Ecology and Evolution}},
	publisher={Springer-Verlag},
	address={Berlin, Germany},
	pages={131-142}
}

@techreport{Boicourt98,
  author={W. C. Boicourt and L. P. Sanford},
	year={1998},
	title={A hydrodynamic study of the {P}atuxent {R}iver estuary},
	institution={Maryland Department of the Environment},
	address={Baltimore, Maryland}
}

@article{Bokde16,
	author={N. Bokde and K. Kulat and M. W. Beck and A. C. Gualberto},
	year={2016},
	title={R package imputeTestbench to compare imputation methods for univariate time series},
	journal={arXiv},
	volume={arXiv preprint arXiv:1608.00476},
	number={},
	pages={}
}

@techreport{Boler01,
  author={R. Boler},
	year={2001},
	title={Surface water quality 1999-2000 {H}illsborough {C}ounty, {F}lorida},
	institution={Environmental Protection Commission of Hillsborough County},
	address={Tampa, Florida, USA}
}

@article{Borja09,
	author={A. Borja and A. Ranasinghe and S. B. Weisberg},
	year={2009},
	title={Assessing ecological integrity in marine waters, using multiple indices and ecosystem components: Challenges for the future},
	journal={Marine Pollution Bulletin},
	volume={59},
	number={1-3},
	pages={1-4}
}

@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}
}

@book{Borman01,
	author={S. Borman and R. Korth and J. Temte},
	year={2001},
	title={Through the Looking Glass: A Field Guide to Aquatic Plants},
	publisher={Wisconsin Lakes Partnership, Reindl Printing, Inc.},
	address={Stevens Point, Wisconsin},
	pages={248}
}

@article{Borman09,
	author={S. C. Borman and S. M. Galatowitsch and R. M. Newman},
	year={2009},
	title={The effects of species immigrations and changing conditions on isoetid communities},
	journal={Aquatic Botany},
	volume={91},
	number={3},
	pages={143-150}
}

@article{Borsuk04b,
	author={M. E. Borsuk and C. A. Stow and K. H. Reckhow},
	year={2004},
	title={Confounding effect of flow on estuarine response to nitrogen loading},
	journal={Journal of Environmental Engineering-ASCE},
	volume={130},
	number={6},
	pages={605-614}
}

@article{Borsuk04,
	author={M. E. Borsuk and C. A. Stow and K. H. Reckhow},
	year={2004},
	title={A {B}ayesian network of eutrophication models for synthesis, prediction, and uncertainty analysis},
	journal={Ecological Modelling},
	volume={173},
	number={2-3},
	pages={219-239}
}

@article{Borsuk01,
	author={M. E. Borsuk and C. A. Stow and Leuttich, Jr., R. A. and H. W. Pearl and J. L. Pinckney},
	year={2001},
	title={Modelling oxygen dynamics in an intermittently stratified estuary: Estimation of process rates using field data},
	journal={Estuarine, Coastal and Shelf Science},
	volume={52},
	number={1},
	pages={33-49}
}

@incollection{Bowden06,
	author={G. J. Bowden and G. C. Dandy and H. R. Maier},
	editor={F. Recknagel},
	year={2006},
	title={An evaluation of methods for the selection of inputs for an artificial neural network based river model},
	booktitle={Ecological Informatics: Scope, Techniques and Applications},
	publisher={Springer-Verlag},
	edition={2nd},
	address={Berlin, Germany},
	pages={275-292}
}

@article{Bowes09,
	author={M. J. Bowes and J. T. Smith and C. Neal},
	year={2009},
	title={The value of high resolution nutrient monitoring: a case study of the {R}iver {F}rome, {D}orset, {UK}},
	journal={Journal of Hydrology},
	volume={378},
	number={},
	pages={82-96}
}

@article{Boyer02,
  author={E. W. Boyer and C. L. Goodale and N. A. Jaworski and R. W. Howarth},
	year={2002},
	title={Anthropogenic nitrogen sources and relationships to riverine nitrogen export in the northeastern {U.S.A.}},
	journal={Biogeochemistry},
	volume={57},
	number={1},
	pages={137-169}
}

@article{Brabec02,
	author={E. Brabec and S. Schulte and P. L. Richards},
	year={2002},
	title={Impervious surfaces and water quality: {A} review of current literature and its implications for watershed planning},
	journal={Journal of Planning Literature},
	volume={16},
	number={4},
	pages={499-514}
}

@article{Brauns11,
	author={M. Brauns and B. G\"{u}cker and C. Wagner and X. F. Garcia and N. Walz and M. T. Pusch},
	year={2011},
	title={Human lakeshore development alters the structure and trophic basis of littoral food webs},
	journal={Journal of Applied Ecology},
	volume={48},
	number={4},
	pages={916-925}
}

@book{Breiman84,
  author={L. Breiman and J. H. Friedman and R. A. Olshen and C. J. Stone},
	year={1984},
	title={Classification and Regression Trees},
	publisher={Wadsworth International Group},
	address={Belmont, California},
	pages={358}
}

@article{Breiman01,
  author={L. Breiman},
	year={2001},
	title={Random forests},
	journal={Machine Learning},
	volume={45},
	pages={5-32}
}

@article{Breine04,
	author={J. Breine and I. Simoens and P. Goethals and P. Quataert and D. Ercken and C. Van Liefferinghe and C. Belpaire},
	year={2004},
	title={A fish-based index of biotic integrity for upstream brooks in {F}landers ({B}elgium)},
	journal={Hydrobiologia},
	volume={522},
	number={1-3},
	pages={133-148}
}

@article{Brosse01,
	author={S. Brosse and S. Lek and C. R. Townsend},
	year={2001},
	title={Abundance, diversity, and structure of freshwater invertebrates and fish communities: An artificial neural network approach},
	journal={New Zealand Journal of Marine and Freshwater Research},
	volume={35},
	number={1},
	pages={135-145}
}

@article{Brun01,
	author={R. Brun and P. Reichert and H. R. K\"{u}nsch},
	year={2001},
	title={Practical identifiability analysis of large environmental simulation models},
	journal={Water Resources Research},
	volume={37},
	number={4},
	pages={1015-1030}
}

@article{Bryan92,
	author={M. D. Bryan and D. L. Scarnecchia},
	year={1992},
	title={Species richness, composition, and abundance of fish larvae and juveniles inhabiting natural and developed shorelines of a glacial {I}owa lake},
	journal={Environmental Biology of Fishes},
	volume={35},
	number={4},
	pages={329-341}
	}

@article{Bulthius95,
  author={D. A. Bulthius},
	year={1995},
	title={Distribution of seagrasses in a north {P}uget {S}ound estuary - {P}adilla {B}ay, {W}ashington, {USA}},
	journal={Aquatic Botany},
	volume={50},
	number={1},
	pages={99-105}
}

@article{Burdick99,
	author={D. M. Burdick and F. T. Short},
	year={1999},
	title={The effects of boat docks on eelgrass beds in coastal waters of {M}assachusetts},
	journal={Environmental Management},
	volume={23},
	number={2},
	pages={231-240}
}

@article{Burke97,
	author={L. Burke and J. P. Ignizio},
	year={1997},
	title={A practical overview of neural networks},
	journal={Journal of Intelligent Manufacturing},
	volume={8},
	number={3},
	pages={157-165}
}

@book{Burrough98,
	author={P. A. Burrough and R. A. McDonnell},
	year={1998},
	title={Principles of Geographical Information Systems},
	publisher={Oxford University Press},
	address={New York, New York},
	edition={second},
	pages={356}
}

@article{Butler08,
	author={R. G. Butler and P. G. {deMaynadier}},
	year={2008},
	title={The significance of littoral and shoreline habitat integrity to the conservation of lacustrine damselflies ({O}donata)},
	journal={Journal of Insect Conservation},
	volume={12},
	number={1},
	pages={23-36}
	}

@article{Byrd95,
	author={R. H. Byrd and P. Lu and J. Nocedal and C. Zhu},
	year={1995},
	title={A limited memory algorithm for bound constrained optimization},
	journal={SIAM Journal on Scientific Computing},
	volume={16},
	number={5},
	pages={1190-1208}
}

@article{Cade03,
	author={B. S. Cade and B. R. Noon},
	year={2003},
	title={A gentle introduction to quantile regression for ecologists},
	journal={Frontiers in Ecology and the Environment},
	volume={1},
	number={8},
	pages={412-420}
}

@article{Cairns01,
	author={D. M. Cairns},
	year={2001},
	title={A comparison of methods for predicting vegetation type},
	journal={Plant Ecology},
	volume={156},
	number={1},
	pages={3-18}
}

@incollection{Caffrey16,
	author={J. M. Caffrey and M. C. Murrell},
	editor={P. M. Glibert and T. M. Kana},
	year={2016},
	title={A historical perspective on eutrophication in the {P}ensacola {B}ay {E}stuary, {FL}, {USA}},
	booktitle={Aquatic Microbial Ecology and Biogeochemistry: A Dual Perspective},
	publisher={Springer International Publishing},
	address={Switzerland},
	pages={199-213}
}


@article{Caffrey03,
  author={J. M. Caffrey},
	year={2003},
	title={Production, respiration and net ecosystem metabolism in {U.S.} estuaries},
	journal={Environmental Monitoring and Assessment},
	volume={81},
	number={1-3},
	pages={207-219}
}

@article{Caffrey04,
	author={J. M. Caffrey},
	year={2004},
	title={Factors controlling net ecosystem metabolism in {U.S.} estuaries},
	journal={Estuaries},
	volume={27},
	number={1},
	pages={90-101}
}

@article{Caffrey14,
	author={J. M. Caffrey and M. C. Murrell and K. S. Amacker and J. Harper and S. Phipps and M. Woodrey},
	year={2013},
	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},
	journal={Estuaries and Coasts},
	volume={37},
	number={1},
	pages={222-241}
}

@article{Camacho14a,
	author={R. A. Camacho and J. L. Martin and B. Watson and M. J. Paul and L. Zheng and J. B. Stribling},
	year={2014},
	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},
	journal={Journal of Environmental Engineering},
	volume={141},
	number={3},
	pages={04014067}
}

@article{Camacho14b,
	author={R. A. Camacho and J. L. Martin and J. Diaz-Ramirez and W. McAnally and H. Rodriguez and P. Suscy and S. Zhang},
	year={2014},
	title={Uncertainty analysis of estuarine hydrodynamic models: an evaluation of input data uncertainty in the {W}eeks {B}ay estuary, {A}labama},
	journal={Applied Ocean Research},
	volume={47},
	number={},
	pages={138-153}
}

@article{Campbell13,
  author={J. L. Campbell and L. E. Rustad and J. H. Porter and J. R. Taylor and E. W. Dereszynski and J. B. Shanley and C. Gries and D. L. Henshaw and M. E. Martin and W. M. Sheldon and E. R. Boose},
	year={2013},
	title={Quantity is nothing without quality: Automated {QA/QC} for streaming environmental sensor data},
	journal={BioScience},
	volume={63},
	number={7},
	pages={574-585}
}

@manual{Cannon15,
  title = {monmlp: Monotone Multi-Layer Perceptron Neural Network},
  author = {Alex J. Cannon},
  year = {2015},
  note = {R package version 1.1.3},
  url = {http://CRAN.R-project.org/package=monmlp},
}

@article{Cannon11,
  title = {Quantile regression neural networks: implementation in R and application to precipitation downscaling},
  author = {Alex J. Cannon},
  year = {2011},
  journal = {Computers \& Geosciences},
  volume = {37},
  pages = {1277-1284. doi:10.1016/j.cageo.2010.07.005},
}

@article{Canuel09,
	author={E. A. Canuel and E. J. Lerberg and R. M. Dickhut and S. A. Kuehl and T. S. Bianchi and S. G. Wakeham},
	year={2009},
	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})},
	journal={Marine Pollution Bulletin},
	volume={59},
	number={4-7},
	pages={154-163}
}

@article{Carlisle09,
	author={D. M. Carlisle and J. Falcone and M. R. Meador},
	year={2009},
	title={Predicting the biological condition of streams: use of geospatial indicators of natural and anthropogenic characteristics of watersheds},
	journal={Environmental Monitoring and Assessment},
	volume={151},
	number={1-4},
	pages={143-160},
	doi={10.1007/s10661-008-0256-z}
}

@article{Carlson77,
	author={R. E. Carlson},
	year={1977},
	title={A trophic state index for lakes},
	journal={Limnology and Oceanography},
	volume={22},
	number={2},
	pages={361-369}
}

@article{Carlton90,
	author={J. T. Carlton and J. K. Thompson and L. E. Schemel and F. H. Nichols},
	year={1990},
	title={Remarkable invasion of {S}an {F}rancisco {B}ay ({C}alifornia, {USA}) by the {A}sian claim \textit{Potamocorbula amurensis}. {I.} {I}ntroduction and dispersal},
	journal={Marine Ecology Progress Series},
	volume={66},
	number={1-2},
	pages={81-94}
}

@article{Carpenter95,
	author={D. O. Carpenter},
	year={1995},
	title={Communicating with the public on issues of science and public health},
	journal={Environmental Health Perspectives},
	volume={103},
	number={S6},
	pages={127-130}
}

@article{Campbell09,
	author={K. R. Campbell and R. Baird},
	year={2009},
	title={The effects of residential docks on light availability and distribution of submerged aquatic vegetation in two {F}lorida lakes},
	journal={Lake and Reservoir Management},
	volume={25},
	number={1},
	pages={87-101}
}

@incollection{Campbell07,
	author={N. Campbell and K. MacKenzie and A. F. Zuur and E. N. Ieno and G. M. Smith},
	editor={A. F. Zuur and E. N. Ieno and G. M. Smith},
	year={2007},
	title={Fish stock identification through neural network analysis of parasite fauna},
	booktitle={Analysing Ecological Data},
	publisher={Springer-Verlag},
	address={New York, New York},
	pages={449-462}
}

@article{Carpenter06,
  author={S. R. Carpenter and W. A. Brock},
	year={2006},
	title={Rising variance: A leading indicator of ecological transition},
	journal={Ecology Letters},
	volume={9},
	number={3},
	pages={308-315}
}

@article{Carpenter00,
	author={J. Carpenter and J. Bithell},
	year={2000},
	title={Bootstrap confidence intervals: When, which, what? {A} guide for medical statisticians},
	journal={Statistics in Medicine},
	volume={19},
	number={9},
	pages={1141-1164}
}

@article{Carpenter98a,
	author={S. R. Carpenter and D. Bolgrien and R. C. Lathrop and C. A. Stow and T. Reed and M. A. Wilson},
	year={1998},
	title={Ecological and economic analysis of lake eutrophication by nonpoint pollution},
	journal={Australian Journal of Ecology},
	volume={23},
	number={1},
	pages={68-79}
}

@article{Carpenter98b,
	author={S. R. Carpenter and N. F. Caraco and D. L. Correll and R. W. Howarth and A. N. Sharpley and V. H. Smith},
	year={1998},
	title={Nonpoint pollution of surface waters with phosphorus and nitrogen},
	journal={Ecological Applications},
	volume={8},
	number={3},
	pages={559-568}
}

@article{Casselman96,
	author={J. M. Casselman and C. A. Lewis},
	year={1996},
	title={Habitat requirements of northern pike (Esox lucius)},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={53},
	number={1},
	pages={161-174}
}

@manual{Castejon14,
    title = {AMORE: A MORE flexible neural network package},
    author = {Manuel Castej\'{o}n Limas and Joaquin B. Ordieres Mer\'{e} and Ana Gonz\'{a}lez Marcos and Francisco Javier Martinez de Pis\'{o}n Ascacibar and Alpha V. Pern\'{i}a Espinoza and Fernando Alba El\'{i}as and Jose Maria Perez Ramos},
    year = {2014},
    note = {R package version 0.2-15},
    url = {http://CRAN.R-project.org/package=AMORE},
  }

@incollection{Castilla08,
	author={G. Castilla and G. J. Hay},
	editor={T. Blaschke and S. Lang and G. J. Hay},
	year={2008},
	title={Image objects and geographic objects},
	booktitle={Object-Based Image Analysis: Spatial Concepts for Knowledge-Driven Remote Sensing Applications},
	publisher={Springer-Verlag},
	address={Heidelberg, Berlin, New York},
	pages={91-110}
}

@misc{CDMO14,
  author={{CDMO (Centralized Data Management Office)}},
	year={2014},
	title={{National Estuarine Research Reserve System}},
	note={\url{http://cdmo.baruch.sc.edu/}. (Accessed January, 2014)}
	}

@techreport{CEC97,
	author={{CEC (Commission for Environmental Cooperation)}},
	year={1997},
	title={Ecological regions of {N}orth {A}merica: Toward a common perspective},
	address={Montreal, Quebec}
	}

@article{Chambers87,
	author={P. A. Chambers},
	year={1987},
	title={Nearshore occurrence of submersed aquatic macrophytes in relation to wave action},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={44},
	number={9},
	pages={1666-1669}
}

@article{Champely97,
	author={S. Champely and S. Doledec},
	year={1997},
	title={How to separate long-term trends from periodic variation in water quality monitoring},
	journal={Water Research},
	volume={31},
	number={11},
	pages={2849-2857}
}

@manual{chang15,
  title = {shiny: Web Application Framework for R},
  author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
  year = {2015},
  note = {R package version 0.11.1},
  url = {http://CRAN.R-project.org/package=shiny},
}

@article{Chang13,
	author={N. B. Chang and Z. Xuan and Y. J. Yang},
	year={2013},
	title={Exploring spatiotemporal patterns of phosphorus concentrations in a coastal bay with {MODIS} images and machine learning models},
	journal={Remote Sensing of Environment},
	volume={134},
	pages={100-110}
}

@article{Chang08,
	author={H. Chang},
	year={2008},
	title={Spatial analysis of water quality trends in the {H}an {R}iver basin, {S}outh {K}orea},
	journal={Water Research},
	volume={42},
	number={13},
	pages={3285-3304}
}

@article{Chandra05,
	author={S. Chandra and M. Jake Vander Zanden and A. C. Heyvaert and B. C. Richards and B. C. Allen and C. R. Goldman},
	year={2005},
	title={The effects of cultural eutrophication on the coupling between pelagic primary producers and benthic producers},
	journal={Limnology and Oceanography},
	volume={50},
	number={5},
	pages={1368-1376}
}

@article{Chase06,
	author={J. M. Chase and T. M. Knight},
	year={2006},
	title={Effects of eutrophication and snails on {E}urasian watermilfoil (\textit{{M}yriophyllum spicatum}) invasion},
	journal={Biological Invasions},
	volume={8},
	number={8},
	pages={1643-1649}
}

@article{Chen14,
	author={K. Chen and R. M. Hughes and S. Xu and J. Zhang and D. Cai and B. Wang},
	year={2014},
	title={Evaluating performance of macroinvertebrate-based adjusted and unadjusted multi-metric indices ({MMI}) using multi-season and multi-year samples},
	journal={Ecological Indicators},
	volume={36},
	number={},
	pages={142-151},
	doi={10.1016/j.ecolind.2013.07.006}
}

@article{Chen07,
  author={Z. Chen and F. E. Muller-Karger and C. Hu},
  year={2007},
	title={Remote sensing of water clarity in {T}ampa {B}ay},
	journal={Remote Sensing of Environment},
	volume={109},
	number={2},
	pages={249-259}
}

@manual{Cheng15,
    title = {leaflet: Create Interactive Web Maps with the JavaScript 'Leaflet' Library},
    author = {Joe Cheng and Yihui Xie},
    year = {2015},
    note = {R package version 1.0.0},
    url = {http://CRAN.R-project.org/package=leaflet},
  }

@article{Cheng94,
	author={B. Cheng and D. M. Titterington},
	year={1994},
	title={Neural networks: A review from a statistical perspective},
	journal={Statistical Science},
	volume={9},
	number={1},
	pages={2-54}
}

@article{Cheruvelil08,
	author={K. S. Cheruvelil and P. A. Soranno},
	year={2008},
	title={Relationships between lake macrophyte cover and lake and landscape features},
	journal={Aquatic Botany},
	volume={88},
	number={3},
	pages={219-227}
}

@techreport{Chipman09,
	author={J. W. Chipman and L. G. Olmanson and A. A. Gitelson},
	year={2009},
	title={Remote sensing methods for lake management: A guide for resource managers and decision-makers},
	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},
	address={Madison, Wisconsin},
	pages={126}
}

@techreport{Chirhart03,
	author={J. Chirhart},
	year={2003},
	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},
	institution={Biological Monitoring Program, Minnesota Pollution Control Agency},
	address={St. Paul, Minnesota},
	pages={45}
}

@article{Choice14,
  author={Z. D. Choice and T. K. Frazer and C. A. Jacoby},
	year={2014},
	title={Light requirements of seagrasses determined from historical records of light attenuation along the {G}ulf coast of peninsular {F}lorida},
	journal={Marine Pollution Bulletin},
	volume={81},
	number={1},
	pages={94-102}
}

@article{Christensen96,
	author={D. L. Christensen and B. R. Herwig and D. E. Schindler and S. R. Carpenter},
	year={1996},
	title={Impacts of lakeshore residential development on coarse woody debris in north temperate lakes},
	journal={Ecological Applications},
	volume={6},
	number={4},
	pages={1143-1149}
}

@article{Clarke93,
	author={K. R. Clarke},
	year={1993},
	title={Non-parametric multivariate analyses of changes in community structure},
	journal={Australian Journal of Ecology},
	volume={18},
	number={1},
	pages={117-143}
}

@article{Clayton06,
	author={J. Clayton and T. Edwards},
	year={2006},
	title={Aquatic plants as environmental indicators of ecological condition in {N}ew {Z}ealand lakes},
	journal={Hydrobiologia},
	volume={570},
	pages={147-151}
}

@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},
	year={2001},
	title={Ecological forecasts: an emerging imperative},
	journal={Science},
	volume={293},
	number={5530},
	pages={657-660}
}

@article{Cleve08,
	author={C. Cleve and M. Kelly and F. R. Kearns and M. Moritz},
	year={2008},
	title={{Classification of the wildland-urban interface: A comparison of pixel- and object-based classifications using high-resolution aerial photography}},
	journal={Computers, Environment and Urban Systems},
	volume={32},
	number={4},
	pages={317-326}
}

@article{Cleveland79,
	author={W. S. Cleveland},
	year={1979},
	title={Robust locally weighted regression and smoothing scatterplots},
	journal={Journal of the American Statistical Association},
	volume={74},
	number={368},
	pages={829-836}
}

@incollection{Cloern15,
	author={J. E. Cloern},
	editor={H. Mooney and E. Zavaleta},
	year={2015},
	title={Life on the edge: {C}alifornia's estuaries},
	booktitle={{Ecosystems of California: A Source Book}},
	publisher={University of California Press},
	address={California},
	pages={359-387}
}

@article{Cloern12b,
  author={J. E. Cloern and A. D. Jassby},
	year={2012},
	title={Drivers of change in estuarine-coastal ecosystems: Discoveries from four decades of study in {S}an {F}rancisco {B}ay},
	journal={Reviews of Geophysics},
	volume={50},
	number={4},
	pages={1-33}
}

@article{Cloern12,
  author={J. E. Cloern and A. D. Jassby and J. Carstensen and W. A. Bennett and W. Kimmerer and R. {Mac Nally} and D. H. Schoellhamer and M. Winder},
	year={2012},
	title={Perils of correlating {CUSUM}-transformed variables to infer ecological relationships ({Breton et al. 2006}; {Glibert 2010})},
	journal={Limnology and Oceanography},
	volume={57},
	number={2},
	pages={665-668}
}

@article{Cloern10,
	author={J. E. Cloern and A. D. Jassby},
	year={2010},
	title={Patterns and scales of phytoplankton variability in estuarine-coastal ecosystems},
	journal={Estuaries and Coasts},
	volume={33},
	number={2},
	pages={230-241}
}

@article{Cloern07,
	author={J. E. Cloern and A. D. Jassby and J. K. Thompson and K. A. Hieb},
	year={2007},
	title={A cold phase of the {E}ast {P}acific triggers new phytoplankton blooms in {S}an {F}rancisco {B}ay},
	journal={Proceedings of the National Academy of Sciences of the United States of America},
	volume={104},
	number={47},
	pages={18561-18565}
}

@article{Cloern05,
	author={J. E. Cloern and T. S. Schraga and C. B. Lopez and N. Knowles and R. G. Labiosa and R. Dugdale},
	year={2005},
	title={Climate anomalies generate an exceptional dinoflagellate bloom in {S}an {F}rancisco {B}ay},
	journal={Geophysical Research Letters},
	volume={32},
	number={14},
	pages={L14608}
}

@article{Cloern01,
  author={J. E. Cloern},
	year={2001},
	title={Our evolving conceptual model of the coastal eutrophication problem},
	journal={Marine Ecology Progress Series},
	volume={210},
	number={},
	pages={223-253}
}

@article{Cloern96,
  author={J. E. Cloern},
	year={1996},
	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},
	journal={Review of Geophysics},
	volume={34},
	number={2},
	pages={127-168}
}

@article{Cloern95,
	author={J. E. Cloern and C. Grenz and L. Vidergar-Lucas},
	year={1995},
	title={An empirical model of the phytoplankton:carbon ratio - the conversion factor between productivity and growth rate},
	journal={Limnology and Oceanography},
	volume={40},
	number={7},
	pages={1313-1321}
}

@article{Cloern83,
	author={J. E. Cloern and A. E. Alpine and B. E. Cole and R. L. J. Wong and J. F. Arthur and M. D. Ball},
	year={1983},
	title={River discharge controls phytoplankton dynamics in the northern {S}an {F}rancisco {B}ay estuary},
	journal={Estuarine, Coastal and Shelf Science},
	volume={16},
	number={4},
	pages={415-426}
}

@article{Cohen60,
	author={J. Cohen},
	year={1960},
	title={A coefficient of agreement for nominal scales},
	journal={Educational Psychology Measurement},
	volume={20},
	number={1},
	pages={37-46}
}

@article{Cohen98,
	author={A. N. Cohen and J. T. Carlton},
	year={1998},
	title={Accelerating invasion rate in a highly invaded estuary},
	journal={Science},
	volume={279},
	number={5350},
	pages={555-558}
}

@article{Cohn92,
  author={T. A. Cohn and D. L. Caulder and E. J. Gilroy and L. D. Zynjuk and R. M. Summers},
	year={1992},
	title={The validity of a simple statistical model for estimating fluvial constituent loads: An empirical study involving nutrient loads entering {C}hesapeake {B}ay},
	journal={Water Resources Research},
	volume={28},
	number={9},
	pages={2353-2363}
}

@article{Cohn89,
	author={T. A. Cohn and L. L. DeLong and E. J. Gilroy and R. M. Hirsch and D. K. Wells},
	year={1989},
	title={Estimating constituent loads},
	journal={Water Resources Research},
	volume={25},
	number={5},
	pages={937-942}
}

@article{Cole84,
	author={B. E. Cole and J. E. Cloern},
	year={1984},
	title={Significance of biomass and light availability to phytoplankton productivity in {S}an {F}rancisco {B}ay},
	journal={Marine Ecology Progress Series},
	volume={17},
	number={1},
	pages={15-24}
}

