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| Original file line number | Diff line number | Diff line change |
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| @article{Anderson1997, | ||
| author = {Anderson, Donald M.}, | ||
| title = {Bloom dynamics of toxic Alexandrium species in the northeastern U.S}, | ||
| journal = {Limnology and Oceanography}, | ||
| volume = {42}, | ||
| number = {5part2}, | ||
| pages = {1009-1022}, | ||
| doi = {https://doi.org/10.4319/lo.1997.42.5\_part\_2.1009}, | ||
| url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.1997.42.5_part_2.1009}, | ||
| eprint = {https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1997.42.5_part_2.1009}, | ||
| year = {1997} | ||
| } | ||
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| @article{Anderson2005, | ||
| title = {Identification and enumeration of Alexandrium spp. from the Gulf of Maine using molecular probes}, | ||
| journal = {Deep Sea Research Part II: Topical Studies in Oceanography}, | ||
| volume = {52}, | ||
| number = {19}, | ||
| pages = {2467-2490}, | ||
| year = {2005}, | ||
| note = {The Ecology and Oceanography of Toxic Alexandrium fundyense Blooms in the Gulf of Maine}, | ||
| issn = {0967-0645}, | ||
| doi = {https://doi.org/10.1016/j.dsr2.2005.06.015}, | ||
| url = {https://www.sciencedirect.com/science/article/pii/S0967064505001621}, | ||
| author = {Donald M. Anderson and David M. Kulis and Bruce A. Keafer and Kristin E. Gribble and Roman Marin and Christopher A. Scholin} | ||
| } | ||
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| @article{Li2009, | ||
| title = {Investigation of the 2006 Alexandrium fundyense bloom in the Gulf of Maine: In-situ observations and numerical modeling}, | ||
| journal = {Continental Shelf Research}, | ||
| volume = {29}, | ||
| number = {17}, | ||
| pages = {2069-2082}, | ||
| year = {2009}, | ||
| issn = {0278-4343}, | ||
| doi = {https://doi.org/10.1016/j.csr.2009.07.012}, | ||
| url = {https://www.sciencedirect.com/science/article/pii/S0278434309002301}, | ||
| author = {Yizhen Li and Ruoying He and Dennis J. McGillicuddy and Donald M. Anderson and Bruce A. Keafer}, | ||
| keywords = {Harmful algal bloom, Coastal circulation, Gulf of Maine, Bio-physical interaction} | ||
| } | ||
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| @article{Li2020, | ||
| title = {Dynamics of an intense Alexandrium catenella red tide in the Gulf of Maine: satellite observations and numerical modeling}, | ||
| journal = {Harmful Algae}, | ||
| volume = {99}, | ||
| pages = {101927}, | ||
| year = {2020}, | ||
| issn = {1568-9883}, | ||
| doi = {https://doi.org/10.1016/j.hal.2020.101927}, | ||
| url = {https://www.sciencedirect.com/science/article/pii/S1568988320302067}, | ||
| author = {Yizhen Li and Richard P. Stumpf and D.J. McGillicuddy and Ruoying He} | ||
| } | ||
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| @article{McGillicuddy2011, | ||
| author = {McGillicuddy, D. J., Jr. and Townsend, D. W. and He, R. and Keafer, B. A. and Kleindinst, J. L. and Li, Y. and Manning, J. P. and Mountain, D. G. and Thomas, M. A. and Anderson, D. M.}, | ||
| title = {Suppression of the 2010 Alexandrium fundyense bloom by changes in physical, biological, and chemical properties of the Gulf of Maine}, | ||
| journal = {Limnology and Oceanography}, | ||
| volume = {56}, | ||
| number = {6}, | ||
| pages = {2411-2426}, | ||
| doi = {https://doi.org/10.4319/lo.2011.56.6.2411}, | ||
| url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2011.56.6.2411}, | ||
| eprint = {https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2011.56.6.2411}, | ||
| year = {2011} | ||
| } | ||
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| @inproceedings{Chung2010, | ||
| title={Measuring paralytic shellfish toxins in mussels from New Hampshire coastal waters using zwitterionic hydrophilic liquid chromatography/electrospray mass spectrometry}, | ||
| author={Lee Lee Chung}, | ||
| year={2010}, | ||
| url={https://scholars.unh.edu/thesis/539} | ||
| } | ||
|
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| @article{Kleindinst2014, | ||
| author = {Kleindinst, Judith L. and Anderson, Donald M. and McGillicuddy, Dennis J. and Stumpf, Richard P. and Fisher, Kathleen M. and Couture, Darcie A. and Michael Hickey, J. and Nash, Christopher}, | ||
| title = {Categorizing the severity of paralytic shellfish poisoning outbreaks in the Gulf of Maine for forecasting and management}, | ||
| journal = {Deep Sea Research Part II: Topical Studies in Oceanography}, | ||
| year = 2014, | ||
| month = may, | ||
| volume = {103}, | ||
| pages = {277-287}, | ||
| doi = {10.1016/j.dsr2.2013.03.027}, | ||
| adsurl = {https://ui.adsabs.harvard.edu/abs/2014DSRII.103..277K}, | ||
| adsnote = {Provided by the SAO/NASA Astrophysics Data System} | ||
| } |
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| @article{Silva2020, | ||
| doi = {10.1111/csp2.274}, | ||
| url = {https://doi.org/10.1111%2Fcsp2.274}, | ||
| year = 2020, | ||
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| publisher = {Wiley}, | ||
| volume = {3}, | ||
| number = {2}, | ||
| author = {Tammy L. Silva and David N. Wiley and Michael A. Thompson and Peter Hong and Les Kaufman and Justin J. Suca and Joel K. Llopiz and Hannes Baumann and Gavin Fay}, | ||
| title = {High collocation of sand lance and protected top predators: Implications for conservation and management}, | ||
| journal = {Conservation Science and Practice} | ||
| } |
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| # Annual SST Cycles | ||
|
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||
| **Description**: Annual SST Cycles | ||
|
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| **Found in**: State of the Ecosystem - Gulf of Maine & Georges Bank (2018), State of the Ecosystem - Mid-Atlantic (2018) | ||
|
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| **Indicator category**: Database pull with analysis | ||