@article{Collins13,
  author={J. R. Collins and P. A. Raymond and W. F. Bohlen and M. M. Howard-Strobel},
	year={2013},
	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},
	journal={Estuaries and Coasts},
	volume={36},
	number={1},
	pages={74-97}
}

@article{Coloso11,
  author={J. J. Coloso and J. J. Cole and M. L. Pace},
	year={2011},
	title={Difficulty in discerning drivers of lake ecosystem metabolism with high-frequency data},
	journal={Ecosystems},
	volume={14},
	number={6},
	pages={935-948}
}

@article{Congalton91,
	author={R. G. Congalton},
	year={1991},
	title={A review of assessing the accuracy of classifications of remotely sensed data},
	journal={Remote Sensing of Environment},
	volume={37},
	number={1},
	pages={35-46}
}

@article{Connell78,
	author={J. H. Connell},
	year={1978},
	title={Diversity in tropical rain forests and coral reefs},
	journal={Science},
	volume={199},
	pages={1302-1310}	
}

@book{Cook99,
	author={R. D. Cook and S. Weisberg},
	year={1999},
	title={Applied Regression Including Computing and Graphics},
	publisher={Wiley},
	address={New York, New York},
	pages={593}
}

@article{Cornwell14,
	author={J. C. Cornwell and P. M. Glibert and M. S. Owens},
	year={2014},
	title={Nutrient fluxes from sediments in the {S}an {F}rancisco {B}ay {D}elta},
	journal={Estuaries and Coasts},
	volume={37},
	number={5},
	pages={1120-1133}
}

@misc{CPC13,
  author={{CPC (Climate Prediction Center)}},
	year={2013},
	title={{N}ational {W}eather {S}ervice {C}limate {P}rediction {C}enter: Cold and warm episodes by season},
	note={\url{http://www.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/ensoyears.shtml}. (Accessed September, 2013)}
}

@techreport{CPE97,
  author={{Coastal Planning and Engineering}},
  year={1997},
	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},
	institution={Coastal Planning and Engineering},
  number={Contract 95W142},
	address={Palatka, Florida}
}

@techreport{Crauder16,
	author={J. S. Crauder and J. K. Thompson and F. Parchaso and R. I. Anduaga and S. A. Pearson and K. Gehrts and H. Fuller and E. Wells},
	year={2016},
	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},
	institution={US Geological Survey}, 
	address={Reston, Virginia}, 
	number={Open-File Report 2016-1005}
}

@techreport{Cronin75,
	author={W. B. Cronin and D. W. Pritchard},
	year={1975},
	title={Additional statistics on the dimensions of the {C}hesapeake {B}ay and its tributaries: Cross-section widths and segment volumes per meter depth},
	institution={Chesapeake Bay Institute, The Johns Hopkins University},
	address={Baltimore, Maryland},
	number={42, Reference 75-3}
}

@article{Cross13,
	author={T. K. Cross and P. C. Jacobson},
	year={2013},
	title={Landscape factors influencing lake phosphorus concentrations across {M}innesota},
	journal={Lake and Reservoir Management},
	volume={29},
	number={1},
	pages={1-12}
}

@techreport{Cross06,
	author={T. Cross and M. McInerny},
	year={2006},
	title={Relationships between aquatic plant cover and fish populations based on {M}innesota lake survey data},
	institution={Fisheries and Wildlife Division, Minnesota Department of Natural Resources},
	address={St. Paul, Minnesota},
	number={537}
}

@book{Cryer08,
  author={J. D. Cryer and K. S. Chan},
	year={2008},
	title={Time Series Analysis with Applications in R},
	publisher={Springer-Verlag},
	address={New York, New York},
  edition={second},
	pages={491}
}

@manual{Csardi15,
  year={2015},
  title={cranlogs: Download Logs from the 'RStudio' 'CRAN' Mirror},
  author={Gabor Csardi},
  note={R package version 2.1.0},
  url={https://github.com/metacran/cranlogs},
}

@article{Cvetkovic10,
	author={M. Cvetkovic and A. Wei and P. Chow-Fraser},
	year={2010},
	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},
	journal={Journal of Great Lakes Research},
	volume={36},
	pages={64-73}
}

@article{Cutler07,
	author={D. R. Cutler and T. C. Edwards Jr. and K. H. Beard and A. Cutler and K. T. Hess and J. Gibson and J. J. Lawler},
	year={2007},
	title={Random forests for classification in ecology},
	journal={Ecology},
	volume={88},
	number={11},
	pages={2783-2792},
	doi={10.1890/07-0539.1}
}

@article{Dahm16,
	author={C. N. Dahm and A. E. Parker and A. E. Adelson and M. A. Christman and B. A. Bergamaschi},
	year={2016},
	title={Nutrient dynamics of the {D}elta: Effects on primary producers},
	journal={San Francisco Estuary and Watershed Science},
	volume={14},
	number={4},
	pages={1-36}
}

@article{Dale02,
	author={M. R. T. Dale and P. Dixon and M. J. Fortin and P. Legendre and D. E. Myers and M. S. Rosenberg},
	year={2002},
	title={Conceptual and mathematical relationships among methods for spatial analysis},
	journal={Ecography},
	volume={25},
	number={5},
	pages={558-577}
}

@article{Danz07,
	author={Nicholas P. Danz and Gerald J. Niemi and Ronald R. Regal and Tom Hollenhorst and Lucinda B. Johnson and JoAnn M. Hanowski and Richard P. Axler and Jan J. H. Ciborowski and Thomas Hrabik and Valerie J. Brady and John R. Kelly and John A. Morrice and John C. Brazner and Robert W. Howe and Carol A. Johnston and George E. Host},
	year={2007},
	title={Integrated measures of anthropogenic stress in the {US Great Lakes} basin},
	journal={Environmental Management},
	volume={39},
	number={5},
	pages={631-647}
}

@article{D'Arcy97,
	author={P. D'Arcy and R. Carignan},
	year={1997},
	title={Influence of catchment topography on water chemistry in southeastern {Q}uebec Shield lakes},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={54},
	number={10},
	pages={2215-2227}
}

@article{Davanzo96,
  author={C. D'Avanzo and J. N. Kremer and S. C. Wainwright},
  year={1996},
	title={Ecosystem production and respiration in response to eutrophication in shallow temperate estuaries},
	journal={Marine Ecology Progress Series},
	volume={141},
	number={1-3},
	pages={263-274}
}

@article{Davies06,
	author={S. P. Davies and S. K. Jackson},
	year={2006},
	title={The biological condition gradient: A descriptive model for interpreting change in aquatic ecosystems},
	journal={Ecological Applications},
	volume={16},
	number={4},
	pages={1251-1266}
}

@article{Dawes10,
  author={C. Dawes and W. Avery},
  year={2010},
	title={Epiphytes of the seagrass {\textit{Halodule wrightii}} in {H}illsborough {B}ay, {F}lorida, a 14 year study in an estuary recovering from eutrophication},
	journal={Florida Scientist},
	volume={73},
	number={3-4},
	pages={185-195}
}

@article{DeKeyser03,
	author={E. DeKeyser and D. R. Kirby and M. J. Ell},
	year={2003},
	title={An index of plant community integrity: Development of the methodology for assessing prairie wetland plant commmunities},
	journal={Ecological Indicators},
	volume={3},
	number={2},
	pages={119-133}
}

@article{Denman03,
	author={K. L. Denman},
	year={2003},
	title={Modelling planktonic ecosystems: parameterizing complexity},
	journal={Progress in Oceanography},
	volume={57},
	number={3-4},
	pages={429-452}
}

@article{Dennison87,
  author={W. C. Dennison},
  year={1987},
	title={Effects of light on seagrass photosynthesis, growth and depth distribution},
	journal={Aquatic Botany},
	volume={27},
	number={1},
	pages={15-26}
}

@article{Dennison93,
  author={W. C. Dennison and R. J. Orth and K. A. Moore and J. C. Stevenson and V. Carter and S. Kollar and P. W. Bergstrom and R. A. Batiuk},
	year={1993},
	title={Assessing water quality with submersed aquatic vegetation},
	journal={Bioscience},
	volume={43},
	number={2},
	pages={86-94}
}

@article{Diaz11,
	author={R. J. Diaz and R. Rosenberg},
	year={2011},
	title={Introduction to environmental and economic consequences of hypoxia},
	journal={International Journal of Water Resources Development},
	volume={27},
	number={1},
	pages={71-82}
}

@article{Diaz08,
	author={R. J. Diaz and R. Rosenberg},
	year={2008},
	title={Spreading dead zones and consequences for marine ecosystems},
	journal={Science},
	volume={321},
	pages={926-929}
}

@article{Diaz95,
	author={R. J. Diaz and R. Rosenberg},
	year={1995},
	title={Marine benthic hypoxia: A review of its ecological effects and the behavioural responses of benthic macrofauna},
	journal={Oceanography and Marine Biology},
	volume={33},
	pages={245-303}
}

@article {Diefenderfer16,
  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.},
  title = {Evidence-based evaluation of the cumulative effects of ecosystem restoration},
  journal = {Ecosphere},
  volume = {7},
  number = {3},
  url = {http://dx.doi.org/10.1002/ecs2.1242},
  pages = {e01242},
  year = {2016}
}

@article{Dix08,
  author={N. G. Dix and E. J. Phlips and R. A. Gleeson},
	year={2008},
	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},
	journal={Journal of Coastal Research},
	volume={55},
	number={SI},
	pages={26-37}
}

@techreport{Dixon95,
  author={L. K. Dixon and J. R. Leverone},
  year={1995},
	title={Light requirements of \textit{Thalassia testudinum} in {T}ampa {B}ay, {F}lorida},
	institution={Number 425, Mote Marine Lab},
	address={Sarasota, Florida},
  pages={77}
}

@article{Dodds09,
	author={W. K. Dodds and W. W. Bouska and J. L. Eitzmann and T. J. Pilger and K. L. Pitts and A. J. Riley and J. T. Schloesser and D. J. Thornbrugh},
	year={2009},
	title={Eutrophication of {U.S.} freshwaters: Analysis of potential economic damages},
	journal={Environmental Science and Technology},
	volume={43},
	number={1},
	pages={12-19}
}

@article{Dodson00,
	author={S. I. Dodson and S. E. Arnott and K. L. Cottingham},
	year={2000},
	title={The relationship in lake communities between primary productivity and species richness},
	journal={Ecology},
	volume={81},
	number={10},
	pages={2662-2679}
}

@article{Dolph10,
	author={C. L. Dolph and A. Y. Sheshukov and C. J. Chizinski and B. Vondracek},
	year={2010},
	title={The index of biological integrity and the bootstrap: Can random sampling error affect stream impairment decisions?},
	journal={Ecological Indicators},
	volume={10},
	number={2},
	pages={527-537}
}

@article{Dolph11,
	author={C. L. Dolph and D. D. Huff and C. J. Chizinski and B. Vondracek},
	year={2011},
	title={Implications of community concordance for assessing stream intregrity at three nested spatial scales in {M}innesota, {U.S.A}},
	journal={Freshwater Biology},
	volume={56},
	pages={1652-1669}
}

@article{Doran07,
	author={H. Doran and D. Bates and P. Bliese},
	year={2007},
	title={Estimating the multilevel {R}asch model: {W}ith the lme4 package},
	journal={Journal of Statistical Software},
	volume={20},
	number={2},
	pages={1-18}
}

@techreport{Dortch07,
	author={M. S. Dortch and M. Zakikhani and M. R. Noel and S. C. Kim},
	year={2007},
	title={Application of a water quality model to {M}ississippi {S}ound to evaluate impacts of freshwater diversions},
	institution={Engineer Research and Development Center},
	address={Vicksburg, Mississippi},
	pages={889}
}

@article{Dortch90,
	author={W. Dortch},
	year={1990},
	title={The interaction between ammonium and nitrate uptake in phytoplankton},
	journal={Marine Ecology Progress Series},
	volume={61},
	number={1/2},
	pages={183-201}
}

@manual{Dowle14,
    title = {data.table: Extension of data.frame},
    author = {M. Dowle and T. Short and S. Lianoglou and A. Srinivasan and R. Saporta and E. Antonyan},
    year = {2014},
    note = {R package version 1.9.4},
    url = {http://CRAN.R-project.org/package=data.table},
  }

@article{Drake05,
	author={M. T. Drake and R. D. Valley},
	year={2005},
	title={Validation and application of a fish-based index of biotic integrity for small central {M}innesota lakes},
	journal={North American Journal of Fisheries Management},
	volume={25},
	number={3},
	pages={1095-1111}
}

@article{Drake02,
	author={M. T. Drake and D. L. Pereira},
	year={2002},
	title={Development of a fish-based index of biotic integrity for small inland lakes in central {M}innesota},
	journal={North American Journal of Fisheries Management},
	volume={22},
	number={4},
	pages={1105-1123}
}

@article{Droop73,
	author={M. R. Droop},
	year={1973},
	title={Some thoughts on nutrient limitation in algae},
	journal={Journal of Phycology},
	volume={9},
	number={},
	pages={264-272}
}

@article{Duan83,
  author={N. Duan},
	year={1983},
	title={Smearing estimate: A nonparametric retransformation method},
	journal={Journal of the American Statistical Association},
	volume={78},
	number={383},
	pages={605-610}
}

@article{Duarte09,
  author={C. M. Duarte and D. J. Conley and J. Carstensen and M. S\'{a}nchez-Camacho},
	year={2009},
	title={Return to \textit{Neverland}: Shifting baseline affect eutrophication restoration targets},
	journal={Estuaries and Coasts},
	volume={32},
	number={1},
	pages={29-36}
}

@article{Duarte95,
	author={C. M. Duarte},
	year={1995},
	title={Submerged aquatic vegetation in relation to different nutrient regimes},
	journal={Ophelia},
	volume={41},
	pages={87-112}
}

@article{Duarte91,
	author={C. M. Duarte},
	year={1991},
	title={Seagrass depth limits},
	journal={Aquatic Botany},
	volume={40},
	number={4},
	pages={363-377}
}

@article{Duarte86,
	author={C. M. Duarte and J. Kalff and R. H. Peters},
	year={1986},
	title={Patterns in biomass and cover of aquatic macrophytes in lakes},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={43},
	pages={1900-1908}
}

@article{Dugdale07,
	author={R. C. Dugdale and F. P. Wilkerson and V. E. Hogue and A. Marchi},
	year={2007},
	title={The role of ammonium and nitrate in spring bloom development in {S}an {F}rancisco {B}ay},
	journal={Estuarine, Coastal, and Shelf Science},
	volume={73},
	number={},
	pages={17-29}
}

@article{Dugdale67,
	author={R. C. Dugdale and J. J. Goering},
	year={1967},
	title={Uptake of new and regenerated nitrogen in primary productivity},
	journal={Limnology and Oceanography},
	volume={12},
	number={},
	pages={196-206}
}

@article{Durand02,
	author={P. Durand and C. Gascuel-Odoux and M. O. Cordier},
	year={2002},
	title={Parameterisation of hydrological models: a review and lessons learned from studies of an agricultural catchment ({N}aisin, {F}rance},
	journal={Agronomie},
	volume={22},
	number={2},
	pages={217-228}
}

@book{Dyer73,
  author={K. R. Dyer},
  year={1973},
	title={Estuaries: A Physical Introduction},
	publisher={Wiley},
	address={London, United Kingdom},
	pages={156}
}

@article{Edwards08,
	author={L. J. Edwards and K. E. Muller and R. D. Wolfinger and B. F. Qaqish and O. Schabenberger},
	year={2008},
	title={An {R}$^2$ statistic for fixed effects in the linear mixed model},
	journal={Statistics in Medicine},
	volume={27},
	number={29},
	pages={6137-6157}
}

@article{Eiswerth00,
	author={M. E. Eiswerth and S. G. Donaldson and W. S. Johnson},
	year={2000},
	title={Potential environmental impacts and economic damages of {E}urasian watermilfoil (\textit{{M}yriophyllum spicatum}) in western {N}evada and northeastern {C}alifornia},
	journal={Weed Technology},
	volume={14},
	number={3},
	pages={511-518}
}

@book{Efron93,
	author={B. Efron and R. Tibshirani},
	year={1993},
	title={An Introduction to the Bootstrap},
	publisher={Chapman and Hall},
	address={New York, New York},
	edition={first},
	pages={436}	
}

@article{Eldridge10,
	author={P. M. Eldridge and D. L. Roelke},
	year={2010},
	title={Origins and scales of hypoxia on the {L}ouisiana shelf: importance of seasonal plankton dynamics and river nutrients and discharge},
	journal={Ecological Modelling},
	volume={221},
	number={7},
	pages={1028-1042}
}

@article{Ellenius00,
	author={J. Ellenius and T. Groth},
	year={2000},
	title={Methods for selection of adequate neural network structures with application to early assessment of chest pain patients by biochemical monitoring},
	journal={International Journal of Medical Informatics},
	volume={57},
	number={2-3},
	pages={181-202}
}

@article{Elsdon09,
  author={T. S. Elsdon and S. D. Connell},
  year={2009},
  title={Spatial and temporal monitoring of coastal water quality: refining the way we consider, gather, and interpret patterns},
	journal={Aquatic Biology},
	volume={5},
	number={2},
	pages={157-166}
}

@article{Emerson13,
  author={J. W. Emerson and W. A. Green and B. Schloerke and J. Crowley and D. Cook and H. Hofmann and H. Wickham},
	year={2013},
	title={The generalized pairs plot},
	journal={Journal of Computational and Graphical Statistics},
	volume={22},
	number={1},
	pages={79-91}
}

@article{Engel94,
	author={S. Engel and S. A. Nichols},
	year={1994},
	title={Aquatic macrophyte growth in a turbid windswept lake},
	journal={Journal of Freshwater Ecology},
	volume={9},
	number={2},
	pages={97-109}
}

@article{Enright09,
	author={C. Enright and S. D. Culberson},
	year={2009},
	title={Salinity trends, variability, and control in the northern reach of the {S}an {F}rancisco {E}stuary},
	journal={San Francisco Estuary and Watershed Science},
	volume={7},
	number={2},
	pages={1-28}
}

@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={R. W. Eppley and J. N. Rogers and J. McCarthy},
	year={1969},
	title={Half-saturation constants for uptake of nitrate and ammonium by marine phytoplankton},
	journal={Limnology and Oceanography},
	volume={14},
	number={6},
	pages={912-920}
}

@techreport{EQB00,
	author={{EQB (Environmental Quality Board)}},
	year={2000},
	title={{M}innesota watermarks: Gauging the flow of progress 2000-2010},
	institution={Minnesota Planning, Environmental Quality Board},
	address={St. Paul, Minnesota},
	pages={49},
	note={\url{http://www.gda.state.mn.us/pdf/2000/eqb/wtr_mrk.pdf}}
}

@misc{ERDAS10,
	author={{ERDAS (Earth Resource Data Analysis System)}},
	year={2010},
	title={{ERDAS Imagine}},
	note={{ERDAS, Hexagon Group}, Atlanta, Georgia}
}

@misc{ESRI12,
	author={{ESRI (Environmental Systems Research Institute)}},
	year={2012},
	title={{ArcGIS v10.1}},
	note={{ESRI}, Redlands, California}
}

@article{Esselman12,
	author={P. C. Esselman and D. M. Infante and L. Wang and D. Wu and A. R. Cooper and W. W. Taylor},
	year={2012},
	title={An index of cumulative disturbance to river fish habitats of the conterminous {U}nited {S}tates from landscape anthropogenic activities},
	journal={Ecological Restoration},
	volume={29},
	number={1-2},
	pages={133-151}
}

@article{Esterby96,
	author={S. R. Esterby},
	year={1996},
	title={Review of methods for the detection and estimation of trends with emphasis on water quality applications},
	journal={Hydrological Processes},
	volume={10},
	number={2},
	pages={127-149}
}

@article{Estrada10,
	author={V. Estrada and M.S. Diaz},
	year={2010},
	title={Global sensitivity analysis in the development of first principle-based eutrophication models},
	journal={Environmental Modelling and Software},
	volume={25},
	number={},
	pages={1539-1551}
}

@article{Fahnenstiel95,
	author={G. L. Fahnenstiel and M. J. McCormick and G. A. Lang and D. G. Redalje and S. E. Lohrenz and M. Markowitz and B. Wagoner and H. J. Carrick},
	year={1995},
	title={Taxon-specific growth and loss rates for dominant phytoplankton populations from the northern {G}ulf of {M}exico},
	journal={Marine Ecology Progress Series},
	volume={117},
	number={1-3},
	pages={229-239}
}

@incollection{Fanning85,
  author={K. A. Fanning and L. M. Bell},
  editor={S. F. Treat and J. L. Simon and R. R. Lewis and R. L. Whitman},
	year={1985},
	title={Nutrients in {T}ampa {B}ay},
	booktitle={Proceedings of the Tampa Bay Area Scientific Information Symposium},
	publisher={Florida Sea Grant Report No. 65, Bellwether Press},
	address={Tampa, Florida, USA},
	pages={109-129}
}

@article{Fasham06,
	author={M. J. R. Fasham and K. J. Flynn and P. Pondaven and T. R. Anderson and P. W. Boyd},
	year={2006},
	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},
	journal={Deep-Sea Research I},
	volume={53},
	number={},
	pages={333-366}
}

@book{Fassett57,
	author={N. C. Fassett},
	year={1957},
	title={A Manual of Aquatic Plants},
	publisher={University of Wisconsin Press},
	address={Madison, Wisconsin},
	pages={416}
}

@article{Feng02,
	author={C. X. Feng and X. Wang},
	year={2002},
	title={Digitizing uncertainty modeling for reverse engineering applications: regression versus neural networks},
	journal={Journal of Intelligent Manufacturing},
	volume={13},
	number={3},
	pages={189-199}
}

@article{Fennel13,
	author={K. Fennel and J. Hu and A. Laurent and M. Marta-Almeida and R. Hetland},
	year={2013},
	title={Sensitivity of hypoxia predictions for the northern {G}ulf of {M}exico to sediment oxygen consumption and model nesting},
	journal={Journal of Geophysical Research: Oceans},
	volume={118},
	number={2},
	pages={990-1002}
}

@article{Fetscher13,
	author={A. E. Fetscher and R. Stancheva and J. P. Kociolek and R. G. Sheath and E. D. Stein and R. D. Mazor and P. R. Ode and L. B. Busse},
	year={2013},
	title={Development and comparison of stream indices of biotic integrity using diatoms vs. non-diatom algae vs. a combination},
	journal={Journal of Applied Phycology},
	volume={26},
	number={1},
	pages={433-450},
	doi={10.1007/s10811-013-0088-2}
}

@article{Feyrer03,
	author={F. Feyrer and B. Herbold and S. A. Matern and P. B. Moyle},
	year={2003},
	title={Dietary shifts in a stressed fish assemblage: Consequences of a bivalve invasion in the {S}an {F}rancisco {E}stuary},
	journal={Environmental Biology of Fishes},
	volume={67},
	number={3},
	pages={277-288}
}

@article{Figuerola12,
	author={B. Figuerola and A. Maceda-Veiga and A. De Sostoa},
	year={2012},
	title={Assessing the effects of sewage effluents in a {M}editerranean creek: Fish population features and biotic indices},
	journal={Hydrobiologia},
	volume={694},
	number={1},
	pages={75-86}
}

@techreport{FLDEP12,
  author={{(FLDEP) Florida Department of Environmental Protection}},
  year={2012},
  title={Site-specific information in support of establishing numeric nutrient criteria for {C}hoctawhatchee {B}ay},
	institution={Florida Department of Environmental Protection},
	address={Tallahassee, Florida},
  pages={118}
}

@article{Flynn05,
	author={K. J. Flynn},
	year={2005},
	title={Castles built on sand: dysfunctionality in plankton models and the inadequacy of dialogue between biologists and modellers},
	journal={Journal of Plankton Research},
	volume={27},
	number={12},
	pages={1205-1210}
}

@article{Flynn03,
	author={K. J. Flynn},
	year={2003},
	title={Modelling multi-nutrient interactions in phytoplankton; balancing simplicity and realism},
	journal={Progress in Oceanography},
	volume={56},
	number={2},
	pages={249-279}
}

@article{Fore09,
	author={L. S. Fore and J. R. Karr and W. S. Fisher and P. Bradley and W. S. Davis},
	year={2009},
	title={Heeding a call to action for {US} coral reefs: The untapped potential of the {C}lean {W}ater {A}ct},
	journal={Marine Pollution Bulletin},
	volume={58},
	number={10},
	pages={1421-1423}
}

@article{Fore94,
	author={L. S. Fore and J. R. Karr and L. L. Conquest},
	year={1994},
	title={Statistical properties of an index of biological integrity used to evaluate water resources},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={51},
	number={5},
	pages={1077-1087}
}

@book{Fox11,
	author={J. Fox and S. Weisberg},
	year={2011},
	title={An {R} Companion to Applied Regression},
	publisher={{SAGE} Publications Inc.},
	address={Thousand Oaks, California},
	pages={449} 
}

@article{Foreman89,
  author={M. G. G. Foreman and R. F. Henry},
	year={1989},
	title={The harmonic analysis of tidal model time series},
	journal={Advances in Water Resources},
	volume={12},
	number={3},
	pages={109-120}
}

@article{Francis06,
	author={T. B. Francis and D. E. Schindler},
	year={2006},
	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},
	journal={AMBIO: A Journal of the Human Environment},
	volume={35},
	number={6},
	pages={274-280}
}

@article{Franks97,
	author={S. W. Franks and K. J. Beven and P. F. Quinn and I. R. Wright},
	year={1997},
	title={On the sensitivity of soil-vegetation-atmosphere transfer ({SVAT}) schemes: Equifinality and the problem of robust calibration},
	journal={Agricultural and Forest Meteorology},
	volume={86},
	number={1-2},
	pages={63-75}
}

@article{Frieden14,
	author={J. C. Frieden and E. E. Peterson and J. A. Webb and P. M. Negus},
	year={2014},
	title={Improving the predictive power of spatial statistical models of stream macroinvertebrates using weighted autocovariance functions},
	journal={Environmental Modelling \& Sofware},
	volume={60},
	number={},
	pages={320-330}
}

@article{Fries08,
  author={D. P. Fries and S. Z. Ivanov and P. H. Bhanushali and J. A. wilson and H. A. Broadbent and A. C. Sanderson},
  year={2008},
	title={Broadband, low-cost, coastal sensor nets},
	journal={Oceanography},
	volume={20},
	number={4},
	pages={150-155}
}

@article{Frissell86,
	author={C. A. Frissell and W. J. Liss and C. E. Warren and M. D. Hurley},
	year={1986},
	title={A hierarchical framework for stream habitat classification: Viewing streams in a watershed context},
	journal={Environmental Management},
	volume={10},
	number={2},
	pages={199-214}
}

@manual{Fritsch12,
  title = {neuralnet: Training of neural networks},
  author = {Stefan Fritsch and Frauke Guenther},
  year = {2012},
  note = {R package version 1.32},
  url = {http://CRAN.R-project.org/package=neuralnet},
  }

@article{Fry11,
	author={J. Fry and G. Xian and S. Jin and J. Dewitz and C. Homer and L. Yang and C. Barnes and N. Herold and J. Wickham},
	year={2011},
	title={Completion of the 2006 {National Land Cover Database} for the conterminous {United States}},
	journal={Photogrammetric Engineering and Remote Sensing},
	volume={77},
	number={9},
	pages={858-864}
	}

@article{Gaarder27,
  title={Investigations of the production of plankton in the Oslo Fjord},
  author={T. Gaarder and H. H. Gran},
  year={1927},
  journal={Rapports et Proc\'{e}s-Verbaux des R\'{e}unions du Conseil Permanent International pour l'Exploration de le Mer}, 
  volume={42},
  pages={1-48}
}

@article{Gaeta11,
	author={J. W. Gaeta and M. J. Gaurascio and G. G. Sass and S. R. Carpenter},
	year={2011},
	title={Lakeshore residential development and growth of largemouth bass (\textit{Micropterus salmoides}): A cross-lakes comparison},
	journal={Ecology of Freshwater Fish},
	volume={20},
	number={1},
	pages={92-101}
} 

@article{Gallagher07,
	author={M. Gallagher and J. Doherty},
	year={2007},
	title={Parameter estimation and uncertainty analysis for a watershed model},
	journal={Environmental Modelling and Software},
	volume={22},
	number={7},
	pages={1000-1020}
}

@article{Ganju16,
	author={N. K. Ganju and M. J. Brush and B. Rashleigh, and A. L. Aretxabaleta and P. del Barrio and J. S. Grear and L. A. Harris and S. J. Lake and G. McCardell and J. O'Donnell and D. K. Ralston and R. P. Signell and J. M. Testa and J. M. P. Vaudrey},
	year={2016},
	title={Progress and challenges in coupled hydrodynamic-ecological estuarine modeling},
	journal={Estuaries and Coasts},
	volume={39},
	number={2},
	pages={311-332}
}

@article{Garcia13,
	author={S. Garc\'{i}a and J. Luengo and J. A. S\'{a}ez and V. L\'{o}pez and F. Herrera},
	year={2013},
	title={A survey of discretization techniques: Taxonomy and empirical analysis in supervised learning},
	journal={IEEE Transactions on Knowledge and Data Engineering},
	volume={25},
	number={4},
	pages={734-750}
}

@techreport{Garrison05,
	author={P. J. Garrison and D. W. Marshall and L. S. Thompson and P. L. Cicero and P. D. Dearlove},
	year={2005},
	title={Effects of pier shading on littoral zone habitat and communities in lakes {R}ipley and {R}ock, {J}efferson county, {W}isconsin},
	number={PUB-SS-1006},
	institution={Wisconsin Department of Natural Resources, Jefferson County Land and Water Conservation Department, and Lake Ripley Management District},
	address={Madison, Wisconsin},
	pages={18}
}

@article{Garson91,
	author={G. D. Garson},
	year={1991},
	title={Interpreting neural network connection weights},
	journal={Artificial Intelligence Expert},
	volume={6},
	number={4},
	pages={46-51}
}

@article{Geider97,
	author={R. J. Geider and H. L. MacIntyre and T. M. Kana},
	year={1997},
	title={A dynamic model of phytoplankton growth and acclimation: responses of the balanced growth rate and the chlorophyll \textit{a}:carbon ratio to light, nutrient-limitation and temperature},
	journal={Marine Ecology Progress Series},
	volume={148},
	pages={187-200}
}

@article{Geider98,
	author={R. J. Geider and H. L. MacIntyre and T. M. Kana},
	year={1998},
	title={A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature},
	journal={Limnology and Oceanography},
	volume={43},
	number={4},
	pages={679-694}
}

@article{Gelbrecht05,
	author={J. Gelbrecht and H. Lengsfeld and R. Pothig and D. Opitz},
	year={2005},
	title={Temporal and spatial variation of phosphorus input, retention and loss in a small catchment of {NE} {Germany}},
	journal={Journal of Hydrology},
	volume={304},
	pages={151-165}
}

@techreport{Genet04,
	author={J. Genet and J. Chirhart},
	year={2004},
	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},
	institution={Biological Monitoring Program, Minnesota Pollution Control Agency},
	address={St. Paul, Minnesota},
	pages={23}
}

@techreport{Genet06,
	author={J. Genet and M. Bourdaghs},
	year={2006},
	title={Development and validation of indices of biological integrity ({IBI}) for depressional wetlands in the temperate prairies ecoregion},
	institution={Biological Monitoring Program, Minnesota Pollution Control Agency},
	address={St. Paul, Minnesota},
	pages={136}
}

@article{Genkai-Cato05,
	author={M. Genkai-Cato and S. R. Carpenter},
	year={2005},
	title={Eutrophication due to phosphorus recycling in relation to lake morphometry, temperature, and macrophytes},
	journal={Ecology},
	volume={86},
	number={1},
	pages={210-219}
}

@techreport{Gernes02,
	author={M. C. Gernes and J. C. Helgen},
	year={2002},
	title={Indexes of biological integrity ({IBI}) for large depressional wetlands in {M}innesota},
	institution={Biological Monitoring Program, Minnesota Pollution Control Agency},
	address={St. Paul, Minnesota},
	pages={86}
}

@incollection{Gershenfeld93,
	author={N. A. Gershenfeld and A. S. Weigend},
	editor={A. S. Weigend and N. A. Gershenfeld},
	year={1993},
	title={The future of time series: Learning and understanding},
	booktitle={Time Series Prediction: Forecasting the Future and Understanding the Past},
	publisher={Addison-Wesley},
	address={Santa Fe, New Mexico},
	edition={Second},
	pages={1-70}
}

@incollection{Gevrey06,
	author={M. Gevrey and S. Lek and T. Oberdorff},
	editor={F. Recknagel},
	year={2006},
	title={Utility of sensitivity analysis by artificial neural network models to study patterns of endemic fish species},
	booktitle={Ecological Informatics: Scope, Techniques and Applications},
	publisher={Springer-Verlag},
	edition={2nd},
	address={Berlin, Germany},
	pages={293-306}
}

@article{Gevrey03,
	author={M. Gevrey and I. Dimopoulos and S. Lek},
	year={2003},
	title={Review and comparison of methods to study the contribution of variables in artificial neural network models},
	journal={Ecological Modelling},
	volume={160},
	number={3},
	pages={249-264}
}

@book{Gilbert87,
  author={R. O. Gilbert},
  year={1987},
	title={Statistical Methods for Environmental Pollution Monitoring},
	publisher={Van Nostrand Reinhold},
	address={New York, USA},
	pages={320}
}

@article{Gittleman90,
  author = {J. L. Gittleman and M. Kot}, 
  year = {1990},
  title = {Adaptation: statistics and a null model for estimating phylogenetic effects},
  journal = {Systematic Biology},
  volume = {39}, 
  number = {3},
  pages = {227-241}
}

@article{Glasgow04,
  author={H. B. Glasgow and J. M. Burkholder and R. E. Reed and A. J. Lewitus and J. E. Kleinman},
	year={2004},
	title={Real-time remote monitoring of water quality: a review of current applications, and advancements in sensor, telemetry, and computing technologies},
	journal={Journal of Experimental Marine Biology and Ecology},
	volume={300},
	number={1-2},
	pages={409-448}
}

@article{Glibert14,
	author={P. M. Glibert and R. C. Dugdale and F. Wilkerson and A. E. Parker and J. Alexander and E. Antell and S. Blaser and A. Johnson and J. Lee and T. Lee and S. Murasko and S. Strong},
	year={2014},
	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},
	journal={Journal fo Experimental Marine Biology and Ecology},
	volume={460},
	number={},
	pages={8-18}
}

@article{Glibert13,
	author={P. M. Glibert and D. C. Hinkle and B. Sturgis and R. V. Jesien},
	year={2013},
	title={Eutrophication of a {M}aryland/{V}irginia coastal lagoon: A tipping point, ecosytem changes, and potential causes},
	journal={Estuaries and Coasts},
	volume={},
	number={},
	pages={}
}

@article{Glibert10,
	author={P. M. Glibert},
	year={2010},
	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},
	journal={Reviews in Fisheries Science},
	volume={18},
	number={2},
	pages={211-232}
}

@article{Goh95,
	author={A. T. C. Goh},
	year={1995},
	title={Back-propagation neural networks for modeling complex systems},
	journal={Artificial Intelligence in Engineering},
	volume={9},
	number={3},
	pages={143-151}
}

@article{Goldberg83,
	author={D. E. Goldberg and P. A. Werner},
	year={1983},
	title={Equivalence of competitors in plant communities: {A} null hypothesis and a field experimental approach},
	journal={American Journal of Botany},
	volume={70},
	number={7},
	pages={1098-1104}
}

@techreport{Goodwin87,
  author={C. R. Goodwin},
	year={1987},
	title={Tidal-flow, circulation, and flushing changes caused by dredge and fill in {T}ampa {B}ay, {F}lorida},
	institution={US Geological Survey},
	address={Denver, Colorado},
  number={Water-Supply Paper 2282},
	url={http://pubs.usgs.gov/wsp/2282/report.pdf}
}

@article{Greene09,
	author={R. M. Greene and J. C. Lehrter and J. D. Hagy},
	year={2009},
	title={Multiple regression models for hindcasting and forecasting midsummer hypoxia in the {G}ulf of {M}exico},
	journal={Ecological Applications},
	volume={19},
	number={5},
	pages={1161-1175}
}

@article{Greening06,
	author={H. Greening and A. Janicki},
	year={2006},
	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}},
	journal={Environmental Management},
	volume={38},
	number={2},
	pages={163-178}
}

@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{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}
}

@article{Greve05,
  author={T. Greve and D. Krause-Jensen},
  year={2005},
	title={Stability of eelgrass (\textit{{Z}ostera marine {L}.}) depth limits: influence of habitat type},
	journal={Marine Biology},
	volume={147},
	number={3},
	pages={803-812}
}

@misc{HADS15,
  title = {Hydrometeorological Automated Data System website},
  author = {National Weather Service, National Oceanic and Atmospheric Administration},
  year = {2015},
  note = {\url{http://www.nws.noaa.gov/oh/hads/}. (Accessed March, 2015)}
}

@mastersthesis{Hagythes,
  author={J. D. Hagy},
	year={1996},
	title={Residence times and net ecosystem processes in {P}atuxent {R}iver estuary},
	school={University of Maryland},
	address={College Park, Maryland}, 
	pages={205}
}

@phdthesis{Hagydiss,
  author={J. D. Hagy},
	year={2002},
	title={Eutrophication, hypoxia, and trophic transfer efficiency in {C}hesapeake {B}ay},
	school={University of Maryland},
	address={College Park, Maryland}
}

@article{Hagy06,
	author={J. D. Hagy and J. C. Lehrter and M. C. Murrell},
	year={2006},
	title={Effects of hurricanee {I}van on water quality in {P}ensacola {B}ay, {F}lorida},
	journal={Estuaries and Coasts},
	volume={29},
	number={6A},
	pages={919-925}
}

@article{Hagy07,
	author={J. D. Hagy and M. C. Murrell},
	year={2007},
	title={Susceptibility of a northern {G}ulf of {M}exico estuary to hypoxia: An analysis using box models},
	journal={Estuarine Coastal and Shelf Science},
	volume={74},
	pages={239-253}
}

@techreport{Hagy08,
	author={J. D. Hagy and J. C. Kurtz and R. M. Greene},
	year={2008},
	title={An approach for developing numeric nutrient criteria for a {G}ulf {C}oast estuary},
	institution={US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Gulf Ecology Division},
	address={Gulf Breeze, Florida},
	number={EPA/600/R-08/004}
}

@article{Hale04,
  author={J. A. Hale and T. K. Frazer and D. A. Tomasko and M. O. Hall},
	year={2004},
	title={Changes in the distribution of seagrass species along {F}lorida's central gulf coast: {I}verson and {B}ittaker revisited},
	journal={Estuaries},
	volume={27},
	number={1},
	pages={36-43}
}

@article{Hall00,
	author={L. W. Hall and J. M. Giddings},
	year={2000},
	title={The need for multiple lines of evidence for predicting site-specific ecological effects},
	journal={Human and Ecological Risk Assessment},
	volume={6},
	number={4},
	pages={679-710}
}

@article{Hall90,
  author={M. O. Hall and M. J. Durako and J. W. Fourqurean and J. C. Zieman},
	year={1990},
	title={Decadal changes in seagrass distribution and abundance in {F}lorida {B}ay},
	journal={Estuaries},
	volume={22},
	number={2B},
	pages={445-459}
}

@article{Halliday12,
  author={S. J. Halliday and A. J. Wade and R. A. Skeffington and C. Neal and B. Reynolds and P. Rowland and M. Neal and D. Norris},
  year={2012},
	title={An analysis of long-term trends, seasonality and short-term dynamics in water quality data from {P}lynlimon, {W}ales},
	journal={Science of the Total Environment},
	volume={434},
	number={},
	pages={186-200}
}

@article{Hammerstrom93,
	author={D. Hammerstrom},
	year={1993},
	title={Working with neural networks},
	journal={IEEE Spectrum},
	volume={30},
	number={7},
	pages={46-53}
}

@article{Hampton13,
	author={S. E. Hampton and C. A. Strasser and J. J. Tewksbury and W. K. Gram and A. E. Budden and A. L. Batcheller and C. S. Duke and J. H. Porter},
	year={2013},
	title={Big data and the future of ecology},
	journal={Frontiers in Ecology and the Environment},
	volume={11},
	number={3},
	pages={156-162}
}

@article{Haraguchi15,
	author={L. Haraguchi and J. Carstensen and P. C. Abreu and C. Odebrecht},
	year={2015},
	title={Long-term changes of the phytoplankton community and biomass in the subtropical shallow {P}atos {L}agoon {E}stuary, {B}razil},
	journal={Estuarine, Coastal and Shelf Science},
	volume={162},
	number={SI},
	pages={76-87}
}

@article{Harding16,
	author={L. W. Harding and C. L. Gallegos and E. S. Perry and W. D. Miller and J. E. Adolf and M. E. Mallonee and H. W. Paerl},
	year={2016},
	title={Long-term trends of nutrients and phytoplankton in {C}hesapeake {B}ay},
	journal={Estuaries and Coasts},
	volume={39},
	number={},
	pages={664-681}
}

@article{Harding13,
  author={L. W. Harding and R. A. Batiuk and T. R. Fisher and C. L. Gallegos and T. C. Mallone and W. D. Miller and M. R. Mulholland and H. w. Paerl and E. S. Perry and P. Tango},
	year={2013},
	title={Scientific bases for numerical chlorophyll criteria in {C}hesapeake {B}ay},
	journal={Estuaries and Coasts},
	volume={37},
	number={1},
	pages={134-148}
}

@article{Harding94,
  author={L. W. Harding},
  year={1994},
  title={Long-term trends in the distribution of phytoplankton in {C}hesapeake {B}ay - roles of light, nutrients, and streamflow},
  journal={Marine Ecology Progress Series},
  volume={104},
  numer={3},
  pages={267-291}
}

@article{Hartigan79,
	author={J. A. Hartigan and M. A. Wong},
	year={1979},
	title={A K-means clustering algorithm},
	journal={Applied Statistics},
	volume={28},
	number={1},
	pages={100-108}
}

@book{Harvey89,
  author={A. C. Harvey},
  year={1989},
  title={Forecasting, Structural Time Series Models and the Kalman Filter},
	publisher={Cambridge University Press},
	address={Cambridge, United Kingdom},
	pages={572}
}

@article{Harvey00,
	author={L. D. D. Harvey},
	year={2000},
	title={Upscaling in global change research},
	journal={Climatic Change},
	volume={44},
	number={3},
	pages={225-263}
}

@book{Hastie09,
  author={T. Hastie and R. Tibshirani and J. Friedman},
	year={2009},
	title={The elements of statistical learning: data mining, inference, and prediction},
	edition={2nd},
	publisher={Springer},
	address={New York},
	pages={745}
}

@book{Hastie90,
  author={T. Hastie and R. Tibshirani},
	year={1990},
	title={Generalized Additive Models},
	publisher={Chapman and Hall},
	address={London, New York},
	pages={335}
}

@techreport{Hauxwell10,
	author={J. Hauxwell and S. Knight and K. Wagner and A. Mikulyuk and M. Nault and M. Porzky and S. Chase},
	year={2010},
	title={Recommended baseline monitoring of aquatic plants in {W}isconsin: Sampling design, field and laboratory procedures, data entry and analysis, 		and applications},
	institution={Wisconsin Department of Natural Resources},
	address={Madison, Wisconsin},
	number={PUB SS-1068 2010}
}

@article{Hawkins00,
	author={C. P. Hawkins and R. H. Norris and J. Gerritsen and R. M. Hughes and S. K. Jackson and R. K. Johnson and R. J. Stevenson},
	year={2000},
	title={Evaluation of the use of landscape classifications for the prediction of freshwater biota: Synthesis and recommendations},
	journal={Journal of the North American Benthological Society},
	volume={19},
	number={3},
	pages={541-556}
}

@incollection{Hay08,
	author={G. J. Hay and G. Castilla},
	editor={T. Blaschke and S. Lang and G. J. Hay},
	year={2008},
	title={Geographic object-based image analysis ({GEOBIA}): A new name for a new discipline},
	booktitle={Object-Based Image Analysis: Spatial Concepts for Knowledge-Driven Remote Sensing Applications},
	publisher={Springer-Verlag},
	address={Heidelberg, Berlin, New York},
	pages={75-89}
}

@article{Heiskary08,
	author={S. Heiskary and B. Wilson},
	year={2008},
	title={Minnesota's approach to lake nutrient criteria development},
	journal={Lake and Reservoir Management},
	volume={24},
	number={3},
	pages={282-297}
}

@book{Helsel12,
  author={D. R. Helsel},
	year={2012},
	title={Statistics for Censored Environmental Data Using Minitab and R},
	publisher={John Wiley \& Sons, Inc.},
	edition={2nd}, 
	address={Hoboken New Jersey},
	pages={344}
}

@article{Hestir13,
	author={E. L. Hestir and D. H. Schoellhamer and T. Morgan-King and S. L. Ustin},
	year={2013},
	title={A step decrease in sediment concentration in a highly modifed tidal river delta following the 1983 {E}l Ni\~{n}o floods},
	journal={Marine Geology},
	volume={345},
	number={1},
	pages={304-313}
}

@article{Heugens01,
	author={E. H. W. Heugens and A. J. Hendriks and T. Dekker and N. M. van Straalen and W. Admiraal},
	year={2001},
	title={A review of the effects of multiple stressors on aquatic organisms and analysis of uncertainty factors for use in risk assessment},
	journal={Critical Reviews in Toxicology},
	volume={31},
	number={3},
	pages={247-284}
}

@book{Hilborn97,
	author={R. Hilborn and M. Mangel},
	year={1997},
	title={The Ecological Detective: Confronting Models with Data},
	publisher={Princeton University Press},
	address={Princeton, New Jersey},
	pages={315}
}

@article{Hill17,
	author={R. A. Hill and E. W. Fox and S. G. Leibowitz and A. R. Olsen and D. J. Thornbrugh and M. H. Weber},
	year={2017},
	title={Predictive mapping of the biotic condition of conterminous {U.S.} rivers and streams},
	journal={Ecological Applications},
	volume={27},
	number={8},
	pages={2397-2415},
	doi={10.1002/eap.1617}
}

@article{Hill16,
	author={R. A. Hill and M. H. Weber and S. G. Leibowitz and A. R. Olsen and D. J. Thornbrugh},
	year={2016},
	title={The {S}tream-{C}atchment ({S}tream{C}at) dataset: A database of watershed metrics for the conterminous {U}nited {S}tates},
	journal={Journal of the American Water Resources Assocation},
	volume={52},
	number={},
	pages={120-128},
	doi={10.1111/1752-1688.12372}
}

@article{Hirsch82,
  author={R. M. Hirsch and J. R. Slack and R. A. Smith},
  year={1982},
  title={Techniques of trend analysis for monthly water quality data},
  journal={Water Resources Research},
  volume={18},
  numer={1},
  pages={107-121}
}

@article{Hirsch91,
  author={R. M. Hirsch and R. B. Alexander and R. A. Smith},
  year={1991},
  title={Selection of methods for the detection and estimation of trends in water quality},
  journal={Water Resources Research},
  volume={27},
  numer={5},
  pages={803-813}
}

@article{Hirsch10,
	author={R. M. Hirsch and D. L. Moyer and S. A. Archfield},
	year={2010},
	title={Weighted regressions on time, discharge, and season ({WRTDS}), with an application to {C}hesapeake {B}ay river inputs},
	journal={Journal of the American Water Resources Association},
	volume={46},
	number={5},
	pages={857-880}
}

@techreport{Hirsch14,
  author={R. M. Hirsch and L. {De Cicco}},
  year={2014},
  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},
  institution={US Geological Survey},
	address={Reston, Virginia},
  number={Techniques and Methods book 4, ch. A10},
	pages={94}, 
  note={\url{http://pubs.usgs.gov/tm/04/a10/}}
}

@article{Hirsch14b,
	author={R. M. Hirsch},
	year={2014},
	title={Large biases in regression-based constituent flux estimates: causes and diagnostic tools},
	journal={Journal of the American Water Resources Association},
	volume={50},
	number={6},
	pages={1401-1424}
}

@article{Hirsch15, 
  author={R. M. Hirsch and S. A. Archfield and L. A. {De Cicco}}, 
  year={2015}, 
  title={A bootstrap method for estimating uncertainty of water quality trends}, 
  journal={Environmental Modelling and Software}, 
  volume={73}, 
  number={}, 
  pages={148-166}
}

@incollection{Hoang06,
	author={H. Hoang and F. Recknagel and J. Marshall and S. Choy},
	editor={F. Recknagel},
	year={2006},
	title={Elucidation of hypothetical relationships between habitat conditions and macroinvertebrate assemblages in freshwater streams by artificial neural networks},
	booktitle={Ecological Informatics: Scope, Techniques and Applications},
	publisher={Springer-Verlag},
	edition={2nd},
	address={Berlin, Germany},
	pages={239-251}
}

@article{Hoang01,
	author={H. Hoang and F. Recknagel and J. Marshall and S. Choy},
	year={2001},
	title={Predictive modelling of macroinvertebrate assemblages for stream habitat assessments in {Q}ueensland ({A}ustraila)},
	journal={Ecological Modelling},
	volume={195},
	number={1-3},
	pages={195-206}
}

@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={R. M. Hodur},
	year={1997},
	title={The {N}aval {R}esearch {L}aboratory's {C}oupled {O}cean/{A}tmosphere {M}esoscale {P}rediction {S}ystem ({COAMPS})},
	journal={Monthly Weather Review},
	volume={125},
	number={},
	pages={1414-1430}
}

@article{Holmes99,
  author={R. M. Holmes and A. Amino and R. Kerouel and B. A. Hooker and B. J. Peterson},
  year={1999},
	title={A simple precise method for measuring ammonium in marine and freshwater ecosystems},
	journal={Journal of Fisheries and Aquatic Sciences},
	volume={56},
	number={10},
	pages={1801-1808}
}

@article{Holmes70,
  author={R. W. Holmes},
  year={1970},
	title={The secchi disk in turbid coastal waters},
	journal={Limnology and Oceanography},
	volume={15},
	number={5},
	pages={688-694}
}

@article{Homer07,
	author={C. Homer and J. Dewitz and J. Fry and M. Coan and N. Hossain and C. Larson and N. Herold and A. McKerrow and J. N. VanDriel and J. Wickham},
	year={2007},
	title={Completion of the 2001 {National Land Cover Database} for the conterminous {United States}},
	journal={Photogrammetric Engineering and Remote Sensing},
	volume={73},
	number={4},
	pages={337-341}
}

@incollection{Hopkinson05,
  author={C. S. Hopkinson and E. M. Smith},
	editor={P. A. Del Giorgio and P. Williams},
	year={2005},
	title={Estuarine respiration: an overview of benthic, pelagic, and whole system respiration},
	booktitle={Respiration in Aquatic Ecosystems},
	publisher={Oxford Press},
	address={Oxford, United Kingdom},
	pages={122-146}
}

@article{Hornik91,
  author={K. Hornik},
	year={1991},
	title={Approximation capabilities of multilayer feedforward networks},
	journal={Neural Networks},
	volume={4},
	number={2},
	pages={251-257}
}

@article{Horppila01,
	author={J. Horppila and L. Nurminen},
	year={2001},
	title={The effect of an emergent macrophyte (\textit{{T}ypha angustifolia}) on sediment resuspension in a shallow north temperate lake},
	journal={Freshwater Biology},
	volume={46},
	number={11},
	pages={1447-1455}
}

@article{Host05,
	author={G. E. Host and J. Schuldt and J. J. H. Ciborowski and L. B. Johnson and T. Hollenhorst and C. Richards},
	year={2005},
	title={Use of {GIS} and remotely sensed data for a priori identification of reference areas for {G}reat {L}akes coastal ecosystems},
	journal={International Journal of Remote Sensing},
	volume={26},
	number={23},
	pages={5325-5341}
}

@article{Howard15,
  author={J. K. Howard and K. R. Klausmeyer and K. A. Fesenmyer and J. Furnish and T. Gardali and T. Grantham and J. V. E. Katz and S. Kupferberg and P. McIntyre and P. B. Moyle and P. R. Ode and R. Peek and R. M. Qui\~{n}ones and A. C. Rehn and N. Santos and S. Schoenig and L. Serpa and J. D. Shedd and J. Slusark and J. H. Viers and A. Wright and S. A. Morrison},
	year={2015},
	title={Patterns of freshwater species richness, endemism, and vulnerability in {C}alifornia},
	journal={PLOS ONE},
	volume={10},
	number={7},
	pages={e0130710},
	doi={10.1371/journal.pone.0130710}
}

@techreport{Howard09,
	author={J. Howard and C. Revenga},
	year={2000},
	title={California's freshwater biodiveristy in a continental context. {S}cience for {C}onservation {T}echnical {B}rief {S}eries},
	institution={The Nature Conservancy of California}, 
	address={San Francisco, CA},
	pages={29 + Appendices}
}

@article{Howarth96,
  author={R. W. Howarth and G. Billen and D. Swaney and A. Townsend and N. Jaworski and K. Lajtha and J. A. Downing and R. Elmgren and N. Caraco and T. Jordan and F. Berendse and J. Freney and V. Kudeyarov and P. Murdoch and Z. Zhao-Liang},
	year={1996},
	title={Regional nitrogen budgets and riverine {N} \& {P} fluxes for the drainages to the {N}orth {A}tlantic {O}cean: natural and human influences},
	journal={Biogeochemistry},
	volume={35},
	number={1},
	pages={75-139}
}

@article{Howarth14,
  author={R. W. Howarth and M. Hayn and R. M. Marino and N. Ganju and K. Foreman and K. McGlathery and A. E. Giblin and P. Berg and J. D. Walker},
	year={2014},
	title={Metabolism of a nitrogen-enriched coastal marine lagoon during the summertime},
	journal={Biogeochemistry},
	volume={118},
	number={1-3},
	pages={1-20}
}

@article{Hughes09,
  author={A. R. Hughes and S. L. Williams and C. M. Duarte and K. L. Heck and M. Waycott},
  year={2009},
  title={Associations of concern: declining seagrasses and threatened dependent species},
	journal={Frontiers in Ecology and the Environment},
	volume={7},
	number={5},
	pages={242-246}
}

@article{Hunt02,
	author={J. Hunt and C. A. Annett},
	year={2002},
	title={Effects of habitat manipulation on reproducive success of individual largemouth bass in an {O}zark reservoir},
	journal={North American Journal of Fisheries Management},
	volume={22},
	number={4},
	pages={1201-1208}
}

@article{Hyndman08,
	author={R. J. Hyndman and Y. Khandakar},
	year={2008},
	title={Automatic time series forecasting: The forecast package for R},
	journal={Journal of Statistical Software},
	volume={26},
	number={3},
	pages={1-22}
}

@article{Ibarra03,
	author={A. A. Ibarra and M. Gevrey and Y. S. Park and P. Lim and S. Lek},
	year={2003},
	title={Modelling the factors that influence fish guilds composition using a back-propagation network: Assessment of metrics for indices of biotic integrity},
	journal={Ecological Modelling},
	volume={160},
	number={3},
	pages={281-290}
}

@article{Idso74,
  author={S. B. Idso and R. G. Gilbert},
  year={1974},
	title={On the universality of the {P}oole and {A}tkins secchi disk-light extinction equation},
	journal={Journal of Applied Ecology},
	volume={11},
	number={1},
	pages={399-401}
}

@misc{IEP13,
  title = {{IEP Bay-Delta Monitoring and Analysis Section, Discrete Water Quality Metadata}},
  author = {IEP},
  year = {2013},
  note = {\url{http://water.ca.gov/bdma/meta/discrete.cfm}}
}

@misc{IEP16,
  title = {{Dayflow: An estimate of daily average Delta outflow. Interagency Ecological Program for the San Francisco Estuary}},
  author = {IEP},
  year = {2016},
  note = {\url{http://www.water.ca.gov/dayflow/}}
}

@article{Iverson86,
  author={R. L. Iverson and H. F. Bittaker},
	year={1986},
	title={Seagrass distribution and abundance in eastern {G}ulf of {M}exico coastal waters},
	journal={Estuarine, Coastal and Shelf Science},
	volume={22},
	number={5},
	pages={577-602}
}

@techreport{Jabusch16,
	author={T. Jabusch and P. Bresnahan and P. Trowbridge and E. Novick and A. Wong and M. Salomon and D. Senn},
	year={2016},
	title={Summary and evaluation of {D}elta subregions for nutrient monitoring and assessment},
	institution={San Francisco Estuary Institute},
	number={},
	address={Richmond, CA},
	url={http://sfbaynutrients.sfei.org/books/dsp-nutrient-monitoring-and-assessment}
}

@techreport{Jabusch09,
	author={T. Jabusch and A. N. Gilbreath},
	year={2009},
	title={Summary of current water quality monitoring programs in the {D}elta},
	institution={San Francisco Estuary Institute},
	number={},
	address={Richmond, CA},
	url={http://www.waterboards.ca.gov/centralvalley/water_issues/delta_water_quality/delta_regional_monitoring/studies_reports/drmp_wq_monitoring_progs_sum.pdf}
}

@article{Jackson93,
	author={D. A. Jackson},
	year={1993},
	title={Multivariate analysis of benthic invertebrate communities: The implication of choosing particular data standardizations, measures of association, and ordination methods},
	journal={Hydrobiologia},
	volume={268},
	pages={9-26}
}

@article{Jackson01,
	author={D. A. Jackson and P. R. Peres-Neto and J. D. Olden},
	year={2001},
	title={What controls who is where in freshwater fish communities - the roles of biotic, abiotic, and spatial factors},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={58},
	number={1},
	pages={157-170}
}

@article{Jain00,
  author={A. K. Jain and R. P. W. Duin and J. C. Mao},
  year={2000},
  title={Statistical pattern recognition: A review},
  journal={{IEEE} Transactions on Pattern Analysis and Machine Intelligence},
  volume={22},
  number={1},
  pages={4-37}
}

@techreport{Janicki96,
  author={A. Janicki and D. Wade},
  year={1996},
	title={Estimating critical external nitrogen loads for the {T}ampa {B}ay estuary: An empirically based approach to setting management targets},
	institution={Tampa Bay National Estuary Program},
	address={St. Petersburg, Florida},
  number={06-96},
	pages={200}
}

@manual{Jassby14,
  title = {wq: Exploring water quality monitoring data},
  author = {Alan D. Jassby and James E. Cloern},
  year = {2014},
  note = {R package version 0.4-1},
  url = {http://CRAN.R-project.org/package=wq},
}

@article{Jassby08, 
  author={A. D. Jassby},
	year={2008},
	title={Phytoplankton in the {U}pper {S}an {F}rancisco {E}stuary: Recent biomass trends, their causes, and their trophic significance},
	journal={San Francisco Estuary and Watershed Science},
	volume={6},
	number={1},
	pages={1-24}
}

@article{Jassby02,
  author={A. D. Jassby and J. E. Cloern and B. E. Cole},
	year={2002},
	title={Annual primary production: Patterns and mechanisms of change in a nutrient-rich tidal ecosystem},
	journal={Limnology and Oceanography},
	volume={47},
	number={3},
	pages={698-712}
}

@article{Jassby00,
  author={A. D. Jassby and J. E. Cloern},
	year={2000},
	title={Organic matter sources and rehabilitations of the {S}acramento-{S}an {J}oaquin {D}elta ({C}alifornia, {USA})},
	journal={Aquatic Conservation: Marine and Freshwater Ecosystems},
	volume={10},
	number={},
	pages={323-352}
}

@article{Jennings03,
	author={M. J. Jennings and E. E. Emmons and G. R. Hatzenbeler and C. Edwards and M. A. Bozek},
	year={2003},
	title={Is littoral habitat affected by residential development and land use in watersheds of {W}isconsin lakes?},
	journal={Lake and Reservoir Management},
	volume={19},
	number={3},
	pages={272-279}
}

@article{Jennings99,
	author={M. J. Jennings and M. A. Bozek and G. R. Hatzenbeler and E. E. Emmons and M. D. Staggs},
	year={1999},
	title={Cumulative effects of incremental shoreline habitat modification on fish assemblages in north temperate lakes},
	journal={North American Journal of Fisheries Management},
	volume={19},
	number={1},
	pages={18-27}
}

@incollection{Jensen09,
	author={J. R. Jensen and J. Im and P. Hardin and R. R. Jensen},
	editor={T. A. Warner and M. D. Nellis and G. M. Foody},
	year={2009},
	title={Image classification},
	booktitle={The SAGE Handbook of Remote Sensing},
	publisher={SAGE Publications},
	address={Los Angeles, California},
	pages={269-281}
}

@book{Jeppesen98,
	editor={E. Jeppesen and M. S{\o}ndergaard and M. S{\o}ndergaard and K Christoffersen},
	year={1998},
	title={The Structuring Role of Submerged Macrophytes in Lakes, Ecological Studies, Vol. 131},
	publisher={Springer-Verlag},
	address={New York, New York}
}

@article{Johansson92,
  author={J. O. R. Johansson and R. R. {Lewis III}},
  year={1992},
	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}},
	journal={Marine Coastal Eutrophication},
	volume={Proceedings of an International Conference, Bologna, Italy, 21-24 March 1990},
	number={},
	pages={1199-1215}
}

@article{Johansson91,
  author={J. O. R. Johansson},
  year={1991},
	title={Long-term trends of nitrogen loading, water quality and biological indicators in {H}illsborough {B}ay, {F}lorida},
	editor={S. F. Treat and P. A. Clark},
  booktitle={Proceedings of the Tampa Bay Area Scientific Information Symposium 2},
	publisher={Tampa Bay Area Study Group Project at Scholar Commons},
	address={Tampa, Florida, USA},
	pages={157-176}
}

@article{Johnstone85,
	author={I. M. Johnstone and B. T. Coffey and C. Howard-Williams},
	year={1985},
	title={The role of recreational boat traffic in interlake dispersal of macrophytes: A {N}ew {Z}ealand case study},
	journal={Journal of Environmental Management},
	volume={20},
	number={3},
	pages={263-279}
}

@article{Jones94,
  author={C. G. Jones and J. H. Lawton and M. Shachak},
  year={1994},
	title={Organisms as ecosystem engineers},
	journal={OIKOS},
	volume={69},
	number={3},
	pages={373-386}
}

@article{Jordan03,
  author={T. E. Jordan and D. E. Weller and D. L. Correll},
  year={2003},
	title={Sources of nutrient inputs to the {P}atuxent {R}iver estuary},
	journal={Estuaries and Coasts},
	volume={26},
	number={2A},
	pages={226-243}
}

@article{Jurca12,
	author={T. Jurca and L. Donohue and D. Laketic and S. Radulovic and K. Irvine},
	year={2012},
	title={Importance of the shoreline diversity features for littoral macroinvertebrate assemblages},
	journal={Fundamental and Applied Limnology},
	volume={180},
	number={2},
	pages={175-184}
}

@article{Justic87,
  author={D. Just\'{i}c and T. Legov\'{i}c and L. Rottini-Sandrini},
  year={1987},
	title={Trends in oxygen content 1911--1984 and occurrence of benthic mortality in the northern {A}driatic {S}ea},
	journal={Estuarine, Coastal and Shelf Science},
	volume={25},
	number={4},
	pages={435-445}
}

@article{Kahle13,
  author = {David Kahle and Hadley Wickham},
  title = {ggmap: Spatial Visualization with ggplot2},
  journal = {The R Journal},
  year = {2013},
  volume = {5},
  number = {1},
  pages = {144-161},
  url = {http://journal.r-project.org/archive/2013-1/kahle-wickham.pdf},
}

@article{Kanninen13,
	author={A. Kanninen and S. Hellsten and H. H\"{a}m\"{a}l\"{a}inen},
	year={2013},
	title={Comparing stressor-specific indices and general measures of taxonomic composition for assessing the status of boreal lacustrine macrophyte communities},
	journal={Ecological Indicators},
	volume={27},
	pages={29-43}
}

@book{Karr99,
	author={J. R. Karr and E. W. Chu},
	year={1999},
	title={Restoring Life in Running Waters: Better Biological Monitoring},
	publisher={Island Press},
	address={Washington, DC},
	pages={206}
}
	
@techreport{Karr86,
	author={J. R. Karr and K. D. Fausch and P. L. Angermeier and P. R. Yant and I. J. Schlosser},
	year={1986},
	title={Assessing biological integrity in running waters: a method and its rationale},
	number={Special Publication 5},
	institution={Illinois Natural History Survey},
	address={Champaign, Illinois}
}

@article{KarrDud81,
	author={J. R. Karr and D. R. Dudley},
	year={1981},
	title={Ecological perspective on water quality goals},
	journal={Environmental Management},
	volume={5},
	pages={55-68}
}

@article{Karr81,
	author={J. R. Karr},
	year={1981},
	title={Assessment of biotic integrity using fish communities},
	journal={Fisheries},
	volume={6},
	number={6},
	pages={21-27}
}

@incollection{Karul06,
	author={C. Karul and S. Soyupak},
	editor={F. Recknagel},
	year={2006},
	title={A comparison between neural network based and multiple regression models for {C}hlorophyll-\textit{a} estimation},
	booktitle={Ecological Informatics: Scope, Techniques and Applications},
	publisher={Springer-Verlag},
	edition={2nd},
	address={Berlin, Germany},
	pages={309-323}
}
	
@article{Keddy82,
	author={P. A. Keddy},
	year={1982},
	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},
	journal={Aquatic Botany},
	volume={14},
	number={1},
	pages={41-58}
}

@article{Kell03,
	author={D. B. Kell and S. G. Oliver},
	year={2003},
	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},
	journal={BioEssays},
	volume={26},
	number={1},
	pages={99-105}
}

@misc{Kelley14,
  title = {oce: Analysis of Oceanographic data, {R} package version 0.9-15},
  author = {Dan Kelley and Clark Richards},
  year = {2014},
  note = {\url{http://dankelley.github.com/oce/}}
}

@article{Kelling09,
  author={S. Kelling and W. M. Hochachka and D. Fink and M. Riedewald and R. Caruana and G. Ballard and G. Hooker},
  year={2009},
	title={Data-intensive science: A new paradigm for biodiversity studies},
	journal={BioScience},
	volume={59},
	number={7},
	pages={613-620}
}

@incollection{Kemp12,
  author={W. M. Kemp and J. M. Testa},
	editor={E. Wolanski and D. S. McLusky},
	year={2012},
	title={Metabolic balance between ecosystem production and consumption},
	booktitle={Treatise on Estuarine and Coastal Science},
	publisher={Academic Press},
  address={New York},
	pages={83-118}
}

@article{Kemp09,
  author={W. M. Kemp and J. M. Testa and D. J. Conley and D. Gilbert and J. D. Hagy},
	year={2009},
	title={Temporal responses of coastal hypoxia to nutrient loading and physical controls},
	journal={Biogeosciences},
	volume={6},
	number={12},
	pages={2985-3008}
}

@article{Kemp05,
  author={W. M. Kemp and W. R. Boynton and J. E. Adolf and D. F Boesch and W. C. Boicourt and G. Brush and J. C. Cornwell and T. R. Fisher and P. M. Glibert and J. D. Hagy and L. W. Harding and E. D. Houde and D. G. Kimmel and W. D. Miller and R. I. E. Newell and M. R. Roman and E. M. Smith and J. C. Stevenson},
	year={2005},
	title={Eutrophication of {C}hesapeake {B}ay: historical trends and ecological interactions},
	journal={Marine Ecology Progress Series},
	volume={303},
	number={},
	pages={1-29}
}

@article{Kemp04,
  author={W. C. Kemp and R. Batiuk and R. Bartleson and P. Bergstrom and V. Carter and C. L. Gallegos and W. Hunley and L. Karrh and E. W. Koch and J. M. Landwehr and K. A. Moore and L. Murray and M. Naylor and N. B. Rybicki and J. C. Stevenson and D. J. Wilcox},
  year={2004},
	title={Habitat requirements for submerged aquatic vegetation in {C}hesapeake {B}ay: Water quality, light regime, and physical-chemical factors},
	journal={Estuaries},
	volume={27},
	number={3},
	pages={363-377}
}

@article{Kemp80,
  author={W. M. Kemp and W. R. Boynton},
  year={1980},
  title={Influence of biological and physical processes on dissolved oxygen dynamics in an estuarine system: Implications for the measurement of community metabolism},
	journal={Estuarine and Coastal Marine Science},
	volume={11},
	number={4},
	pages={407-431}
}

@book{Kendall83,
  author={M. Kendall and A. Stuart},
  year={1983},
  title={The Advanced Theory of Statistics},
  publisher={MacMillan Publishing Company},
  volume={3},
	address={New York, New York},
	pages={410-414}
}

@article{Kennard06,
	author={M. J. Kennard and B. D. Harch and B. J. Pusey and A. H. Arthington},
	year={2006},
	title={Accurately defining the reference condition for summary biotic metrics: A comparison of four approaches},
	journal={Hydrobiologia},
	volume={572},
	pages={151-170}
}

@article{Kenney12,
	author={M. A. Kenney and P. R. Wilcock and B. F. Hobbs and N. E. Flores and D. C. Mart\'{i}nez},
	year={2012},
	title={Is urban stream restoration worth it?},
	journal={Journal of the American Water Resources Association},
	volume={48},
	number={3},
	pages={603-615},
	doi={10.1111/j.1752-1688.2011.00635.x}
}

@article{Kenworthy96,
  author={W. J. Kenworthy and M. S. Fonseca},
	year={1996},
	title={Light requirements of seagrasses \textit{Halodule wrightii} and \textit{Syringodium filiforme} derived from the relationship between diffuse light attenuation and maximum depth distribution},
	journal={Estuaries},
	volume={19},
	number={3},
	pages={740-750}
}

@article{Kerans94,
	author={B. L. Kerans and J. R. Karr},
	year={1994},
	title={A benthic index of biotic integrity {(B-IBI)} for rivers of the {T}ennessee {V}alley},
	journal={Ecological Applications},
	volume={4},
	number={4},
	pages={768-785}
}

@article{Killick14,
	author={R. Killick and I. A. Eckley},
	year={2014},
	title={changepoint: An {R} package for changepoint analysis},
	journal={Journal of Statistical Software},
	volume={58},
	number={3},
	pages={1-19}
}

@article{Kim12,
	author={C. K. Kim and K. Park},
	year={2012},
	title={A modeling study of water and salt exchange for a micro-tidal, stratified northern {G}ulf of {M}exico estuary},
	journal={Journal of Marine Systems},
	volume={96-97},
	number={},
	pages={103-115}
}

@article{Kimmerer05,
	author={W. Kimmerer},
	year={2005},
	title={Long-term changes in apparent uptake of silica in the {S}an {F}rancisco {E}stuary},
	journal={Limnology and Oceanography},
	volume={50},
	number={3},
	pages={793-798}
}

@article{Kimmerer12,
	author={W. J. Kimmerer and A. E. Parker and U. E. Lidstrom and E. J. Carpenter},
	year={2012},
	title={Short-term and interannual variability in primary production in the low-salinity zone of the {S}an {F}rancisco {E}stuary},
	journal={Estuaries and Coasts},
	volume={35},
	number={},
	pages={913-929}
}

@article{Kimmerer14,
	author={W. J. Kimmerer and J. K. Thompson},
	year={2014},
	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},
	journal={Estuaries and Coasts},
	volume={37},
	number={},
	pages={1202-1218}
}

@article{Kirchner06,
	author={J. W. Kirchner},
	year={2006},
	title={Getting the right answers for the right reasons: Linking measurements, analyses, and models to advance the science of hydrology},
	journal={Water Resources Research},
	volume={42},
	number={3},
	pages={W03S04}
}

@manual{Klima15,
  title = {FCNN4R: Fast Compressed Neural Networks for R},
  author = {Grzegorz Klima},
  year = {2015},
  note = {R package version 0.4.1},
}

@article{Knapton99,
	author={R. W. Knapton and S. A. Petrie},
	year={1999},
	title={Changes in distribution and abundance of submerged macrophytes in the {I}nner {B}ay at {L}ong {P}oint, {L}ake {E}rie: Implications for foraging waterfowl},
	journal={Journal of Great Lakes Research},
	volume={25},
	number={4},
	pages={783-798}
}

@book{Knuth92,
  author={D. E. Knuth},
  year={1992},
	title={Literate Programming},
	publisher={Center for the Study of Language and Information, Leland Stanford Junior University},
	edition={second},
	address={Stanford, California},
	pages={368}
}

@article{Koch01,
  author={E. W. Koch},
	year={2001},
	title={Beyond light: Physical, geological, and geochemical parameters as possible submersed aquatic vegetation habitat requirements},
	journal={Estuaries},
	volume={24},
	number={1},
	pages={1-17}
}

@misc{Koenker13,
  author={R. Koenker},
  year={2013},
	title={quantreg: {Q}uantile Regression {R} package 5.05.},
	note={\url{http://CRAN.R-project.org/package=quantreg}}
}

@article{Koenker08,
  author={R. Koenker},
  year={2008},
  title={Censored quantile regression redux},
  journal={Journal of Statistical Software},
  volume={27},
  number={6},
  pages={1-25}
  }

@article{Koenker99,
  author={R. Koenker and J. A. F. Machado},
  year={1999},
  title={Goodness of fit and related inference processes for quantile regression},
  journal={Journal of the American Statistical Association},
  volume={94},
  number={448},
  pages={1296-1310}
  }

@article{Kosten09,
	author={S. Kosten and A. Kamarainen and E. Jeppesen and E. H. van Nes and E. T. H. M. Peeters and N. Mazzeo and L. Sass and J. Hauxwell and N. Hansel-Welch and T. L. Lauridsen and M. S{\o}ndergaard and R. W. Bachmann and G. Lacerot and M. Scheffer},
	year={2009},
	title={Climate-related differences in the dominance of submerged macrophytes in shallow lakes},
	journal={Global Change Biology},
	volume={15},
	number={10},
	pages={2503-2517}
}

@article{Kratz97,
	author={T. K. Kratz and K. E. Webster and C. J. Bowser and J. J. Magnuson and B. J. Benson},
	year={1997},
	title={The influence of landscape position on lakes in northern {W}isconsin},
	journal={Freshwater Biology},
	volume={37},
	number={1},
	pages={209-217}
}

@techreport{Krysel03,
	author={C. Krysel and E. M. Boyer and C. Parson and P. Welle},
	year={2003},
	title={Lakeshore property values and water quality: Evidence from property sales in the {M}ississippi headwaters region},
	number={},
	institution={Legislative Commission on Minnesota Resources, Mississippi Headwaters Board, and Bemidji State University},
	address={Bemidji, Minnesota},
	pages={57}
}

@manual{Kuhn15,
  title = {caret: Classification and Regression Training},
  author = {Max Kuhn},
  year = {2015},
  note = {R package version 6.0-52},
  url = {http://CRAN.R-project.org/package=caret},
}

@article{Lacoul06,
	author={P. Lacoul and B. Freedman},
	year={2006},
	title={Environmental influences on aquatic plants in freshwater ecosystems},
	journal={Environmental Reviews},
	volume={14},
	pages={89-136}
}

@article{Lance67,
	author={G. N. Lance and W. T. Williams},
	year={1967},
	title={A general theory of classificatory sorting strategies: 1. Hierarchical systems},
	journal={Computer Journal},
	volume={9},
	pages={373-380}
}

@incollection{Lang08,
	author={S. Lang},
	editor={T. Blaschke and S. Lang and G. J. Hay},
	year={2008},
	title={Object-based image analysis for remote sensing applications: Modeling reality - dealing with complexity},
	booktitle={Object-Based Image Analysis: Spatial Concepts for Knowledge-Driven Remote Sensing Applications},
	publisher={Springer-Verlag},
	address={Heidelberg, Berlin, New York},
	pages={3-27}
}

@article{Lauridsen93,
	author={T. L. Lauridsen and E. Jeppesen and F. O. Andersen},
	year={1993},
	title={Colonization of submerged macrophytes in shallow fish manipulated lake {V}aeng: Impact of sediment composition and waterfowl grazing},
	journal={Aquatic Botany},
	volume={46},
	number={1},
	pages={1-15}	
}

@article{Lee05,
	author={Z. P. Lee and K. P. Du and R. Arnone},
	year={2005},
	title={A model for the diffuse attenuation of downwelling irradiance},
	journal={Journal of Geophysical Research},
	volume={110},
	number={C2},
	pages={1-15}
}

@article{Le17,
	author={C. Le and J. C. Lehrter and C. Hu and H. MacIntyre and M. W. Beck},
	year={2017},
	title={Satellite observation of particulate organic carbon dynamics on the {L}ouisiana continental shelf},
	journal={Journal of Geophysical Research: Oceans},
	volume={122},
	number={1},
	pages={555-569},
	doi={10.1002/2016JC012275}
}

@article{Le16,
	author={C. Le and J. C. Lehrter and B. Schaeffer and C. Hu and M. C. Murrell and J. D. {Hagy III} and R. M. Greene and M. W. Beck},
	year={2016},
	title={Bio-optical water quality dynamics observed from {MERIS} in {P}ensacola {B}ay, {F}lorida},
	journal={Estuarine Coastal and Shelf Science},
	volume={173},
	pages={26-38},
	doi={10.1016/j.ecss.2016.02.003}
}

@book{Legendre98,
	author={P. Legendre and L. Legendre},
	year={1998},
	title={Numerical Ecology},
	publisher={Elsevier},
	address={Amsterdam, Holland},
	edition={second},
	pages={853}
}

@article{Lehman75,
	author={J. T. Lehman and D. B. Botkin and G. E. Likens},
	year={1975},
	title={The assumptions and rationales of a computer model of phytoplankton population dynamics},
	journal={Limnology and Oceanography},
	volume={20},
	number={3},
	pages={343-364}
}

@article{Lehman00,
	author={P. W. Lehman},
	year={2000},
	title={The influence of climate on phytoplankton community biomass in {S}an {F}rancisco {B}ay {E}stuary},
	journal={Limnology and Oceanography},
	volume={45},
	number={3},
	pages={580-590}
}

@article{Lehman92,
	author={P. W. Lehman},
	year={1992},
	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},
	journal={Estuaries},
	volume={15},
	number={3},
	pages={335-348}
}

@article{Lehman05,
	author={P. W. Lehman and G. Boyer and C. Hall and S. Waller and K. Gehrts},
	year={2005},
	title={Distribution and toxicity of a new colonial \textit{{M}icrocystis aeruginosa} bloom in the {S}an {F}rancisco {B}ay {E}stuary, {C}alifornia},
	journal={Hydrobiologia},
	volume={541},
	number={},
	pages={87-99}
}

@article{Lehman10,
	author={P. W. Lehman and S. J. Teh and G. L. Boyer and M. L. Nobriga and E. Bass and C. Hogle},
	year={2010},
	title={Initial impacts of \textit{{M}icrocystis aeruginosa} blooms on the aquatic food web in the {S}an {F}rancisco {E}stuary},
	journal={Hydrobiologia},
	volume={637},
	number={1},
	pages={229-248}
}

@article{Lehman15,
	author={P. W. Lehman and C. Kendall and M. A. Guerin and M. B. Young and S. R. Silva and G. L. Boyer and S. J. Teh},
	year={2015},
	title={Characterization of the \textit{{M}icrocystis} bloom and its nitrogen supply in {S}an {F}rancisco {E}stuary using stable isotopes},
	journal={Estuaries and Coasts},
	volume={38},
	number={1},
	pages={165-178}
}

@incollection{Lehrter17,
	author={J. C. Lehrter and D. S. Ko and L. L. Lowe and B. Penta},
	editor={{Justic et al.}},
	year={2017},
	title={Predicted effects of climate change on northern {G}ulf of {M}exico hypoxia},
	booktitle={Modeling Coastal Hypoxia: Numerical Simulations of Patterns, Controls, and Effect of Dissolved Oxygen Dynamics},
	publisher={Springer},
	address={New York},
	pages={173-204}
}

@article{Lehrter13,
	author={J. C. Lehrter and D. S. Ko and M. C. Murrell and J. D. {Hagy III} and B. A. Schaeffer and R. M. Greene and R. W. Gould and B. Penta},
	year={2013},
	title={Nutrient distributions, transports, and budgets on the inner margin of a river-dominated continental shelf},
	journal={Journal of Geophysical Research},
	volume={118},
	number={10},
	pages={4822-4838}
}

@article{Lehrter12,
	author={J. C. Lehrter and D. L. Beddick and R. Devereux and D. F. Yates and M. C. Murrell},
	year={2012},
	title={Sediment-water fluxes of dissolved inorganic carbon, {O}$_2$, nutrients, and {N}$_2$ from the hypoxic region of the {L}ousiana continental shelf},
	journal={Biogeochemistry},
	volume={109},
	number={1-3},
	pages={233-252}
}

@article{Lehrter10,
	author={J. C. Lehrter and J. Cebrian},
	year={2010},
	title={Uncertainty propagation in an ecosystem nutrient budget},
	journal={Ecological Applications},
	volume={20},
	number={2},
	pages={508-524}
}

@book{Lek00,
	author={S. Lek and J. F. Gu\'{e}gan},
	year={2000},
	title={Artificial Neuronal Networks: Application to Ecology and Evolution},
	publisher={Springer-Verlag},
	address={Berlin, Germany}
}

@incollection{Lek00b,
	author={S. Lek and J. L. Giraudel and J. F. Gu\'{e}gan},
	editor={S. Lek and J. F. Gu\'{e}gan},
	year={2000},
	title={Neuronal Networks: Algorithms and architectures for ecologists and evolutionary ecologists},
	booktitle={Artificial Neuronal Networks: Application to Ecology and Evolution},
	publisher={Springer-Verlag},
	address={Berlin, Germany},
	pages={3-27}
}

@article{Lek99,
	author={S. Lek and J. F. Gu\'{e}gan},
	year={1999},
	title={Artificial neural networks as a tool in ecological modelling, an introduction},
	journal={Ecological Modelling},
	volume={120},
	number={2-3},
	pages={65-73}
}

@article{Lek96,
	author={S. Lek and M. Delacoste and P. Baran and I. Dimopoulos and J. Lauga and S. Aulagnier},
	year={1996},
	title={Application of neural networks to modelling nonlinear relationships in ecology},
	journal={Ecological Modelling},
	volume={90},
	number={1},
	pages={39-52}
}

@article{Leps15,
	author={M. Leps and J. D. Tonkin and V. Dahm and P. Haase and A. Sundermann},
	year={2015},
	title={Disentangling environmental drivers of benthic invertebrate assemblages: The role of spatial scale and riverscape heterogeneity in a multiple stressor environment},
	journal={Science of the Total Environment},
	volume={536},
	pages={546-556},
	doi={10.1016/j.scitotenv.2015.07.083}
}

@article{Levin92,
	author={S. A. Levin},
	year={1992},
	title={The problem of pattern and scale in ecology},
	journal={Ecology},
	volume={73},
	number={6},
	pages={1943-1967}
}

@article{Levins66,
	author={R. Levins},
	year={1966},
	title={The strategy of model building in population biology},
	journal={American Scientist},
	volume={54},
	number={4},
	pages={421-431}
}

@techreport{Lewis88,
  author={R. R. Lewis and E. D. Estevez},
  year={1988},
  title={The ecology of {T}ampa {B}ay, {F}lorida: An estuarine profile},
  institution={US Fish and Wildlife Service, Washington DC, USA},
  number={Biological Report 85(7.18)}
}

@incollection{Lewis85,
  author={R. R. Lewis and R. L. Whitman},
	editor={S. F. Treat and J. L. Simon and R. R. Lewis and R. L. Whitman},
	year={1985},
	title={A new geographic description of the boundaries and subdivisions of {T}ampa {B}ay},
	booktitle={Proceedings of the Tampa Bay Area Scientific Information Symposium},
	publisher={Florida Sea Grant Report No. 65, Bellwether Press},
	address={Tampa, Florida, USA},
	pages={10-18}
}

@article{Li03,
	author={R. Li and K. Di and R. Ma},
	year={2003},
	title={{3-D} shoreline extraction from {IKONOS} satellite imagery},
	journal={Marine Geodesy},
	volume={26},
	number={1-2},
	pages={107-115}
}

@article{Liaw02,
  title={Classification and Regression by randomForest},
  author={Andy Liaw and Matthew Wiener},
  journal={R News},
  year={2002},
  volume={2},
  number={3},
  pages={18-22},
  url={http://CRAN.R-project.org/doc/Rnews/}
}

@article{Lipp01,
	author={E. K. Lipp and N. Schmidt and M. E. Luther and J. B. Rose},
	year={2001},
	title={Determining the effects of {E}l {N}i\~{n}o-{S}outhern {O}scillation events on coastal water quality},
	journal={Estuaries and Coasts},
	volume={24},
	number={4},
	pages={491-497}
}

@article{Lipton03,
	author={D. Lipton and R. Hicks},
	year={2003},
	title={The cost of stress: low dissolved oxygen and eocnomic benefits of recreational striped bass (\textit{Morone saxatilis}) fishing in the {P}atuxent {R}iver},
	journal={Estuaries},
	volume={26},
	number={2A},
	pages={310-315}
}

@article{Liu11,
	author={H. Liu and L. Wang and D. J. Sherman and Q. Wu and H. Su},
	year={2011},
	title={Algorithmic foundation and software tools for extracting shoreline features from remote sensing imagery and {LiDAR} data},
	journal={Journal of Geographic Information System},
	volume={3},
	number={2},
	pages={99-119}
}

@article{Logez13,
	author={M. Logez and D. Pont},
	year={2013},
	title={Global warming and potential shift in reference conditions: The case of functional fish-based metrics},
	journal={Hydrobiologia},
	volume={704},
	number={1},
	pages={417-436}
}

@article{Lohrenz08,
	author={S. E. Lohrenz and D. G. Redalje and W. J. Cai and J. Acker and M. Dagg},
	year={2008},
	title={A retrospective analysis of nutrients and phytoplankton productivity in the {M}ississippi {R}iver plume},
	journal={Continental Shelf Research},
	volume={28},
	number={12},
	pages={1466-1475}
}

@article{Lorenz07,
	author={D. L. Lorenz and G. N. Delin},
	year={2007},
	title={A regression model to estimate regional ground water recharge},
	journal={Ground Water},
	volume={45},
	number={2},
	pages={196-208}
}

@article{Lottig14,
  author={N. R. Lottig and T. Wagner and E. N. Henry and K. S. Cheruvelil and K. E. Webster and J. A. Downing and C. A. Stow},
	year={2014},
	title={Long-term citizen-collected data reveal geographical patterns and temporal trends in water clarity},
	journal={PLoS ONE},
	volume={9},
	number={4},
	pages={1-8}
}

@article{Lougheed02,
	author={V. L. Lougheed and P. C. Chow-Fraser},
	year={2002},
	title={Development and use of a zooplankton index of wetland quality in the {L}aurentian {G}reat {L}akes basin},
	journal={Ecological Applications},
	volume={12},
	number={2},
	pages={474-486}
}

@article{Lung03,
	author={W. Lung and S. Bai},
	year={2003},
	title={A water quality model for the {P}atuxent estuary: Current conditions and predictions under changing land-use scenarios},
	journal={Estuaries},
	volume={26},
	number={2A},
	pages={267-279}
}

@article{Mackay10,
	author={S. J. Mackay and C. S. James and A. H. Arthington},
	year={2010},
	title={Macrophytes as indicators of stream condition in the wet tropics region, {N}orthern {Q}ueensland, {A}ustralia},
	journal={Ecological Indicators},
	volume={10},
	pages={330-340}
}

@article{Mackay03,
	author={S. J. Mackay and A. H. Arthington and M. J. Kennard and B. J. Pusey},
	year={2003},
	title={Spatial variation in the distribution and abundance of submersed macrophytes in an {A}ustralian subtropical river},
	journal={Aquatic Botany},
	volume={77},
	pages={169-186}
}

@article{MacNally10,
  author={R. {Mac Nally} and J. R. Thompson and W. J. Kimmerer and F. Feyrer and K. B. Newman and A. Sih and W. A. Bennett and L. Brown and E. Fleishman and S. D. Culberson and G. Castillo},
	year={2010},
	title={Analysis of pelagic species decline in the upper {S}an {F}rancisco {E}stuary using multivariate autoregressive modeling ({MAR})},
	journal={Ecological Applications},
	volume={20},
	number={5},
	pages={1417-1430}
}


@techreport{Madsen99,
	author={J. D. Madsen},
  year={1999},
  title={Point intercept and line intercept methods for aquatic plant management},
  institution={U.S. Army Engineer Center, Vicksburg, Missouri},
  number={TN APCRP-M1-02, APCRP Technical notes collection}
}

@article{Madsen97,
	author={T. V. Madsen and H. Brix},
	year={1997},
	title={Growth, photosynthesis and acclimation by two submerged macrophytes in relation to temperature},
	journal={Oecologia},
	volume={110},
	number={3},
	pages={320-327}
}

@misc{Maechler05,
	author={M. Maechler and P. Rousseeuw and A. Struyf and M. Hubert},
	year={2005},
	title={Cluster analysis and basics and extensions, {R} package.},
	note={\url{http://CRAN.R-project.org/package=cluster}}
}

@article{Maier00,
	author={H. R. Maier and G. C. Dandy},
	year={2000},
	title={Neural networks for the prediction and forecasting of water resources variables: A review of modelling issues and applications},
	journal={Environmental Modelling and Software},
	volume={15},
	number={1},
	pages={101-124}
}

@article{Makela04,
	author={S. M\"{a}kel\"{a} and E. Huitu and L. Arvola},
	year={2004},
	title={Spatial patterns in aquatic vegetation composition and environmental covariates along chains of lakes in the {K}okem\"{a}enjoki watershed ({S}. {F}inland)},
	journal={Aquatic Botany},
	volume={80},
	pages={253-269}
}

@article{Manolakos07,
	author={E. Manolakos and H. Virani and V. Novotny},
	year={2007},
	title={Extracting knowledge on the links between the water body stressors and biotic integrity},
	journal={Water Research},
	volume={41},
	pages={4041-4050}
}

@article{Mantel67,
  author={N. Mantel},
  year={1967},
	title={The detection of disease clustering and a generalized regression approach},
	journal={Cancer Research},
	volume={27},
	number={1},
	pages={209-220}
}

@article{Maravelias03,
	author={C. D. Maravelias and J. Haralabous and C. Papaconstantinou},
	year={2003},
	title={Predicting demersal fish species distributions in the {M}editerranean {S}ea using artificial neural networks},
	journal={Marine Ecology Progress Series},
	volume={255},
	pages={249-258}
}

@article{Marburg06,
	author={A. E. Marburg and M. G. Turner and T. K. Kratz},
	year={2006},
	title={Natural and anthropogenic variation in coarse wood among and within lakes},
	journal={Journal of Ecology},
	volume={94},
	number={3},
	pages={558-568}
}

@techreport{Martin00,
	author={P. J. Martin},
	year={2000},
	title={Description of the navy coastal ocean model version 1.0},
	institution={Naval Research Lab, Stennis Space Center},
	number={NRL/FR/7322-00-9962},
	address={Mississippi}
}

@article{Mateus15,
	author={M. D. Mateus and G. Franz},
	year={2015},
	title={Sensitivity analysis in a complex marine ecological model},
	journal={Water},
	volume={7},
	number={},
	pages={2060-2081}
}

@article{May03,
	author={C. L. May and J. R. Koseff and L. V. Lucas  and J. E. Cloern and D. H. Schoellhamer},
	year={2003},
	title={Effects of spatial and temporal variability of turbidity on phytoplankton blooms},
	journal={Marine Ecology Progress Series},
	volume={254},
	number={},
	pages={111-128}
}

@article{Mazor16,
	author={R. D. Mazor and A. C. Rehn and P. R. Ode and M. Engeln and K. C. Schiff and E. D. Stein and D. J. Gillett and D. B. Herbst and C. P. Hawkins},
	year={2016},
	title={Bioassessment in complex environments: designing an index for consistent meaning in different settings},
	journal={Freshwater Science},
	volume={35},
	number={1},
	pages={249-271}
}

@article{McCormick01,
	author={F. H. McCormick and R. M. Hughes and P. R. Kaufmann and D. V. Peck and J. L. Stoddard  and A. T. Herlihy},
	year={2001},
	title={Development of an index of biotic integrity for the {M}id-{A}tlantic {H}ighlands region},
	journal={Transactions of the American Fisheries Society},
	volume={130},
	number={5},
	pages={857-877}
}

@article{McCulloch43,
  author={W. S. McCulloch and W. Pitts},
	year={1943},
	title={A logical calculus of the ideas imminent in nervous activity},
	journal={Bulletin of Mathematical Biophysics},
	volume={5},
	pages={115-133}
}

@book{McCullagh89,
	author={P. McCullagh and J. Nelder},
	year={1989},
	title={Generalized Linear Models},
	publisher={Chapman and Hall},
	address={London, United Kingdom},
	edition={second},
	pages={532}	
}

@book{McCune02,
	author={B. McCune and J. B. Grace},
	year={2002},
	title={Analysis of Ecological Communities},
	publisher={MjM Software Design},
	address={Gleneden Beach, Oregon}
}

@article{McKenna05,
	author={J. E. McKenna},
	year={2005},
	title={Application of neural networks to prediction of fish diversity and salmonid production in the {L}ake {O}ntario basin},
	journal={Transactions of the American Fisheries Society},
	volume={134},
	number={1},
	pages={28-43}
}

@manual{McLeod14,
  title={cents: Censored time series},
  author={A.I. McLeod and Nagham M. Mohammad and Justin Veenstra and Abdel El-Shaarawi},
  year={2014},
  note={R package version 0.1-41},
  url={http://CRAN.R-project.org/package=cents},
}

@article{Medalie12,
	author={L. Medalie and R. M. Hirsch and S. A. Archfield},
	year={2012},
	title={Use of flow-normalization to evaluate nutrient concentration and flux changes in {L}ake {C}hamplain tributaries, 1990-2009},
	journal={Journal of Great Lakes Research},
	volume={38},
	number={SI},
	pages={58-67}
}

@manual{Meinshausen17,
  title={quantregForest: Quantile Regression Forests},
  author={Nicolai Meinshausen},
  year={2017},
  note={R package version 1.3-7},
  url={https://CRAN.R-project.org/package=quantregForest},
}

@article{Meinshausen06,
	author={N. Meinshausen},
	year={2006},
	title={Quantile regression forests},
	journal={Journal of Machine Learning Research},
	volume={7},
	pages={983-999}
}

@article{Melzer99,
	author={A. Melzer},
	year={1999},
	title={Aquatic macrophytes as tools for lake management},
	journal={Hydrobiologia},
	volume={395/396},
	pages={181-190}
}

@misc{MGDC07,
	author={{MGDC (Minnesota Geographic Data Clearinghouse)}},
	year={2007},
	title={Regional ground water recharge estimates for {M}innesota},
	note={\url{http://geogateway.state.mn.us/documents/}. (Accessed January, 2009)}
}

@article{Michener12,
	author={W. K. Michener and M. B. Jones},
	year={2012},
	title={Ecoinformatics: supporting ecology as a data-intensive science},
	journal={Trends in Ecology and Evolution},
	volume={27},
	number={2},
	pages={85-93}
}

@article{Mikulyuk11,
	author={A. Mikulyuk and S. Sharma and S. {Van Egeren} and E. Erdmann and M. E. Nault and J. Hauxwell},
	year={2011},
	title={The relative role of environmental, spatial, and land-use patterns in explaining aquatic macrophyte community composition},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={68},
	number={10},
	pages={1778-1789}
}

@techreport{Milburn07,
	author={S. A. Milburn and M. Bourdaghs and J. J. Husveth},
	year={2007},
	title={Floristic quality assessment for {M}innesota wetlands},
	institution={Minnesota Pollution Control Agency},
	number={wq-bwm2-01},
	address={St. Paul, Minnesota},
	url={http://www.pca.state.mn.us/index.php/view-document.html?gid=13346}
}

@book{Millard13,
  title={EnvStats:  An R Package for Environmental Statistics},
  author={Steven P. Millard},
  year={2013},
  publisher={Springer},
  address={New York},
  isbn={978-1-4614-8455-4},
  url={http://www.springer.com},
}
  
@article{Miller88,
	author={D. L. Miller and P. M. Leonard and R. M. Hughes and J. R. Karr and P. B. Moyle and L. H. Schrader and B. A. Thompson and R. A. Daniels and 
	K. D. Fausch and G. A. Fitzhugh and J. R. Gammon and D. B. Halliwell 	and P. L. Angermeier and D. J. Orth},
	year={1988},
	title={Regional applications of an index of biotic integrity for use in water resource management},
	journal={Fisheries},
	volume={13},
	number={5},
	pages={12-20}
}

@article{Miller06,
	author={S. J. Miller and D. H. Wardrop and W. M. Mahaney and R. R. Brooks},
	year={2006},
	title={A plant-based index of biological integrity ({IBI}) for headwater wetlands in central {P}ennsylvania},
	journal={Ecological Indicators},
	volume={6},
	number={2},
	pages={290-312}
}

@article{Millie13,
  author={D. F. Millie and G. R. Weckman and W. A. Young and J. E. Ivey and D. P. Fries and E. Ardjmand and G. L. Fahnenstiel},
  year={2013},
	title={Coastal `big data' and nature-inspired computation: prediction potentials, uncertainties, and knowledge derivation of neural networks for an algal metric},
	journal={Estuarine, Coastal and Shelf Science},
	volume={125},
	pages={57-67}
}

@article{Milligan89,
	author={G. W. Milligan},
	year={1989},
	title={A study of the beta-flexible clustering method},
	journal={Multivariate Behavioral Research},
	volume={24},
	pages={163-176}
}

@article{Minns94,
	author={C. K. Minns and V. W. Cairns and R. G. Randall and J. E. Moore},
	year={1994},
	title={An index of biotic integrity ({IBI}) for fish assemblages in the littoral zone of {G}reat {L}akes' areas of concern},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={51},
	number={8},
	pages={1804-1822}
}

@misc{MNDNR11,
	author={{MNDNR (Minnesota Department of Natural Resources)}},
	year={2011},
	title={{Docks and Access in Public Waters}},
	note={\url{http://files.dnr.state.mn.us/publications/waters/shoreline_alterations_water_access.pdf}. (Accessed June, 2012)}
}

@misc{MNDNR12a,
	author={{MNDNR (Minnesota Department of Natural Resources)}},
	year={2012},
	title={{MNDNR Data Deli}},
	note={\url{http://deli.dnr.state.mn.us/}. (Accessed January, 2010)}
}

@misc{MNDNR12b,
	author={{MNDNR (Minnesota Department of Natural Resources)}},
	year={2012},
	title={{Shoreland Management: Aquatic Plant Regulations}},
	note={\url{http://www.dnr.state.mn.us/shorelandmgmt/apg/regulations.html}. (Accessed June, 2012)}
}

@techreport{MNDOC02,
	author={{MNDOC (Minnesota Department of Commerce)}},
	year={2002},
	title={14th Wind Resource Analysis Program Report},
	institution={Minnesota Department of Commerce},
	address={St. Paul, Minnesota}
}

@misc{MNGEO13,
  author={{MnGeo (Minnesota Geospatial Information Office)}},
	year={2013},
	title={{Minnesota Geographic Data Clearinghouse}},
	note={\url{http://www.mngeo.state.mn.us/chouse/}. (Accessed July, 2012)}
}
	
@misc{MNPCA12,
	author={{MNPCA (Minnesota Pollution Control Agency)}},
	year={2012},
	title={{Minnesota Pollution Control Agency, Surface Water Data Submittal, Review, and Reports}},
	address={St. Paul, Minnesota},
	note={\url{http://www.pca.state.mn.us/index.php/water/}. (Accessed January, 2010)}
	}

@article{Molloy09,
  author={J. C. Molloy},
  year={2009},
  title={The {O}pen {K}nowledge {F}oundation: open data means better science},
	journal={{PLoS} Biology},
	volume={9},
	number={12},
	pages={1-4}
}

@article{Monbet92,
  author={Y. Monbet},
	year={1992},
	title={Control of phytoplankton biomass in estuaries: A comparative analysis of microtidal and macrotidal estuaries},
	journal={Estuaries},
	volume={15},
	number={4},
	pages={563-571}
}

@article{Montgomery95,
  author={D. R. Montgomery and G. E. Grant and K. Sullivan},
  year={1995},
  title={Watershed analysis as a framework for implementing ecosystem management},
  journal={Water Resources Bulletin},
  volume={31},
  number={3},
  pages={369-386}
}

@book{Montgomery92,
  author={D. C. Montgomery and E. A. Peck},
	year={1992},
	title={Introduction to Linear Regression Analysis},
	publisher={Wiley},
	address={New York, New York},
	pages={504}
}

@article{Moore12,
	author={M. J. C. Moore and H. A. Langrehr and T. R. Angradi},
	year={2012},
	title={A submersed macrophyte index of condition for the {U}pper {M}ississippi river},
	journal={Ecological Indicators},
	volume={13},
	pages={196-205}
}

@article{Morgan05,
	Author = {R. P. Morgan and S. E. Cushman},
	Title = {Urbanization effects on stream fish assemblages in {M}aryland, {USA}},
	Journal = {Journal of the North American Benthological Society},
	Year = {2005},
	Volume = {24},
	Number = {3},
	Pages = {643-655}
}

@article{Morrison06,
	Author = {G. Morrison and E. T. Sherwood and R. Boler and J. Barron},
	Title = {Variations in water clarity and chlorophyll\textit{a} in {T}ampa {B}ay, {F}lorida, in response to annual rainfall, 1985-2004},
	Journal = {Estuaries and Coasts},
	Year = {2006},
	Volume = {29},
	Number = {6},
	Pages = {926-931}
}

@incollection{Morrison99,
	author={M. Morrison and M. S. Morgan},
	editor={M. S. Morgan and M. Morrison},
	year={1999},
	title={Models as mediating agents},
	booktitle={Models as Mediators},
	address={Cambridge University Press, Cambridge},
	pages={401}
}

@article{Moss03,
	author={B. Moss and D. Stephen and C. Alvarez and E. Becares and W. Van de Bund and S. E. Collings and E. Van Donk and E. De Eyto and T. Feldmann and C. Alaez-Fernandez and M. Alaez-Fernandez and R. J. M. Franken and F. Garcia-Criado and E. M. Gross and M. Gyllstrom and L. A. Hansson and K. Irvine and A. Jarvalt and J. P. Jensen and E. Jeppesen and T. Kairesalo and R. Kornijow and T. Krause and H. Kunnap and A. Laas and E. Lille and B. Lorens and H. Luup and M. R. Miracle and P. Noges and T. Noges and M. Nykanen and I. Ott and W. Peczula and E. T. H. M. Peeters and G. Phillips and S. Romo and V. Russell and J. Salujoe and M. Scheffer and K. Siewertsen and H. Smal and C. Tesch and H. Timm and L. Tuvikene and I. Tonno and T. Virro and E. Vicente and D. Wilson},
	year={2003},
	title={A tested system ({ECOFRAME}) for implementation of the {E}uropean {W}ater {F}ramework {D}irective},
	journal={Aquatic Conservation: Marine and Freshwater Ecosystems},
	volume={13},
	pages={507-549}
}

@techreport{Moyer12,
  author={D. L. Moyer and R. M. Hirsch and K. E. Hyer},
	year={2012},
	title={Comparison of two regression-based approaches for determining nutrient and sediment fluxes and trends in the {C}hesapeake {B}ay Watershed},
	institution={US Geological Survey, US Department of the Interior},
  number={Scientific Investigations Report 2012-544},
	address={Reston, Virginia},
	pages={118}
}

@article{Moyle56,
	author={J. B. Moyle},
	year={1956},
	title={Relationships between the chemistry of {M}innesota surface waters and wildlife management},
	journal={The Journal of Wildlife Management},
	volume={20},
	number={3},
	pages={303-320}
}

@article{Moyle45,
	author={J. B. Moyle},
	year={1945},
	title={Some chemical factors influencing the distribution of aquatic plants in {M}innesota},
	journal={American Midland Naturalist},
	volume={34},
	number={2},
	pages={402-420}
}

@article{MurrellIR,
	author={M. C. Murrell and J. C. Caffrey and D. T. Marcovich and M. W. Beck and B. M. Jarvis and J. D. {Hagy III}},
	year={in revision},
	title={Seasonal oxygen dynamics in a warm temperate estuary: Effects of hydrologic variability on measurements of primary production, respiration, and net metabolism},
	journal={Estuaries and Coasts},
	volume={-},
	number={-},
	pages={-}
}

@techreport{Murrell14,
	author={M. C. Murrell and D. L. Beddick and R. Devereux and R. M. Greene and J. D. {Hagy III} and B. M. Jarvis and J. C. Kurtz and J. C. Lehrter and D. F. Yates},
	year={2014},
	title={Gulf of Mexico hypoxia research program data report: 2002-2007},
	number={EPA/600/R-13/257},
	institution={US Environmental Protection Agency},
	address={Washington, DC}
}

@article{Murrell13,
	author={M. C. Murrell and R. S. Stanley and J. C. Lehrter and J. D. Hagy},
	year={2013},
	title={Plankton community respiration, net ecosystem metabolism, and oxygen dynamics on the {L}ouisiana continental shelf: Implications for hypoxia},
	journal={Continental Shelf Research},
	volume={52},
	pages={27-38}
}

@article{Murrell09,
	author={M. C. Murrell and J. G. Campbell and J. D. Hagy and J. M. Caffrey},
	year={2009},
	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}},
	journal={Estuarine, Coastal and Shelf Science},
	volume={81},
	pages={501-512}
}

@article{Murrell07,
  author={M. C. Murrell and J. D. Hagy and E. M. Lores and R. M. Greene},
  year={2007},
  title={Phytoplankton production and nutrient distributions in a subtropical esuary: Importance of freshwater flow},
  journal={Estuaries and Coasts},
  volume={30},
  number={3},
  pages={390-402}
}

@misc{NDBC15,
  author={{NDBC (National Data Buoy Center)}},
  year={2015},
  title={{National Oceanic and Atmospheric Administration's National Data Buoy Center}},
	note={\url{http://www.ndbc.noaa.gov/}. (Accessed March, 2015)}
	}

@article{Neckles12,
  author={H. A. Neckles and B. S. Kopp and B. J. Peterson and P. S. Pooler},
	year={2012},
	title={Integrating scales of seagrass monitoring to meet conservation needs},
	journal={Estuaries and Coasts},
	volume={35},
	number={1},
	pages={23-46}
}

@incollection{Needoba12,
  author={J. A. Needoba and T. D. Peterson and K. S. Johnson},
	editor={S. M. Tiquia-Arashiro},
	year={2012},
	title={Method for the quantification of aquatic primary production and net ecosystem metabolism using in situ dissolved oxygen sensors},
	booktitle={Molecular Biological Technologies for Ocean Sensing},
	publisher={Springer-Verlag},
	address={New York},
	pages={73-101}
}

@article{Nelder77,
	author={J. A. Nelder},
	year={1977},
	title={A reformulation of linear models},
	journal={Journal of the Royal Statistical Society},
	volume={140},
	number={1},
	pages={48-77}
}

@article{Newall00,
	author={P. Newall and F. Wells},
	year={2000},
	title={Potential for delineating indicator-defined regions for streams in {V}ictoria, {A}ustralia},
	journal={Journal of the North American Benthological Society},
	volume={19},
	number={3},
	pages={557-571}
}

@article{Nichols85,
	author={F. H. Nichols},
	year={1985},
	title={Increased benthic grazing: An alternative explanation for low phytoplankton biomass in northern {S}an {F}rancisco {B}ay during the 1976-1977 drought},
	journal={Estuarine, Coastal and Shelf Science},
	volume={21},
	number={3},
	pages={379-388}
}

@article{Nichols90,
	author={F. H. Nichols and J. K. Thompson and L. E. Schemel},
	year={1990},
	title={Remarkable invasion of {S}an {F}rancisco {B}ay ({C}alifornia, {USA}) by the {A}sian claim \textit{Potamocorbula amurensis}. {II.} {D}isplacement of a former community},
	journal={Marine Ecology Progress Series},
	volume={66},
	number={1-2},
	pages={95-101}
}

@article{Nichols00,
	author={S. Nichols and S. Weber and B. Shaw},
	year={2000},
	title={A proposed aquatic plant community biotic index for {W}isconsin lakes},
	journal={Environmental Management},
	volume={26},
	number={5},
	pages={491-502}
}

@article{Nichols99,
	author={S. Nichols},
	year={1999},
	title={Floristic quality assessment of {W}isconsin lake plant communities with example applications},
	journal={Journal of Lake and Reservoir Management},
	volume={15},
	number={2},
	pages={133-141}
}

@article{Nidzieko14,
  author={N. J. Nidzieko and J. A. Needoba and S. G. Monismith and K. S. Johnson},
	year={2014},
	title={Fortnightly tidal modulations affect net community production in a mesotidal estuary},
	journal={Estuaries and Coasts},
	volume={37},
	number={1},
	pages={91-110}
}

@techreport{Niemela00,
	author={S. Niemela and M. Feist},
	year={2000},
	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},
	institution={Biological Monitoring Program, Minnesota Pollution Control Agency},
	address={St. Paul, Minnesota},
	pages={47}
}

@techreport{Niemela02,
	author={S. Niemela and M. Feist},
	year={2002},
	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},
	institution={Biological Monitoring Program, Minnesota Pollution Control Agency},
	address={St. Paul, Minnesota},
	pages={56}
}

@article{Niemi04,
	author={G. J. Niemi and M. E. McDonald},
	year={2004},
	title={Application of ecological indicators},
	journal={Annual Review of Ecology, Evolution, and Systematics},
	volume={35},
	pages={89-111}
}

@article{Nisbet14,
  author={E. G. Nisbet and E. J. Dlugokencky and P. Bousquet},
	year={2014},
	title={Methane on the rise -- again},
	journal={Science},
	volume={343},
	number={6170},
	pages={493-495}
}

@article{Nixon95,
  author={S. W. Nixon},
	year={1995},
	title={Coastal marine eutrophication: A definition, social causes, and future concerns},
	journal={Ophelia},
	volume={41},
	number={},
	pages={199-219}
}

@book{Nocedal06,
  author={J. Nocedal and S. J. Wright},
	year={2006},
	title={Numerical Optimization},
	publisher={Springer-Verlag},
	edition={2nd},
	address={New York, New York},
	pages={664}
}

@article{Norton00,
	author={S. B. Norton and S. M. Cormier and M. Smith and R. C. Jones},
	year={2000},
	title={Can biological assessments discriminate among types of stress? {A} case study from the {E}astern {C}orn {B}elt {P}lains ecoregion},
	journal={Environmental Toxicology and Chemistry},
	volume={19},
	number={4},
	pages={1113-1119}
}

@article{Nossent12,
	author={J. Nossent and W. Bauwens},
	year={2012},
	title={Multi-variable sensitivity and identifiability analysis for a complex environmental model in view of integrated water quantity and water quality modeling},
	journal={Water Science \& Technology},
	volume={65},
	number={3},
	pages={539-549}
}

@techreport{Novick15,
	author={E. Novick and R. Holleman and T. Jabusch and J. Sun and P. Trowbridge and D. Senn and M. Guerin and C. Kendall and M. Young and S. Peek},
	year={2015},
	title={Characterizing and quantifying nutrient sources, sinks and transformations in the {D}elta: synthesis, modeling, and recommendations for monitoring},
	institution={San Francisco Estuary Institute},
	number={Contribution Number 785},
	address={Richmond, CA},
	url={http://www.sfei.org/documents/characterizing-and-quantifying-nutrient-sources-sinks-and-transformations-delta-synthesis}
}

@techreport{Novick14,
	author={E. Novick and D. Senn},
	year={2014},
	title={External nutrient loads to {S}an {F}rancisco {B}ay},
	institution={San Francisco Estuary Institute},
	number={Contribution Number 704},
	address={Richmond, CA},
	url={http://www.sfei.org/sites/default/files/biblio_files/NutrientLoadsFINAL_FINAL_Jan232014_0.pdf}
}

@article{Novotny05,
	author={V. Novotny and A. Barto\u{s}ov\'{a} and N. O'Reilly and T. Ehlinger},
	year={2005},
	title={Unlocking the relationship of biotic integrity of impaired waters to anthropogenic stresses},
	journal={Water Research},
	volume={39},
	number={1},
	pages={184-198},
	doi={10.1016/j.watres.2004.09.002}
}

@article{Novotny09,
	author={V. Novotny and D. Bedoya and H. Virani and E. Manolakos},
	year={2009},
	title={Linking indices of biotic integrity to environmental and land use variables: Multimetric clustering and predictive models},
	journal={Water Science and Technology},
	volume={59},
	number={1},
	pages={1-8}
}

@book{NRC00,
  author={{NRC (National Research Council}},
  year={2000},
	title={Clean Coastal Waters: Understanding and Reducing the Effects of Nutrient Pollution},
	publisher={National Academy Press},
	address={Washington, DC},
	pages={405}
}

@book{NRC90,
  author={{National Research Council}},
  year={1990},
  title={Managing Troubled Waters: The Role of Environmental Monitoring},
	publisher={National Academy Press},
	address={Washington, DC},
	pages={136}
}

@misc{NRCS10,
	author={{NRCS (Natural Resource Conservation Service)}},
	year={2010},
	title={Soil {S}urvey {G}eographic ({SSURGO}) {D}atabase for {M}innesota},
	note={Soil Survey Staff, Natural Resource Conservation Service, US Department of Agriculture. \url{http://soildatamart.nrcs.usda.gov/}. (Accessed January, 2010)}
}

@misc{NRCS06,
	author={{NRCS (Natural Resource Conservation Service)}},
	year={2006},
	title={U{S} {G}eneral {S}oil {M}ap ({STATSGO2})},
	note={Soil Survey Staff, Natural Resource Conservation Service, US Department of Agriculture. \url{http://soildatamart.nrcs.usda.gov/}. (Accessed January, 2010)}
}

@article{Obenour15,
	author={D. R. Obenour and A. M. Michalak and D. Scavia},
	year={2015},
	title={Assessing biophysical controls on {G}ulf of {M}exico hypoxia through probabilistic modeling},
	journal={Ecological Applications},
	volume={25},
	number={2},
	pages={492-505}
}

@article{Ode16,
	author={P. R. Ode and A. C. Rehn and R. D. Mazor and K. C. Schiff and E. D. Stein and J. T. May and L. R. Brown and D. B. Herbst and D. Gillett and K. Lunde and C. P. Hawkins},
	year={2016},
	title={Evaluating the adequacy of a reference-site pool for ecological assessments in environmentally complex regions},
	journal={Freshwater Science},
	volume={35},
	number={1},
	pages={237-248}
}

@misc{Ode07,
	author={P. R. Ode},
	year={2007},
	title={Standard operating procedures for collecting benthic macroinvertebrate samples and associated physical and chemical data for ambient bioassessment in {C}alifornia},
	address={Surface Water Ambient Monitoring Program. Sacramento, CA}
}

@article{Odum56,
	author={H. T. Odum},
	year={1956},
	title={Primary production in flowing waters},
	journal={Limnology and Oceanography},
	volume={1},
	number={2},
	pages={102-117}
}

@book{Ojakangas82,
	author={R. W. Ojakangas and C. L. Matsch},
	year={1982},
	title={Minnesota's Geology},
	publisher={The University of Minnesota Press},
	address={Minneapolis, Minnesota}
}

@misc{Oksanen10,
	author={J. Oksanen and F. Guillaume Blanchet and R. Kindt and P. Legendre and R. B. 0'Hara and G. L. Simpson and P. Solymos and M. Henry and H. 
		Stevens and H. Wagener},
	year={2010},
	title={Vegan: community ecology package, {R} package version 1.17-2},
	note={\url{http://CRAN.R-project.org/package=vegan}}
}

@article{Olden01,
	author={J. D. Olden and D. A. Jackson},
	year={2001},
	title={Fish-habitat relationships in lakes: Gaining perspective and explanatory insight by using artificial neural networks},
	journal={Transactions of the American Fisheries Society},
	volume={130},
	number={5},
	pages={878-897}
}

@article{Olden02,
	author={J. D. Olden and D. A. Jackson},
	year={2002},
	title={Illuminating the ``black box'': A randomization approach for understanding variable contributions in artifical neural networks},
	journal={Ecological Modelling},
	volume={154},
	number={1-2},
	pages={135-150}
}

@article{Olden04,
	author={J. D. Olden and M. K. Joy and R. G. Death},
	year={2004},
	title={An accurate comparison of methods for quantifying variable importance in artificial neural networks using simulated data},
	journal={Ecological Modelling},
	volume={178},
	number={3-4},
	pages={389-397}
}

@article{Olmanson11,
	author={L. G. Olmanson and P. L. Brezonik and M. E. Bauer},
	year={2011},
	title={Evaluation of medium to low resolution satellite imagery for regional lake water quality assessments},
	journal={Water Resources Research},
	volume={47},
	number={W09515},
	pages={1-14}
}

@article{Olmanson08,
	author={L. G. Olmanson and M. E. Bauer and P. L. Brezonik},
	year={2008},
	title={A 20-year {L}andsat water clarity census of {M}innesota's 10,000 lakes},
	journal={Remote Sensing of Environment},
	volume={112},
	number={11},
	pages={4086-4097}
}

@article{Oneill89,
	author={R. V. O`Neill and A. R. Johnson and A. W. King},
	year={1989},
	title={A hierarchical framework for the analysis of scale},
	journal={Landscape Ecology},
	volume={3},
	number={3-4},
	pages={193-205}
}

@article{Omernik87,
	author={J. M. Omernik},
	year={1987},
	title={Ecoregions of the Conterminous {U}nited-{S}tates},
	journal={Annals of the Association of American Geographers},
	volume={77},
	number={1},
	pages={118-125}
}

@article{Omlin01,
	author={M. Omlin and R. Brun and P. Reichert},
	year={2001},
	title={Biogeochemical model of {L}ake {Z}\"{u}rich: sensitivity, identifiability and uncertainty analysis},
	journal={Ecological Modelling},
	volume={141},
	number={1-3},
	pages={105-123}
}

@article{Omlin01b,
	author={M. Omlin and P. Reichert and R. Forster},
	year={2001},
	title={Biogeochemical model of {L}ake {Z}\"{u}rich: model equations and results},
	journal={Ecological Modelling},
	volume={141},
	number={1-3},
	pages={77-103}
}

@article{Orth10,
	author={R. J. Orth and M. R. Williams and S. R. Marion and D. J. Wilcox and T. J. B. Carruthers and K. A. Moore and W. M. Kemp and W. C. Dennison and N. Rybicki and P. Bergstrom and R. A. Batiuk},
	year={2010},
	title={Long-term trends in submersed aquatic vegetation (SAV) in {C}hesapeake {B}ay, {USA}, related to water quality},
	journal={Estuaries and Coasts},
	volume={33},
	number={5},
	pages={1144-1163}
}

@article{Ozesmi06,
	author={S. L. \"{O}zesmi and C. O. Tan and U. \"{O}zesmi},
	year={2006},
	title={Methodological issues in building, training, and testing artificial neural networks in ecological applications},
	journal={Ecological Modelling},
	volume={195},
	number={1-2},
	pages={83-93}
}

@article{Ozesmi99,
	author={S. L. \"{O}zesmi and U. \"{O}zesmi},
	year={1999},
	title={An artificial neural network approach to spatial habitat modelling with interspecific interaction},
	journal={Ecological Modelling},
	volume={116},
	number={1},
	pages={15-31}
}

@article{Paerl14,
	author={H. W. Paerl and N. S. Hall and B. L. Peierls and K. L. Rossignol},
	year={2014},
	title={Evolving paradigms and challenges in estuarine and coastal eutrophication dynamics in a culturally and climatically stressed world},
	journal={Estuaries and Coasts},
	volume={37},
	number={2},
	pages={243-258}
}

@article{Paerl06,
	author={H. W. Paerl},
	year={2006},
	title={Assessing and managing nutrient-enhanced eutrophication in estuarine and coastal waters: Interacive effects of human and climatic perturbations},
	journal={Ecological Engineering},
	volume={26},
	number={1},
	pages={40-54}
}

@article{Paerl98,
	author={H. W. Paerl and J. L. Pinckney and J. M. Fear and B. L. Peierls},
	year={1998},
	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}},
	journal={Marine Ecology Progress Series},
	volume={166},
	number={},
	pages={17-25}
}

@book{Parsons85,
  author={T. R. Parsons and Y. Maita and C. M. Lalli},
	year={1985},
	title={A manual of chemical methods for seawater analysis},
	publisher={Pergamon Press},
	address={New York},
	pages={188}
}

@article{Pauer16,
  author={J. J. Pauer and T. J. Feist and A. M. Anstead and P. A. DePetro and W. Melendez and J. C. Lehrter and M. C. Murrell and X. Zhang and D. S. Ko},
	year={2016},
	title={A modeling study examining the impact of nutrient boundaries on primary production on the {L}ouisiana continental shelf},
	journal={Ecological Modelling},
	volume={328},
	number={},
	pages={136-147}
}

@article{Pamatmat97,
  author={M. M. Pamatmat},
	year={1997},
	title={Non-photosynthetic oxygen production and non-respiratory oxygen uptake in the dark: A theory of oxygen dynamics in plankton communities},
	journal={Marine Biology},
	volume={129},
	number={4},
	pages={735-746}
}

@article{Parchaso02,
	author={F. Parchaso and J. K. Thompson},
	year={2002},
	title={Influence of hydrologic processes on reproduction of the introduced bivalve \textit{{P}otamocorbula amurensis} in northern {S}an {F}rancisco {B}ay, {C}alifornia},
	journal={Pacific Science},
	volume={56},
	number={3},
	pages={329-345}
}

@article{Parker12,
	author={A. E. Parker and V. E. Hogue and F. P. Wilkerson and R. C. Dugdale},
	year={2012},
	title={The effect of inorganic nitrogen speciation on primary production in the {S}an {F}rancisco {E}stuary},
	journal={Estuarine, Coastal, and Shelf Science},
	volume={104},
	number={},
	pages={91-101}
}

@article{Paruelo97,
	author={J. M. Paruelo and F. Tomasel},
	year={1997},
	title={Prediction of functional characteristics of ecosystems: A comparison of artificial neural networks and regression models},
	journal={Ecological Modelling},
	volume={98},
	number={2-3},
	pages={173-186}
}

@article{Pebesma04,
	author={E. J. Pebesma},
	year={2004},
	title={Multivariable geostatistics in {S}: the gstat package},
	journal={Computers and Geosciences},
	volume={30},
	number={7},
	pages={683-691}
}

@article{Pellerin14,
	author={B. A. Pellerin and B. A. Bergamaschi and R. J. Gilliom and C. G. Crawford and J. F. Saraceno and  C. P. Frederick and B. D. Downing and J. C. Murphy},
	year={2014},
	title={{M}ississippi {R}iver nitrate loads from high frequency sensor measurements and regression-based load estimation},
	journal={Environmental Science and Technology},
	volume={48},
	number={},
	pages={12612-12619}
}

@article{Penning08,
	author={W. E. Penning and B. Dudley and M. Mjelde and S. Hellsten and J. Hanganu and A. Kolada and M. van den Berg and S. Poikane and G. Phillips and N. Willby and F. Ecke},
	year={2008},
	title={Using aquatic macrophyte community indices to define the ecological status of {E}uropean lakes},
	journal={Aquatic Ecology},
	volume={42},
	pages={253-264}
}

@article{Penta08,
	author={B. Penta and Z. Lee and R. M. Kudela and S. L. Palacios and D. J. Gray and J. K. Jolliff and I. G. Shulman},
	year={2008},
	title={An underwater light attenuation scheme for marine ecosystem models},
	journal={Optical Express},
	volume={16},
	number={21},
	pages={16581-16591}
}

@article{Penta09,
	author={B. Penta and Z. Lee and R. M. Kudela and S. L. Palacios and D. J. Gray and J. K. Jolliff and I. G. Shulman},
	year={2009},
	title={An underwater light attenuation scheme for marine ecosystem models: errata},
	journal={Optical Express},
	volume={17},
	number={25},
	pages={23351-23351}
}

@article{Peres-Neto06,
	author={P. R. Peres-Neto and P. Legendre and S. Dray and D. Borcard},
	year={2006},
	title={Variation partitioning of species data matrices: {E}stimation and comparison of fractions},
	journal={Ecology},
	volume={87},
	number={10},
	pages={2614-2625}
}

@techreport{Perleberg12,
	author={D. Perleberg and P. Radomski and S. Simon},
	year={2012},
	title={Score your shore, citizen shoreline description survey},
	number={version 2, January 2012},
	institution={Division of Ecological and Water Resources, Minnesota Department of Natural Resources},
	address={St. Paul, Minnesota},
	pages={48}	
}

@article{Perry02,
	author={J. N. Perry and A. M. Liebhold and M. S. Rosenberg and J. Dungan and M. Miriti and A. Jakomulska and S. Citron-Pousty},
	year={2002},
	title={Illustrations and guidelines for selecting statistical methods for quantifying spatial pattern in ecological data},
	journal={Ecography},
	volume={25},
	number={5},
	pages={578-600}
}

@article{Petrucci14,
	author={G. Petrucci and C. Bonhomme},
	year={2014},
	title={The dilemma of spatial representation for urban hydrology semi-distributed modelling: trade-offs among complexity, calibration and geographical data},
	journal={Journal of Hydrology},
	volume={517},
	pages={997-1007}
}

@article{Pierce86,
	author={D. A. Pierce and D. W. Schafer},
	year={1986},
	title={Residuals in generalized linear models},
	journal={Journal of the American Statistical Association},
	volume={81},
	number={396},
	pages={977-986}
}

@article{Pitts47,
  author={W. Pitts and W. S. McCulloch},
  year={1947},
	title={How we know universals: The perception of auditory and visual forms},
	journal={Bulletin of Mathematical Biophysics},
	volume={9},
  number={3},
	pages={127-147}
}

@techreport{Plafkin89,
	author={J. L. Plafkin and M. T. Barbour and K. D. Porter and S. K. Gross and R. M. Hughes},
	year={1989},
	number={EPA 841-B-99-002},
	title={Rapid bioassessment protocols for use in streams and rivers. Benthic macroinvertebrates and fish},
	institution={U.S. Environmental Protection Agency},
	address={Washington, DC}
}

@article{Platt80,
  author={T. Platt and C. L. Gallegos and W. G. Harrison},
  year={1980},
	title={Photoinhibition of photosynthesis in natural assemblages of marine phytoplankton},
	journal={Journal of Marine Research},
	volume={38},
  number={},
	pages={687-701}
}

@techreport{Poe05,
  author={A. Poe and K. Hackett and S. Janicki and R. Pribble and A. Janicki},
	year={2005},
	title={Estimates of total nitrogen, total phosphorus, total suspended solids, and biochemical oxygen demand loadings to {T}ampa {B}ay, {F}lorida: 1999-2003},
  number={\#02-05},
	institution={Tampa Bay Estuary Program}, 
	address={St. Petersburg, Florida, USA}
}

@article{Poff97,
	author={N. L. Poff},
	year={1997},
	title={Landscape filters and species traits: Towards mechanistic understanding and prediction in stream ecology},
	journal={Journal of the North American Benthological Society},
	volume={16},
	number={2},
	pages={391-409}
}

@article{Pollard98,
	author={P. Pollard and M. Huxham},
	year={1998},
	title={The {E}uropean {W}ater {F}ramework {D}irective: A new era in the management of aquatic ecosystem health?},
	journal={Aquatic Conservation: Marine and Freshwater Ecosystems},
	volume={8},
	number={6},
	pages={773-792}
}

@article{Poole29,
  author={H. H. Poole and W. R. G. Atkins},
  year={1929},
  title={Photo-electric measurements of submarine illumination throughout the year},
	journal={Journal of the Marine Biological Association of the United Kingdom},
	volume={16},
	number={},
	pages={297-324}
}

@article{Poor01,
	author={P. J. Poor and K. J. Boyle and L. O. Taylor and R. Bouchard},
	year={2001},
	title={Objective versus subjective measures of water clarity in hedonic property value models},
	journal={Land Economics},
	volume={77},
	number={4},
	pages={482-493}
}

@article{Portnoy03,
  author={S. Portnoy},
  year={2003},
	title={Censored regression quantiles},
	journal={Journal of the American Statistical Association},
	volume={98},
	number={464},
	pages={1001-1012}
}

@article{Post02,
	author={J. R. Post and M. Sullivan and S. Cox and N. P. Lester and C. J. Walters and E. A. Parkinson and A. J. Paul and L. Jackson and B. J. Shuter},
	year={2002},
	title={{C}anada's recreational fisheries: The invisible collapse?},
	journal={Fisheries},
	volume={27},
	number={1},
	pages={6-17}
}

@article{Powers05,
  author={S. P. Powers and C. H. Peterson and R. R. Christian and E. Sullivan and M. J. Powers and M. J. Bishop and C. P. Buzzelli},
	year={2005},
	title={Effects of eutrophication on bottom habitat and prey resources of demersal fishes},
	journal={Marine Ecology Progress Series},
	volume={302},
	number={},
	pages={233-243}
}

@techreport{Pribble01,
  author={R. Pribble and A. Janicki and H. Zarbock and S. Janicki and M. Winowitch},
  year={2001},
	title={Estimates of total nitrogen, total phosphorus, total suspended solids, and biochemical oxygen demand loadings to {T}ampa {B}ay, {F}lorida: 1995-1998},
  number={\#05-01},
	institution={Tampa Bay Estuary Program}, 
	address={St. Petersburg, Florida, USA}
}

@article{Rabalais02,
  author={N. N. Rabalais and R. E. Turner and D. Scavia},
	year={2002},
	title={Beyond science into policy: {G}ulf of {M}exico hypoxia and the {M}ississippi river},
	journal={BioScience},
	volume={52},
	number={2},
	pages={129-142}
}

@article{Rabotyagov2014,
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{Radomski01,
	author={P. Radomski and T. J. Goeman},
	year={2001},
	title={Consequences of human lakeshore development on emergent and floating-leaf vegetation abundance},
	journal={North American Journal of Fisheries Management},
	volume={21},
	number={1},
	pages={46-61}
}

@article{Radomski06,
	author={P. Radomski},
	year={2006},
	title={Historical changes in abundance of floating-leaf and emergent vegetation in {M}innesota lakes},
	journal={North American Journal of Fisheries Management},
	volume={26},
	number={4},
	pages={932-940}
}

@article{Radomski10,
	author={P. Radomski and L. A. Bergquist and M. Duval and A. Williquett},
	year={2010},
	title={Potential impacts of docks on littoral habitats in {M}innesota lakes},
	journal={Fisheries},
	volume={35},
	number={10},
	pages={489-495}
}

@article{Radomski12,
	author={P. Radomski and D. Perleberg},
	year={2012},
	title={Application of a versatile aquatic macrophyte integrity index for {M}innesota lakes},
	journal={Ecological Indicators},
	volume={20},
	pages={252-268}
	}

@article{Ramstack04,
	author={J. M. Ramstack and S. C. Fritz and D. R. Engstrom},
	year={2004},
	title={Twentieth century water quality trends in Minnesota lakes compared to presettlment variability},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={61},
	pages={561-576}
}

@article{Rasmussen05,
	author={P. Rasmussen and N. J. Anderson},
	year={2005},
	title={Natural and anthropogenic forcing of aquatic macrophyte development in a shallow {D}anish lake during the last 7000 years},
	journal={Journal of Biogeography},
	volume={32},
	number={11},
	pages={1993-2005}
}

@article{Razi05,
	author={M. A. Razi and K. Athappilly},
	year={2005},
	title={A comparative predictive analysis of neural networks ({NN}s), nonlinear regression and classification and regression tree ({CART}) models},
	journal={Expert Systems and Applications},
	volume={29},
	number={1},
	pages={65-74}
}

@misc{RDCT17,
  	author={{RDCT (R Development Core Team)}},
	year={2017},
  	title={{R: A language and environment for statistical computing, v3.3.2. R Foundation for Statistical Computing, Vienna, Austria}},
  	note={\url{http://www.R-project.org}}
}

@book{Recknagel06,
  author={F. Recknagel},
	year={2006},
	title={Ecological Informatics: Scope, Techniques and Applications},
	publisher={Springer-Verlag},
	edition={2nd},
	address={Berlin, Germany},
	pages={496}
}

@incollection{Recknagel00,
	author={F. Recknagel and H. Wilson},
	editor={S. Lek and J. F. Gu\'{e}gan},
	year={2000},
	title={Elucidation and prediction of aquatic ecosystems by artificial neuronal networks},
	booktitle={{Artificial Neuronal Networks: Application to Ecology and Evolution}},
	publisher={Springer-Verlag},
	address={Berlin, Germany},
	pages={143-155}
}

@article{Reckhow90,
	author={K. H. Reckhow and J. T. Clements and R. C. Dodd},
	year={1990},
	title={Statistical evaluation of mechanistic water-quality models},
	journal={Journal of Environmental Engineering},
	volume={116},
	number={2},
	pages={250-268}
	}

@incollection{Reed10,
  author={R. E. Reed and J. M. Burkholder and E. H. Allen},
	year={2010},
	title={Current online monitoring technology for surveillance of algal blooms, potential toxicity, and physicalechemical structure in rivers, reservoirs, and lakes},
	booktitle={{American Water Works Association Manual M57, Algae}},
	publisher={American Water Works Association},
	address={Denver, Colorado},
	pages={1-24}
}

@article{Reed09,
	author={J. R. Reed and D. L. Pereira},
	year={2009},
	title={Relationships between shoreline development and nest site selection by black crappie and largemouth bass},
	journal={North American Journal of Fisheries Management},
	volume={29},
	number={4},
	pages={943-948}
	}

@article{Refsgaard07,
	author={J. C. Refsgaard and J. P. van der Sluijs and A. L. H{\o}jberg and P. A. Vanrolleghem},
	year={2007},
	title={Uncertainty in the environmental modelling process - A framework and guidance},
	journal={Environmental Modelling \& Software},
	volume={22},
	number={11},
	pages={1543-1556}
}

@article{Reichert97,
  author={P. Reichert and M. Omlin},
  year={1997},
  title={On the usefulness of over parameterized ecological models},
  journal={Ecological Modelling},
  volume={95},
  number={2},
  pages={289-299}
  }

@article{Reichert01,
	author={P. Reichert and P. Vanrolleghem},
	year={2001},
	title={Identifiability and uncertainty analysis of the {R}iver {W}ater {Q}uality {M}odel {N}o. 1 {RWQM1}},
	journal={Water Science and Technology},
	volume={43},
	number={7},
	pages={329-338}
	}

@techreport{Reschke06,
	author={C. Reschke and G. E. Host and L. B. Johnson},
	year={2006},
	title={Evaluation of {DNR} aquatic vegetation surveys: data summaries and comparative analysis},
	institution={Natural Resources Research Institute, University of Minnesota, Minnesota Department of Natural Resources, CFMS Contract \#A61156},
	address={Duluth, Minnesota}
}

@article{Reynoldson97,
	author={T. B. Reynoldson and R. H. Norris and V. H. Resh and K. E. Day and D. M. Rosenberg},
	year={1997},
	title={The reference condition: a comparison of multimetric and multivariate approaches to assess water-quality impairment using benthic macroinvertebrates},
	journal={Journal of the North American Benthological Society},
	volume={16},
	number={4},
	pages={833-852}
}

@book{Richards06a,
	author={J. A. Richards and X. Jia},
	year={2006},
	title={Remote Sensing Digital Image Analysis},
	publisher={Springer-Verlag, (Chapter 9)},
	address={Berlin},
	edition={fourth}
}

@book{Richards06b,
	author={J. A. Richards and X. Jia},
	year={2006},
	title={Remote Sensing Digital Image Analysis},
	publisher={Springer-Verlag, (Chapter 8)},
	address={Berlin},
	edition={fourth}
}

@article{Riis03,
	author={T. Riis and I. Hawes},
	year={2003},
	title={Effect of wave exposure on vegetation abundance, richness, and depth distribution of shallow water plants in a {N}ew {Z}ealand lake},
	journal={Freshwater Biology},
	volume={48},
	number={1},
	pages={75-87}
}

@book{Ripley96,
	author={B. D. Ripley},
	year={1996},
	title={Pattern Recognition and Neural Networks},
	publisher={Cambridge University Press},
	address={Cambridge, United Kingdom},
	pages={403}
}

@article{Ro06,
  author={K. S. Ro and P. G. Hunt},
	year={2006},
	title={A new unified equation for wind-driven surficial oxygen transfer into stationary water bodies},
	journal={Transactions of the American Society of Agricultural and Biological Engineers},
	volume={49},
	number={5},
	pages={1615-1622}
}

@article{Robertson04,
	author={W. V. Robertson and D. Whitman and K. Q. Zhang and S. P. Leatherman},
	year={2004},
	title={Mapping shoreline position using airborne laser altimetry},
	journal={Journal of Coastal Research},
	volume={20},
	number={3},
	pages={884-892}
}

@article{Roelke99,
	author={D. L. Roelke and P. M. Eldridge and L. A. Cifuentes},
	year={1999},
	title={A model of phytoplankton competition for limiting and non-limiting nutrients: implications for management of dynamic environments},
	journal={Estuaries},
	volume={22},
	number={},
	pages={92-104}
}

@article{Roelke00,
	author={D. L. Roelke},
	year={2000},
	title={Copepod food-quality threshold as a mechanism influencing phytoplankton succession and accumulation of biomass, and secondary productivity: a modeling study with management implications},
	journal={Ecological Modelling},
	volume={134},
	number={},
	pages={245-274}
}

@incollection{Rohlich69,
  author={G. A. Rohlich},
  editor={G. A. Rohlich},
  year={1969},
	title={Introduction, summary, and recommendations},
	booktitle={Eutrophication: Causes, Consequences, and Correctives},
	publisher={National Academy of Sciences},
	address={Washington DC, USA},
	pages={3-16}
}

@article{Rooney00,
	author={N. Rooney and J. Kalff},
	year={2000},
	title={Inter-annual variation in submerged macrophyte community biomass and distribution: the influence of temperature and lake morphometry},
	journal={Aquatic Botany},
	volume={68},
	number={4},
	pages={321-335}
}

@article{Rorslett91,
	author={B. Rorslett},
	year={1991},
	title={Principal determinants of aquatic macrophyte richness in northern {E}uropean lakes},
	journal={Aquatic Botany},
	volume={39},
	number={1-2},
	pages={173-193}
}

@article{Rosenberg85,
  author={R. Rosenberg},
	year={1985},
	title={Eutrophication -- the future marine coastal nuisance?},
	journal={Marine Pollution Bulletin},
	volume={16},
	number={6},
	pages={227-231}
}

@article{Ruaro13,
	author={R. Ruaro and E. Andr\'e Gubiani},
	year={2013},
	title={A scientometric assessment of 30 years of the {I}ndex of {B}iotic {I}ntegrity in aquatic systems: Applications and main flaws},
	journal={Ecological Indicators},
	volume={29},
	pages={105-110}
}

@article{Rumelhart86,
  author={D. E. Rumelhart and G. E. Hinton and R. J. Williams},
	year={1986},
	title={Learning representations by back-propagating errors},
	journal={Nature},
	volume={323},
  number={6088},
	pages={533-536}
}

@article{Russell07,
  author={M. J. Russell and P. A. Montagna},
	year={2007},
	title={Spatial and tepmoral variability and drivers of net ecosystem metabolism in western {G}ulf of {M}exico estuaries},
	journal={Estuaries and Coasts},
	volume={30},
	number={1},
	pages={137-153}
}

@article{Rykiel96,
  author={E. J. Rykiel Jr.},
	year={1996},
	title={Testing ecological models: the meaning of validation},
	journal={Ecological Modelling},
	volume={90},
	number={3},
	pages={229-244}
}

@article{Sakamoto89,
  author={M. Sakamoto and T. Tanaka},
	year={1989},
	title={Phosphorus dynamics associated with phytoplankton blooms in eutrophic {M}ikawa {B}ay, {J}apan},
	journal={Marine Biology},
	volume={101},
	number={2},
	pages={265-271}
}

@techreport{Sanger02,
  author={D. M. Sanger and M. D. Arendt and Y. Chen and E. L. Wenner and A. F. Holland and D. Edwards and J. Caffrey},
	year={2002},
	title={A synthesis of water quality data: National Estuarine Research Reserve System-wide Monitoring Program (1995-2000)},
	institution={National Estuarine Research Reserve Technical Report Series 2002:3. South Carolina Department of Natural Resources, Marine Resources Division Contribution No. 500},
	address={Charleston, South Carolina},
	pages={135}
}

@article{Santos09,
	author={M. J. Santos and S. Khanna and E. L. Hestir and M. E. Andrew},
	year={2009},
	title={Use of hyperspectral remote sensing to evaluate efficacy of aquatic plant management},
	journal={Invasive Plant Science and Management},
	volume={2},
	number={3},
	pages={216-229}
}

@article{Saeys07,
  author={Y. Saeys and I. Inza and P. Larra\~{n}aga},
  year={2007},
  title={A review of feature selection techniques in bioinformatics},
	journal={Bioinformatics},
	volume={23},
	number={19},
	pages={2507-2517}
}

@article{Sanders01,
  author={C. A. Sanders and M. Rodriguez and E. Greenbaum},
  year={2008},
  title={Stand-off tissue-based biosensors for the detection of chemical warfare agents using photosynthetic fluorescence induction},
	journal={Biosensors and Bioelectronics},
	volume={16},
	number={7-8},
	pages={439-446}
}

@article{Santos80,
  author={S. L. Santos and J. L. Simon},
  year={1980},
	title={Marine soft-bottom community establishment following annual defaunation: Larval or adult recruitment},
	journal={Marine Ecology - Progress Series},
	volume={2},
  number={3},
	pages={235-241}
}

@article{Sasaki09,
  author={A. Sasaki and Y. Hagimori and T. Nakatsubo and A. Hoshika},
  year={2009},
	title={Tidal effects on the organic carbon mineralization rate under aerobic conditions in sediments of an intertidal estuary},
	journal={Ecological Research},
	volume={24},
	number={4},
	pages={723-729}
}

@article{Sass10,
	author={L. L. Sass and M. A. Bozek and J. A. Hauxwell and K. Wagner and S. Knight},
	year={2010},
	title={Response of aquatic macrophytes to human land use perturbations in the watersheds of {W}isconsin lakes, {U.S.A.}},
	journal={Aquatic Botany},
	volume={93},
	pages={1-8}
}

@article{Sawaya03,
	author={K. E. Sawaya and L. G. Olmanson and N. J. Heinert and P. L. Brezonik and M. E. Bauer},
	year={2003},
	title={Extending satellite remote sensing to local scales: Land and water resource monitoring using high-resolution imagery},
	journal={Remote Sensing of Environment},
	volume={88},
	number={1-2},
	pages={144-156}
}

@article{Scardi01,
  author={M. Scardi},
	year={2001},
	title={Advances in neural network modeling of phytoplankton primary production},
	journal={Ecological Modelling},
	volume={146},
	number={1-3},
	pages={33-45}
}

@article{Scavia04,
  author={D. Scavia and D. Justic and V. J. Bierman},
	year={2004},
	title={Reducing hypoxia in the {G}ulf of {M}exico: Advice from three models},
	journal={Estuaries},
	volume={27},
	number={3},
	pages={419-425}
}

@article{Schaeffer13,
	author={B. A. Schaeffer and J. D. {Hagy III} and R. P. Stumpf},
	year={2013},
	title={Approach to developing numeric water quality criteria for coastal waters: transition from {SeaWiFS} to {MODIS} and {MERIS} satellites},
	journal={Journal of Applied Remote Sensing},
	volume={7},
	number={1},
	pages={073544}
}

@article{Schaeffer12,
	author={B. A. Schaeffer and J. D. Hagy and R. N. Conmy and J. C. Lehrter and R. P. Stumpf},
	year={2012},
	title={An approach to developing numeric water quality criteria for coastal waters using the {SeaWiFS} satellite data record},
	journal={Environmental Science and Technology},
	volume={46},
	number={2},
	pages={916-922}
}

@article{Scheffer93,
	author={M. Scheffer and S. H. Hosper and M. L. Meijer and B. Moss and E. Jeppesen},
	year={1993},
	title={Alternative equilibria in shallow lakes},
	journal={Trends in Ecology and Evolution},
	volume={8},
	number={8},
	pages={275-279}
}

@article{Scheffer98,
	author={M. Scheffer and S. Carpenter and J. A. Foley and C. Folkes and B. Walker},
	year={1998},
	title={Catastrophic shifts in ecosystems},
	journal={Nature},
	volume={413},
	pages={591-596}
}

@article{Scheuerell04,
	author={M. D. Scheuerell and D. E. Schindler},
	year={2004},
	title={Changes in the spatial distribution of fishes in lakes along a residential development gradient},
	journal={Ecosystems},
	volume={7},
	number={1},
	pages={98-106}
}

@article{Schiff16,
  title = {Regional monitoring programs in the {U}nited {S}tates: Synthesis of four case studies from {P}acific, {A}tlantic, and {G}ulf {C}oasts},
  journal = {Regional Studies in Marine Science},
  volume = {4},
  pages = {A1 - A7},
  year = {2016},
  url = {https://doi.org/10.1016/j.rsma.2015.11.007},
  author = {K. Schiff and P.R. Trowbridge and E.T. Sherwood and P. Tango and R.A. Batiuk}
}

@article{Schindler00,
	author={D. E. Schindler and S. I. Geib and M. R. Williams},
	year={2000},
	title={Patterns of fish growth along a residential development gradient in north temperate lakes},
	journal={Ecosystems},
	volume={3},
	number={3},
	pages={229-237}
}

@article{Schmidt02,
	author={N. Schmidt and M. E. Luther},
	year={2002},
	title={{ENSO} impacts on salinity in {T}ampa {B}ay, {F}lorida},
	journal={Estuaries and Coasts},
	volume={25},
	number={5},
	pages={976-984}
}

@article{Schoellhamer11,
	author={David H. Schoellhamer},
	year={2011},
	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},
	journal={Estuaries and Coasts},
	volume={34},
	number={},
	pages={885-899}
}

@article{Schoolmaster13,
	author={D. R. Schoolmaster Jr. and J. B. Grace and E. W. Schweiger and G. R. Guntenspergen and B. R. Mitchell and K. M. Miller and A. M. Little},
	year={2013},
	title={An algorithmic and information-theoretic approach to multimetric index construction},
	journal={Ecological Indicators},
	volume={26},
	pages={14-23}
}

@incollection{Schopfer08,
	author={E. Sch\"{o}pfer and S. Lang and J. Strobl},
	editor={T. Blaschke and S. Lang and G. J. Hay},
	year={2008},
	title={Segmentation and object-based image analysis},
	booktitle={Object-Based Image Analysis: Spatial Concepts for Knowledge-Driven Remote Sensing Applications},
	publisher={Springer-Verlag},
	address={Heidelberg, Berlin, New York},
	pages={181-192}
}

@misc{Schad11,
	author={D. Schad},
	year={2011},
	title={Game and fish fund: {T}he big picture.},
	note={{Minnesota Department of Natural Resources Roundtable Meeting, January 7-8, 2011, Brooklyn Center, MN}}
	}

@techreport{Schupp92,
	author={D. H. Schupp},
	year={1992},
	title={An ecological classification of {M}innesota lakes with associated fish communities},
	number={41},
	institution={Section of Fisheries, Minnesota Department of Natural Resources},
	address={St. Paul, Minnesota}
}

@book{Sculthorpe67,
	author={C. D. Sculthorpe},
	year={1967},
	title={The Biology of Aquatic Vascular Plants},
	publisher={St. Martin's Press},
	address={New York, New York},
	pages={610}
}

@article{Schultz08,
	author={P. Schultz and N. R. Urban},
	year={2008},
	title={Effects of bacterial dynamics on organic matter decomposition and nutrient release from sediments: A modeling study},
	journal={Ecological Modelling},
	volume={210},
	number={1-2},
	pages={1-14}
}

@misc{SFWMD13,
  author={{SFWMD (Southwest Florida Water Management District)}},
  year={2013},
	title={{GIS, Maps and Survey Shapefile Library for Support of Surface Water Improvement and Management Projects}},
	note={\url{http://www.swfwmd.state.fl.us/data/gis/layer_library/category/swim}. (Accessed October, 2013)}
}

@article{Shanley05,
	author={J. B. Shanley and N. C. Kamman and T. A. Clair and A. Chalmers},
	year={2005},
	title={Physical controls on total methylmercury concentrations in streams and lakes of the northeastern {USA}},
	journal={Ecotoxicology},
	volume={14},
	pages={125-134}
}

@techreport{Shellenbarger08,
  author={G. G. Shellenbarger and D. H. Schoellhamer and T. L. Morgan and J. Y. Takekawa and N. D. Athearn and K. D. Henderson},
	year={2008},
	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},
	institution={US Geological Survey},
	address={Reston, Virginia},
	number={Open-File Report 2008-1097},
	pages={26}
}

@article{Sherwood17,
	author={E. T. Sherwood and H. S. Greening and J. O. R. Johansson and K. Kaufman and G. Raulerson},
	year={2017},
	title={{T}ampa {B}ay ({F}lorida, {USA}): Documenting seagrass recovery since the 1980s and reviewing the benefits},
	journal={Southeastern Geographer},
	volume={57},
	number={3},
	pages={294-319}
}

@article{Shoredits13,
	author={A. S. Shoredits and J. A. Clayton},
	year={2013},
	title={Assessing the practice and challenges of stream restoration in urbanized environments of the {USA}},
	journal={Geography Compass},
	volume={7},
	number={5},
	pages={358-372},
	doi={10.1111/gec3.12039}
}

@article{Short96,
	author={F. T. Short and S. Wyllie-Echeverria},
	year={1996},
	title={Natural and human-induced disturbance of seagrasses},
	journal={Environmental Conservation},
	volume={23},
	number={1},
	pages={17-27}
}

@book{Shumway11,
  author={R. H. Shumway and D. S. Stoffer},
  title={Time Series Analysis and its Applications: With R Examples},
	year={2011},
	edition={3rd},
	publisher={Springer-Verlag},
	address={New York, New York},
  pages={596}
} 

@article{Sleeter11, 
  author={B. M. Sleeter and T. S. Wilson and C. E. Soulard and J. Liu},
  title={Estimation of the late twentieth century land-cover change in {C}alifornia},
  year={2011},
  journal={Environmental Monitoring and Assessment},
  volume={173},
  number={1-4},
  pages={251-266},
  doi={10.1007/s10661-010-1385-8}
}

@article{Smetacek08,
  author={V. Smetacek and J. E. Cloern},
	year={2008},
	title={On phytoplankton trends},
	journal={Science},
	volume={319},
	number={5868},
	pages={1346-1348}
}

@article{Snowling01,
  author={S. D. Snowling and J. R. Kramer},
	year={2001},
	title={Evaluating modelling uncertainty for model selection},
	journal={Ecological Modelling},
	volume={138},
	number={},
	pages={17-30}
}

@article{Soetaert10,
	author={K. Soetaert and T. Petzoldt},
	year={2010},
	title={Inverse modelling, sensitivity, and {M}onte {C}arlo analysis in {R} using package {FME}},
	journal={Journal of Statistical Software},
	volume={33},
	number={3},
	pages={1-28}
}

@article{Sondergaard13,
	author={M. S{\o}ndergaard and G. Phillips and S. Hellsten and A. Kolada and F. Ecke and H. M\"{a}emets and M. Mjelde and M. M. Azzella and A. Oggioni},
	year={2013},
	title={Maximum growing depth of submerged macrophytes in {E}uropean lakes},
	journal={Hydrobiologia},
	volume={704},
	number={1},
	pages={165-177}
}

@book{Soille03,
	author={P. Soille},
	title={Morphological Image Analysis: Principles and Applications},
	year={2003},
	edition={2nd},
	publisher={Springer-Verlag},
	address={Secaucus, New Jersey, USA}
} 

@book{Sokal94,
  author={R. Sokal and F. J. Rohlf},
	title={Biometry},
	year={1994},
	edition={3rd},
	publisher={W. H. Freeman},
	address={San Francisco, California, USA},
  pages={880}
} 

@article{Soranno08,
	author={P. A. Soranno and K. S. Cheruvelil and R. J. Stevenson and S. L. Rollins and S. W. Holden and S. Heaton and E. Torng},
	year={2008},
	title={A framework for developing ecosystem-specific nutrient criteria: Integrating biological thresholds with predictive modeling},
	journal={Limnology and Oceanography},
	volume={53},
	number={2},
	pages={773-787}
}

@article{Southerland07,
	author={M. T. Southerland and G. M. Rogers and M. J. Kline and R. P. Morgan and D. M. Boward and R. Kazyak and R. J. Klauda and S. A. Stranko},
	year={2007},
	title={Improving biological indicators to better assess the condition of streams},
	journal={Ecological Indicators},
	volume={7},
	number={4},
	pages={751-767}
}

@article{Spears09,
  author={B. M. Spears and I. D. M. Gunn and L. Carvalho and I. J. Winfield and B. Dudley and K. Murphy and L. May},
  year={2009},
	title={An evaluation of methods for sampling macrophyte maximum colonisation depth in {L}och {L}even, {S}cotland},
	journal={Aquatic Botany},
	volume={91},
	number={2},
	pages={75-81}
}

@article{Sponseller01,
  author={R. A. Sponseller and E. F. Benfield and H. M. Valett},
  year={2001},
	title={Relationships between land use, spatial scale and stream macroinvertebrate communities},
	journal={Freshwater Biology},
	volume={46},
	number={10},
	pages={1409-1424}, 
	doi={10.1046/j.1365-2427.2001.00758.x}
}

@article{Sprague11,
	author={L. A. Sprague and R. M. Hirsch and B. T. Aulenbach},
	year={2011},
	title={Nitrate in the {M}ississippi {R}iver and its tributaries, 1980 to 2008: Are we making progress?},
	journal={Environmental Science and Technology},
	volume={45},
	number={17},
	pages={7209-7216}
}

@article{Staehr10,
  author={P. A. Staehr and D. Bade and M. C. Van de Bogert and G. R. Koch and C. Williamson and P. Hanson and J. J. Cole and T. Kratz},
	year={2010},
	title={Lake metabolism and the diel oxygen technique: State of the science},
	journal={Limnology and Oceanography: Methods},
	volume={8},
	number={},
	pages={628-644}
}

@article{Stein17,
	author={E. D. Stein and A. Sengupta and R. D. Mazor and K. McCune and B. P. Bledsoe and S. Adams},
	year={2017},
	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}},
	journal={Ecohydrology},
	volume={},
	number={},
	pages={}
}

@article{Stelzer05,
	author={D. Stelzer and S. Schneider and A. Melzer},
	year={2005},
	title={Macrophyte-based assessment of lakes - a contribution to the implementation of the {E}uropean {W}ater {F}ramework {D}irective in {G}ermany},
	journal={International Review of Hydrobiology},
	volume={90},
	number={2},
	pages={223-237}
}

@article{Steward05,
  author={J. S. Steward and R. W. Virnstein and L. J. Morris and E. F. Lowe},
	year={2005},
	title={Setting seagrass depth, coverage, and light targets for the {I}ndian {R}iver {L}agoon System, {F}lorida},
	journal={Estuaries},
	volume={28},
	number={6},
	pages={923-935}
}

@article{Steward07,
  author={J. S. Steward and W. C. Green},
	year={2007},
	title={Setting load limits for nutrients and suspended solids based upon seagrass depth-limit targets},
	journal={Estuaries and Coasts},
	volume={30},
	number={4},
	pages={657-670}
}

@article{Steward10,
	author={J. S. Steward and E. F. Lowe},
	year={2010},
	title={General empirical models for estimating nutrient load limits for {F}lorida's estuaries and inland waters},
	journal={Limnology and Oceanography},
	volume={55},
	number={1},
	pages={433-445}
}

@article{Stoddard06,
	author={J. L. Stoddard and D. P. Larsen and C. P. Hawkins and R. K. Johnson and R. H. Norris},
	year={2006},
	title={Setting expectations for the ecological condition of streams: The concept of reference condition},
	journal={Ecological Applications},
	volume={16},
	number={4},
	pages={1267-1276}
}

@article{Stow05,
	author={C. A. Stow and S. S. Qian and J. K. Craig},
	year={2005},
	title={Declining threshold for hypoxia in the {G}ulf of {M}exico},
	journal={Environmental Science and Technology},
	volume={39},
	number={3},
	pages={716-723}
}

@article{Suter93,
	author={G. W. Suter},
	year={1993},
	title={A critique of ecosystem health concepts and indexes},
	journal={Environmental Toxicology and Chemistry},
	volume={12},
	number={9},
	pages={1533-1539}
}

@article{Sutula17,
	author={M. Sutula and R. Kudela and J. D. {Hagy III} and L. W. Harding Jr. and D. Senn and J. E. Cloern and S. Bricker and G. M. Berg and M. W. Beck},
	year={2017},
	title={Novel analyses of long-term data provide a scientific basis for chlorophyll-a thresholds in {S}an {F}rancisco {B}ay},
	journal={Estuarine, Coastal and Shelf Science},
	volume={197},
	number={},
	pages={107-118}
}

@article{Swanson15,
	author={A. Swanson and M. Kosmala and C. Lintott and R. Simpson and A. Smith and C. Packer},
	year={2015},
	title={{S}napshot {S}erengeti: High-frequency annotated camera trap images of 40 mammalian species in {A}frican savanna},
	journal={Scientific Data},
	volume={2},
	number={},
	pages={150026}
}

@article{Swanson88,
	author={F. J. Swanson and T. K. Kratz and N. Caine and R. G. Woodmansee},
	year={1988},
	title={Landform effects on ecosystem patterns and processes},
	journal={Bioscience},
	volume={38},
	number={2},
	pages={92-98}
}

@book{Swink94,
	author={F. Swink and G. Wilhelm},
	year={1994},
	title={Plants of the {C}hicago Region},
	publisher={Indiana Academy of Science},
	edition={fourth},
	address={Indianapolis, Indiana},
	pages={921}
}

@misc{SWMP14,
  author={{System-Wide Monitoring Program Data Analysis Training}},
  year={2014},
  title={SWMP Data Analysis Training Workshop provided at the 2014 NERRS/NERRA Annual Meeting, November 17, 2014},
  note={\url{http://copepod.org/nerrs-swmp-workshop/}}
}

@misc{TBEP17,
  author={{TBEP (Tampa Bay Estuary Program)}},
	year={2017},
	title={{Tampa Bay Water Atlas}},
	note={\url{http://www.tampabay.wateratlas.usf.edu/}. (Accessed July, 2017)}
}

@techreport{TBRPC86,
  author={{TBRPC (Tampa Bay Regional Planning Council)}},
	year={1986},
	title={Documenting the Economic Importance of {T}ampa {B}ay},
	institution={Tampa Bay Regional Planning Council, Agency on Bay Management},
	address={St. Petersburg, Florida},
	number={Final}
}

@article{Terrell96,
  author={J. W. Terrell and B. S. Cade and J. Carpenter and J. M. Thompson},
	year={1996},
	title={Modeling stream fish habitat limitations from wedge-shaped patterns of variation in standing stock},
	journal={Transactions of the American Fisheries Society},
	volume={125},
	number={1},
	pages={104-117}
}

@article{Testa08a,
  author={J. M. Testa and W. M. Kemp and W. R. Boynton and J. D. Hagy},
  year={2008},
	title={Long-term changes in water quality and productivity in the {P}atuxent {R}iver {E}stuary: 1985 to 2003},
	journal={Estuaries and Coasts},
	volume={31},
	number={6},
	pages={1021-1037}
}

@article{Testa08b,
  author={J. M. Testa and W. M. Kemp},
  year={2008},
  title={Variability of biogeochemical processes and physical transport in a partially stratified estuary: a box-modeling analysis},
	journal={Marine Ecology Progres Series},
	volume={356},
	number={},
	pages={63-79}
}

@article{Tewfik07,
  author={A. Tewfik and J. B. Rasmussen and K. S. McCann},
  year={2007},
  title={Simplification of seagrass food webs across a gradient of nutrient enrichment},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={64},
	number={7},
	pages={956-967}
}

@article{Thebault08,
	author={J. Th\'{e}bault and T. S. Schraga and J. E. Cloern and E. G. Dunlavey},
	year={2008},
	title={Primary production and carrying capacity of former salt ponds after reconnection to {S}an {F}rancisco {B}ay},
	journal={Wetlands},
	volume={28},
	number={3},
	pages={841-851}
}

@article{Thompson11,
	author={S. E. Thompson and N. B. Basu and J. Lascurain Jr. and A. Aubeneau and P. S. C. Rao},
	year={2011},
	title={Relative dominance of hydrologic versus biogeochemical factors on solute export across impact gradients},
	journal={Water Resources Research},
	volume={47},
	number={10},
	pages={W00J05}
}

@article{Thompson08,
  author={J. K. Thompson and J. R. Koseff and S. G. Monismith and L. V. Lucas},
  year={2008}, 
  title={Shallow water processes govern system-wide phytoplankton bloom dynamics: A field study},
  journal={Journal of Marine Systems},
  volume={74},
  number={1-2},
  pages={153-166}
}

@article{Tobin58,
  author={J. Tobin},
  year={1958},
	title={Estimation of relationships for limited dependent variables},
	journal={Econometrica},
	volume={26},
	number={1},
	pages={24-36}
}

@article{Tolonen01,
	author={K. T. Tolonen and H. Hamalainen and I. J. Holopainen and J. Karjalainen},
	year={2001},
	title={Influences of habitat type and environmental variables on littoral macroinvertebrate communities in a large lake system},
	journal={Hydrobiologia},
	volume={152},
	number={1},
	pages={39-67}
}

@article{Tomasko05,
	author={D. A. Tomasko and C. A. Corbett and H. S. Greening and G. E. Raulerson},
	year={2005},
	title={Spatial and temporal variation in seagrass coverage in {S}outhwest {F}lorida: Assessing the relative effects of anthropogenic nutrient load reductions and rainfall in four contiguous estuaries},
	journal={Marine Pollution Bulletin},
	volume={50},
	number={8},
	pages={797-805}
}

@article{Townsend08,
	author={C. R. Townsend and S. S. Uhlmann and C. D. Matthaei},
	year={2008},
	title={Individual and combined responses of stream ecosystems to multiple stressors},
	journal={Journal of Applied Ecology},
	volume={45},
	number={6},
	pages={1810-1819},
	doi={10.1111/j.1365-2664.2008.01548.x}
}

@article{Townshend00,
	author={J. R. G. Townshend and C. Huang and S. N. V. Kalluri and R. S. Defries and S. Liang},
	year={2000},
	title={Beware of per-pixel characterization of land cover},
	journal={International Journal of Remote Sensing},
	volume={21},
	number={4},
	pages={839-843}
}

@article{Tuerlinckx06,
	author={F. Tuerlinckx and F. Rijmen and G. Verbeke and P. DeBoeck},
	year={2006},
	title={Statistical inference in generalized linear mixed models: A review},
	journal={British Journal of Mathematical and Statistical Psychology},
	volume={59},
	pages={225-255}
}

@book{Tukey77,
  author={J. W. Tukey},
  year={1977},
	title={Exploratory Data Analysis},
	publisher={Addison-Wesley},
	address={Reading, Massachusetts},
	pages={688}
}

@techreport{Tyler07,
  author={D. Tyler and D. G. Zawada and A. Nayegandhi and J. C. Brock and M. P. Crane and K. K. Yates and K. E. L. Smith},
  year={2007},
	title={Topobathymetric data for {T}ampa {B}ay, {F}lorida},
	number={Open-File Report 2007-1051 (revised)},
	institution={US Geological Survey, US Department of the Interior},
	address={St. Petersburg, Florida}
}

@misc{USDA11,
	author={{USDA (US Department of Agriculture)}},
	year={2011},
	title={{2008 National Agricultural Imagery Program}},
	note={{Aerial Photography Field Office, Farm Service Agency, United States Department of Agriculture}, Salt Lake City, Utah. \url{http://www.fsa.usda.gov/FSA/apfoapp?area=apfohome&subject=landing&topic=landing}. (Accessed January, 2010)}
}

@misc{USDOC11,
	author={{USDOC (US Department of Commerce)}},
	year={2011},
	title={{National Climatic Data Center}},
	note={\url{http://www.ncdc.noaa.gov/oa/ncdc.html}. (Accessed January, 2010)}
}

@techreport{USEPA98,
  author={{USEPA (US Environmental Protection Agency)}},
  year={1998},
	title={National strategy for the development of regional nutrient criteria},
	institution={Office of Water, Office of Research and Development, US Environmental Protection Agency},
	address={Washington, DC},
	number={EPA-822-R-98-002}
}

@techreport{USEPA98,
  author={{USEPA (US Environmental Protection Agency)}},
  year={1998},
	title={National strategy for the development of regional nutrient criteria},
	institution={Office of Water, Office of Research and Development, US Environmental Protection Agency},
	address={Washington, DC},
	number={EPA-822-R-98-002}
}

@techreport{USEPA00,
	author={{USEPA (US Environmental Protection Agency)}},
	year={2000},
	title={Stressor identification guidance document},
	institution={Office of Water, Office of Research and Development, US Environmental Protection Agency},
	address={Washington, DC},
	number={EPA-822-B-00-025}
}

@techreport{USEPA02,
	author={{USEPA (US Environmental Protection Agency)}},
	year={2002},
	title={Summary of biological assessment programs and biocriteria development for states, tribes, and interstate commissions: Streams and wadeable rivers},
	institution={Office of Environmental Information, Office of Water, US Environmental Protection Agency},
	address={Washington, DC},
	number={EPA-822-R-02-048}
}

@techreport{USEPA06,
  author={{USEPA (US Environmental Protection Agency)}},
  year={2006},
  title={Volunteer estuary monitoring: A methods manual, second edition},
  address={Washington, DC},
	number={EPA-842-B-06-003}
}

@techreport{USEPA10,
  author={{USEPA (US Environmental Protection Agency)}},
  year={2010},
  title={{C}hesapeake {B}ay phase 5.3 community watershed model},
  institution={US Environmental Protection Agency, Chesapeake Bay Program Office},
  address={Annapolis, MD},
	number={EPA903S10002 - CBP/TRS-303-10}
}

@misc{USGS15,
  author={{USGS (US Geological Survey)}},
	year={2015},
	title={{Water Quality Loads and Trends at Nontidal Monitoring Stations in the Chesapeake Bay Watershed}},
	note={\url{http://cbrim.er.usgs.gov/}. (Accessed November, 2015)}
}

@misc{USGS14,
  author={{USGS (US Geological Survey)}},
	year={2014},
	title={{National Hydrography Dataset available on the World Wide Web}},
	note={\url{https://nhd.usgs.gov}. (Accessed August, 2017)}
}

@book{Usinger56,
	author={J. L. Usinger},
	year={1956},
	title={Aquatic Insects of California: With Keys to North American Genera and California Species},
	publisher={University of California Press},
	address={Berkeley, California},
	pages={508},
	doi={10.5962/bhl.title.61952}
}

@article{Vadeboncoeur03,
	author={Y. Vadeboncoeur and E. Jeppesen and M. J. Vander Zanden and H. H. Schierup  and K. Christoffersen and D. M. Lodge},
	year={2003},
	title={From {G}reenland to green lakes: Cultural eutrophication and the loss of benthic pathways in lakes},
	journal={Limnology and Oceanography},
	number={48},
	issue={4},
	pages={1408-1418}
}

@techreport{Valley04,
	author={R. D. Valley and T. K. Cross and P. Radomski},
	year={2004},
	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},
	institution={Division of Fish and Wildlife, Minnesota Department of Natural Resources},
	address={St. Paul, Minnesota},
	number={Special Publication 160}
}

@article{Valley10,
  author={R. D. Valley and M. D. Habrat and E. D. Dibble and M. T. Drake},
	year={2010},
	title={Movement patterns and habitat use of three declining littoral fish species in a north-temperate mesotrophic lake},
	journal={Hydrobiologia},
	number={644},
	issue={1},
	pages={385-389}
}

@article{Valley12,
	author={R. D. Valley and S. Heiskary},
	year={2012},
	title={Short-term declines in curlyleaf pondweed in {M}innesota: Potential influences of snowfall},
	journal={Lake and Reservoir Management},
	volume={28},
	number={4},
	pages={338-345}
}

@techreport{Vaughn09,
	author={S. R. Vaughn},
	year={2009},
	title={{DNR} watershed delineation: Project history, methodology, terminology, and data attribution},
	institution={Division of Waters, Minnesota Department of Natural Resources},
	address={St. Paul, Minnesota},
	number={{D}raft}
}

@book{Venables02,
	title={Modern Applied Statistics with {S}},
	author={W. N. Venables and B. D. Ripley},
	publisher={Springer-Verlag},
	edition={Fourth},
	year={2002},
	address={New York, New York},
	url={http://www.stats.ox.ac.uk/pub/MASS4}
}

@article{Vestergaard00,
	author={O. Vestergaard and K. Sand-Jensen},
	year={2000},
	title={Aquatic macrophyte richness in {D}anish lakes in relation to alkalinity, transparency, and lake area},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={57},
	number={10},
	pages={2022-2031}
}

@article{Vondracek14,
	author={B. Vondracek and J. D. Koch and M. W. Beck},
	year={2014},
	title={A comparison of survey methods to evaluate macrophyte index of biotic integrity performance in {M}innesota lakes},
	journal={Ecological Indicators},
	volume={36},
	pages={178-185},
	doi={10.1016/j.ecolind.2013.07.002}
}

@article{Wade08,
	author={A. J. Wade and B. M. Jackson and D. Butterfield},
	year={2008},
	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},
	journal={Science of the Total Environment},
	volume={400},
	number={1-3},
	pages={52-74}
}

@incollection{Wagener01b,
	author={T. Wagener and M. J. Lees and H. S. Wheater},
	editor={V. P. Singh and D. K. Frevert S. P. Meyer},
	year={2001},
	title={A toolkit for the development and application of parsimonious hydrological models},
	booktitle={Mathematical Models of Small Watershed Hydrology and Applications - Volume 2},
	publisher={Water Resources Publications LLC},
	address={USA},
	pages={91-140}
}

@article{Wagener01,
	author={T. Wagener and D. P. Boyle and M. J. Lees and H. S. Wheater and H. V. Gupta and S. Sorooshian},
	year={2001},
	title={A framework for development and application of hydrological models},
	journal={Hydrology and Earth System Sciences},
	volume={5},
	number={1},
	pages={13-26}
}

@article{Wagner08,
  author={T. Wagner and P. A. Soranno and K. S. Cheruvelil and W. H. Renwick and K. E. Webster and P. Vaux and R. J. Abbitt},
	year={2008},
	title={Quantifying sample biases of inland lake sampling programs in relation to lake surface area and land use/cover},
	journal={Environmental Monitoring and Assessment},
	volume={141},
	number={1-3},
	pages={131-147}
}

@article{Wagner06,
	author={T. Wagner and A. K. Jubar and M. T. Bremigan},
	year={2006},
	title={Can habitat alteration and spring angling explain largemouth bass nest success?},
	journal={Transactions of the American Fisheries Society},
	volume={135},
	number={4},
	pages={843-852}
}

@article{Wan17,
	author={Y. Wan and L. Wan and Y. Li and P. Doering},
	year={2017},
	title={Decadal and seasonal trends of nutrient concentration and export from highly managed coastal catchments},
	journal={Water Research},
	volume={115},
	number={},
	pages={180-194}
}

@article{Wan10,
	author={H. Wan and C. J. Chizinski and C. L. Dolph and B. Vondracek and B. N. Wilson},
	year={2010},
	title={The impact of rare taxa  on a fish index of biotic integrity},
	journal={Ecological Indicators},
	volume={10},
	number={4},
	pages={781-788}
}

@article{Wang10,
	author={L. Z. Wang and K. Wehrly and J. E. Breck and L. S. Kraft},
	year={2010},
	title={Landscape-based assessment of human disturbance for {M}ichigan lakes},
	journal={Environmental Management},
	volume={46},
	number={3},
	pages={471-483}
} 

@article{Wang99,
	author={P. F. Wang and J. Martin and G. Morrison},
	year={1999},
	title={Water quality and eutrophication in {T}ampa {B}ay, {F}lorida},
	journal={Estuarine, Coastal and Shelf Science},
	volume={49},
	number={1},
	pages={1-20}
}

@article{Ward13,
	author={B. A. Ward and M. Schartau and A. Oschlies and A. P. Martin and M. J. Follows and T. R. Anderson},
	year={2013},
	title={When is a biogeochemical model too complex? Objective model reduction and selection for {N}orth {A}tlantic time-series sites},
	journal={Progress in Oceanography},
	volume={116},
	number={},
	pages={49-65}
}

@book{Warner09,
	author={T. A. Warner and M. D. Nellis and G. M. Foody},
	year={2009},
	title={The {SAGE} Handbook of Remote Sensing},
	publisher={{SAGE Publications}},
	address={Thousand Oaks, California}
}

@article{Warner05,
	author={J. C. Warner and W. R. Geyer and J. A. Lerczak},
	year={2005},
	title={Numerical modeling of an estuary: a comprehensive skill assessment},
	journal={Journal of Geophysical Research: Oceans},
	volume={110},
	number={C5},
	pages={13}
}

@techreport{Warren79,
	author={C. E. Warren},
	year={1979},
	title={Toward classification and rationale for watershed management and stream protection},
	number={EPA 600/3-79-059},
	institution={Corvallis Environmental Research Laboratory, U.S Environmental Protection Agency},
	address={Corvallis, Oregon}
}

@article{Wehrly12,
	author={K. E. Wehrly and J. E. Breck and L. Wang and L. Szabo-Kraft},
	year={2012},
	title={Assessing local and landscape patterns of residential shoreline development in {M}ichigan lakes},
	journal={Lake and Reservoir Management},
	volume={28},
	number={2},
	pages={158-169}
}

@techreport{Wenner01,
  author={E. L. Wenner and A. F. Holland and M. D. Arendt and Y. Chen and D. Edwards and C. Miller and M. Meece and J. Caffrey},
  year={2001},
  title={A synthesis of water quality data from the National Estuarine Research Reserve's System-Wide Monitoring Program},
	institution={MRD Contribution No. 459. The Cooperative Institute for Coastal and Estuarine Environmental Technology. NOAA Grant Number: NA97OR0209.},
	address={Charleston, South Carolina},
	pages={276}
}

@article{Wenner04,
  author={E. Wenner and D. Sanger and M. Arendt and A. F. Holland and Y. Chen},
	year={2004},
	title={Variability in dissolved oxygen and other water-quality variables within the {N}ational {E}stuarine {R}esearch {R}eserve {S}ystem},
	journal={Journal of Coastal Research},
	volume={45},
	number={SI},
	pages={17-38}
}

@article{Werner93,
  author={I. Werner and J. T. Hollibaugh},
	year={1993},
	title={\textit{{P}otamocorbula amurensis} - comparison of clearance rates and assimilation efficiencies for phytoplankton and bacterioplankton},
	journal={Limnology and Oceanography},
	volume={38},
	number={5},
	pages={949-964}
}

@book{Wetzel01,
	author={R. G. Wetzel},
	year={2001},
	title={Limnology: Lake and River Ecosystems},
	publisher={Academic Press},
	address={San Diego, California},
	pages={1006}
}

@article{Wheater86,
	author={H. S. Wheater and K. H. Bishop and M. B. Beck},
	year={1986},
	title={The identification of conceptual hydrological models for surface water acidification},
	journal={Hydrological Processes},
	volume={1},
	number={1},
	pages={89-109}
}

@article{Whittier07,
	author={T. R. Whittier and R. M. Hughes and J. L. Stoddard and G. A. Lomnicky and D. V. Peck and A. T. Herlihy},
	year={2007},
	title={A structured approach for developing indices of biotic integrity: {T}hree examples from streams and rivers in the {W}estern {USA}},
	journal={Transactions of the American Fisheries Society},
	volume={136},
	number={3},
	pages={718-735}
}

@incollection{Whittier99,
	author={T. R. Whittier},
	editor={T. P. Simon},
	year={1999},
	title={Development of {IBI} metrics for lakes in southern {N}ew {E}ngland},
	booktitle={Assessing the Sustainability and Biological Integrity of Water Resources Using Fish Communities},
	publisher={CRC Press},
	address={Boca Raton, Florida},
	pages={563-582}
}

@article{Whittier88,
	author={T. R. Whittier and R. M. Hughes and D. P. Larsen},
	year={1988},
	title={Correspondence between ecoregions and spatial patterns in stream ecosystems in {O}regon},
	journal={Canadian Journal of Fisheries and Aquatic Sciences},
	volume={45},
	number={7},
	pages={1264-1278}
}

@manual{Wickham14b,
  title = {nycflights13: Data about flights departing NYC in 2013.},
  author = {H. Wickham},
  year = {2014},
  note = {R package version 0.1},
  url = {http://CRAN.R-project.org/package=nycflights13},
}

@book{Wickham14,
  author={H. Wickham},
	year={2014},
	title={Advanced R},
	publisher={Chapman and Hall, CRC Press},
	address={Boca Raton, Florida},
	pages={476}
}

@book{Wickham09,
  author={Hadley Wickham},
  title={ggplot2: Elegant Graphics for Data Analysis},
  publisher={Springer-Verlag. New York},
  year={2009},
  isbn={978-0-387-98140-6},
  url={http://had.co.nz/ggplot2/book},
}

@article{Wilcox92,
	author={D. A. Wilcox and J. E. Meeker},
	year={1992},
	title={Implications for Faunal Habitat Related to Altered Macrophyte Structure in Regulated Lakes in Northern {M}innesota},
	journal={Wetlands},
	volume={12},
	number={3},
	pages={192-203}
}

@incollection{Williams01,
  author={S. L. Williams and K. L. Heck},
  editor={M. D. Bertness and S. D. Gaines and M. E. Hay},
  year={2001},
  title={Seagrass community ecology},
	booktitle={Marine Community Ecology},
	publisher={Sinauer Associates},
	address={Sunderland, Massachusetts}
}

@article{Wilson13,
  author={M. Wilson and S. D. Meyers and M. E. Luther},
	year={2013},
	title={Synoptic volumetric variations and flushing of the {T}ampa {B}ay estuary},
	journal={Climate Dynamics},
	volume={},
	number={},
	pages={}
}

@article{Winder10,
  author={M. Winder and J. E. Cloern},
	year={2010},
	title={The annual cycles of phytoplankton biomass},
	journal={Philosophical Transactions of the Royal Society B-Biological Sciences},
	volume={365},
	number={1555},
	pages={3215-3226}
}

@article{Winter01,
	author={T. C. Winter},
	year={2001},
	title={The concept of hydrologic landscapes},
	journal={Journal of the American Water Resources Association},
	volume={37},
	number={2},
	pages={335-349}
}

@article{Wiseman97,
	author={W. J. Wiseman and N. N. Rabalais and R. E. Turner and S. P. Dinnel and A. MacNaughton},
	year={1997},
	title={Seasonal and interannual variability within the {L}ouisiana coastal current: stratification and hypoxia},
	journal={Journal of Marine Systems},
	volume={12},
	number={1-4},
	pages={237-248}
}

@article{Wofsy83,
  author={S. C. Wofsy},
	year={1983},
	title={A simple model to predict extinction coefficients and phytoplankton biomass in eutrophic waters},
	journal={Limnology and Oceanography},
	volume={28},
	number={6},
	pages={1144-1155}
}

@article{Wood06b,
  author={S. N. Wood},
	year={2006},
	title={Low-rank scale-invariant tensor product smooths for generalized additive mixed models},
	journal={Biometrics},
	volume={62},
	number={4},
	pages={1025-1036}
}

@book{Wood06,
	author={S. N. Wood},
	year={2006},
	title={Generalized Additive Models: An Introduction with R},
	publisher={Chapman and Hall, CRC Press},
	address={London, United Kingdom},
	pages={410}
}

@article{Woodruff99,
  author={D. L. Woodruff and R. P. Stumpf and J. A. Scope and H. W. Paerl},
  year={1999},
	title={Remote estimation of water clarity in optically complex estuarine waters},
	journal={Remote Sensing of Environment},
	volume={68},
	number={1},
	pages={41-52}
}

@incollection{Wooten85,
  author={G. R. Wooten},
  editor={S. F. Treat and J. L. Simon and R. R. Lewis and R. L. Whitman},
	year={1985},
	title={The meteorology of {T}ampa {B}ay},
	booktitle={Proceedings of the Tampa Bay Area Scientific Information Symposium},
	publisher={Florida Sea Grant Report No. 65, Bellwether Press},
	address={Tampa, Florida, USA},
	pages={19-26}
}

@article{Wright04,
	author={S. A. Wright and D. H. Schoellhamer},
	year={2004},
	title={Trends in the sediment yield of the {S}acramento {R}iver, {C}alifornia, 1957-2001},
	journal={San Francisco Estuary and Watershed Science},
	volume={2},
	number={2},
	pages={1-14}
}

@article{Wu12,
	author={N. Wu and B. Schmalz and N. Fohrer},
	year={2012},
	title={Development and testing of a phytoplankton index of biotic integrity ({P-IBI}) for a {G}erman lowland river},
	journal={Ecological Indicators},
	volume={13},
	number={1},
	pages={158-167}
}

@article{Xian07,
  author={G. Xian and M. Crane and J. Su},
	year={2007},
	title={An analysis of urban development and its environmental impact on the {T}ampa {B}ay watershed},
	journal={Environmental Management},
	volume={85},
	number={4},
	pages={965-976}
}

@article{Ye97,
  author={W. Ye and B. C. Bates and N. R. Viney and M. Sivapalan and A. J. Jakeman},
  year={1997}, 
  title={Performance of conceptual rainfall-runoff models in low yielding ephemeral catchments},
  journal={Water Resources Research},
  volume={33},
  number={1},
  pages={153-166}
}

@article{Yin04,
  author={K. D. Yin and Z. F. Lin and Z. Y. Ke},
  year={2004}, 
  title={Temporal and spatial distribution of dissolved oxygen in the {P}earl {R}iver {E}stuary and adjacent coastal waters},
  journal={Continental Shelf Research},
  volume={24},
  number={16},
  pages={1935-1948}
}

@article{Young11,
  author={W. A. Young and D. F. Millie and G. R. Weckman and J. S. Anderson and D. M. Klarer and G. L. Fahnenstiel},
	year={2011},
	title={Modeling net ecosystem metabolism with an artificial neural network and {B}ayesian belief network},
	journal={Environmental Modelling and Software},
	volume={26},
	number={10},
	pages={1199-1210}
}

@article{Yvon12,
  author={G. Yvon-Durocher and J. M. Caffrey and A. Cescatti and M. Dossena and P. del Giorgio and J. M. Gasol and J. M. Montoya and J. Pumpanen and P. A. Staehr and M. Trimmer and G. Woodward and A. P. Allen},
	year={2012},
	title={Reconciling the temperature dependence of respiration across timescales and ecosystem types},
	journal={Nature},
	volume={487},
	number={7408},
	pages={472-476}
}

@techreport{Zarbock94,
  author={H. Zarbock and A. Janicki and D. Wade and D. Heimbuch and H. Wilson},
	year={1994},
	title={Estimates of total nitrogen, total phosphorus, and total suspended solids loadings ot {T}ampa {B}ay, {F}lorida},
	institution={Prepared for the Tampa Bay National Estuary Program},
	address={St. Petersburg, Florida, USA},
	number={No. 04-94}
}

@manual{Zell98,
  title = {{SNNS}: Stuttgart Neural Network Simulator, User Manual, Version 4.2},
  author = {A. Zell and G. Mamier and M. Vogt and N. Mache and R. H\"{u}bner and S. D\"{o}ring and K. U. Herrmann and T. Soyez and M. Schmalzl and T. Sommer and A. Hatzigeorgiou and D. Posselt and T. Schreiner and B. Kett and G. Clemente and J. Wieland and J. Gatter},
  year = {1998},
  note = {University of Stuttgart and WSI, University of T\"{u}bingen},
  url = {http://www.ra.cs.uni-tuebingen.de/SNNS/},
}

@article{Zhang16,
	author={Q. Zhang and C. J. Harman and W. P. Ball},
	year={2016},
	title={An improved method for interpretation of riverine concentration-discharge relationships indicates long-term shifts in reservoir sediment trapping},
	journal={Geophysical Research Letters},
	volume={43},
	number={10},
	pages={215-224}
}

@article{Zhang15,
  author={Q. Zhang and D. C. Brady and W. R. Boynton and W. P. Ball},
	year={2015},
	title={Long-term trends of nutrients and sediment from the nontidal {C}hesapeake watershed: An assessment of progress by river and season},
	journal={Journal of the American Water Resources Association},
	volume={51},
	number={6},
	pages={1534-1555}
}

@article{Zhang13,
  author={Q. Zhang and D. C. Brady and W. P. Ball},
	year={2013},
	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},
	journal={Science of the Total Environment},
	volume={452-453},
	number={},
	pages={208-221}
}

@article{Zhao10,
  author={L. Zhao and C. Chen and J. Vallino and C. Hopkinson and R. C. Beardsley and H. Lin and J. Lerczak},
	year={2010},
	title={Wetland-estuarine-shelf interactions on the {P}lum {I}sland {S}ound and {M}errimack {R}iver in the {M}assachusetts coast},
	journal={Journal of Geophysical Research},
	volume={115},
	number={C10},
	pages={13}
}

@article{Zhu07,
	author={B. Zhu and D. G. Fitzgerald and S. B. Hoskins and L. G. Rudstam and C. M. Mayer and E. L. Mills},
	year={2007},
	title={Quantification of historical changes of submerged aquatic vegetation cover in two bays of {L}ake {O}ntario with three complementary methods},
	journal={Journal of Great Lakes Research},
	volume={33},
	number={1},
	pages={122-135}
}

@article{Ziegler98,
  author={S. Ziegler and R. Benner},
	year={1998},
	title={Ecosystem metabolism in a subtropical, seagrass-dominated lagoon},
	journal={Marine Ecology Progress Series},
	volume={173},
	number={},
	pages={1-12}
}

@book{Zumberge52,
	author={J. H. Zumberge},
	year={1952},
	title={The Lakes of {M}innesota: Their Origin and Classification},
	publisher={Bulletin 35, University of Minnesota Geological Survey, The University of Minnesota Press},
	address={Minneapolis, Minnesota}
}

@book{Zuur07,
	author={A. F. Zuur and E. N. Ieno and G. M. Smith},
	year={2007},
	title={Analysing Ecological Data},
	publisher={Springer-Verlag},
	address={New York, New York},
	pages={672}
}

@book{Zuur09,
	author={A. F. Zuur and E. N. Ieno and N. J. Walker and A. A. Saveliev and G. M. Smith},
	year={2009},
	title={Mixed Effects Models and Extensions in Ecology with R},
	publisher={Springer-Verlag},
	address={New York, New York},
	pages={574}
}

@book{Zuur09R,
	author={A. F. Zuur and E. N. Ieno and E. Meesters},
	year={2009},
	title={A Beginner's Guide to R (Use R!)},
	publisher={Springer-Verlag},
	address={New York, London},
	pages={236}
}

@article{Zuur10,
	author={A. F. Zuur and E. N. Ieno and C. S. Elphick},
	year={2010},
	title={A protocol for data exploration to avoid common statistical problems},
	journal={Methods in Ecology and Evolution},
	volume={1},
	number={1},
	pages={3-14}
}

@book{Zuur12,
	author={A. F. Zuur},
	year={2012},
	title={A Beginner's Guide to Generalized Additive Models in R},
	publisher={Highland Statistics Ltd.},
	address={Newburgh, United Kingdom},
	pages={184}
}