|
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| **Contributor(s)**: Sean Hardison, Vincent Saba | ||
|
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| **Data steward**: Kimberly Bastille, <[email protected]> | ||
|
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| **Point of contact**: Kimberly Bastille, <[email protected]> | ||
|
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| **Public availability statement**: Source data are available [here](https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.highres.html). | ||
|
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| ## Methods | ||
|
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| ### Data sources | ||
| Data for annual sea surface tempature (SST) cycles were derived from the NOAA optimum interpolation sea surface temperature (OISST) high resolution dataset ([NOAA OISST V2 dataset](https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.highres.html)) provided by NOAA's Earth System Research Laboratory's Physical Sciences Devision, Boulder, CO. The data extend from 1981 to present, and provide a 0.25° x 0.25° global grid of SST measurements [@Reynolds2007]. Gridded SST data were masked according to the extent of Ecological Production Units (EPU) in the Northeast Large Marine Ecosystem (NE-LME) (See ["EPU_Extended" shapefiles](https://github.com/NOAA-EDAB/tech-doc/tree/master/gis)). | ||
|
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||
|
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| ### Data extraction | ||
| Daily mean sea surface temperature data for 2017 and for each year during the period of 1981-2012 were downloaded from the NOAA [OI SST V2 site](https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.highres.html) to derive the long-term climatological mean for the period. The use of a 30-year climatological reference period is a standard procedure for metereological observing [@WMO2017]. These reference periods serve as benchmarks for comparing current or recent observations, and for the development of standard anomaly data sets. The reference period of 1982-2012 was chosen to be consistent with previous versions of the State of the Ecosystem report. | ||
|
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| R code used in extraction and processing can be found [here](https://github.com/NOAA-EDAB/tech-doc/blob/master/R/stored_scripts/annual_sst_cycles_extraction_and_processing.R) | ||
|
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|
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| ### Data analysis | ||
| We calculated the long-term mean and standard deviation of SST over the period of 1982-2012 for each EPU, as well as the daily mean for 2017. | ||
|
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| R code used for analysis and plotting can be found [here](https://github.com/NOAA-EDAB/tech-doc/blob/master/R/stored_scripts/annual_sst_cycles_analysis_and_plotting.R) | ||
|
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| ```{r , fig.width=5, fig.asp = 0.45, fig.cap = "Long-term mean SSTs for the Mid-Atlantic Bight (A), Georges Bank (B), and Gulf of Maine (C). Orange and cyan shading show where the 2017 daily SST values were above or below the long-term mean respectively; red and dark blue shades indicate days when the 2017 mean exceeded +/- 1 standard deviation from the long-term mean.", echo = F, fig.align="center", eval=T } | ||
| knitr::include_graphics(file.path(image.dir, "annual_SST_cycle_plot.png")) | ||
| # Annual SST Cycles | ||
|
|
||
| **Description**: Annual SST Cycles | ||
|
|
||
| **Found in**: State of the Ecosystem - Gulf of Maine & Georges Bank (2018), State of the Ecosystem - Mid-Atlantic (2018) | ||
|
|
||
| **Indicator category**: Database pull with analysis | ||
|
|
||
| **Contributor(s)**: Sean Hardison, Vincent Saba | ||
|
|
||
| **Data steward**: Kimberly Bastille, <[email protected]> | ||
|
|
||
| **Point of contact**: Kimberly Bastille, <[email protected]> | ||
|
|
||
| **Public availability statement**: Source data are available [here](https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.highres.html). | ||
|
|
||
| ## Methods | ||
|
|
||
| ### Data sources | ||
| Data for annual sea surface tempature (SST) cycles were derived from the NOAA optimum interpolation sea surface temperature (OISST) high resolution dataset ([NOAA OISST V2 dataset](https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.highres.html)) provided by NOAA's Earth System Research Laboratory's Physical Sciences Devision, Boulder, CO. The data extend from 1981 to present, and provide a 0.25° x 0.25° global grid of SST measurements [@Reynolds2007]. Gridded SST data were masked according to the extent of Ecological Production Units (EPU) in the Northeast Large Marine Ecosystem (NE-LME) (See ["EPU_Extended" shapefiles](https://github.com/NOAA-EDAB/tech-doc/tree/master/gis)). | ||
|
|
||
|
|
||
| ### Data extraction | ||
| Daily mean sea surface temperature data for 2017 and for each year during the period of 1981-2012 were downloaded from the NOAA [OI SST V2 site](https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.highres.html) to derive the long-term climatological mean for the period. The use of a 30-year climatological reference period is a standard procedure for metereological observing [@WMO2017]. These reference periods serve as benchmarks for comparing current or recent observations, and for the development of standard anomaly data sets. The reference period of 1982-2012 was chosen to be consistent with previous versions of the State of the Ecosystem report. | ||
|
|
||
| R code used in extraction and processing can be found [here](https://github.com/NOAA-EDAB/tech-doc/blob/master/R/stored_scripts/annual_sst_cycles_extraction_and_processing.R) | ||
|
|
||
|
|
||
| ### Data analysis | ||
| We calculated the long-term mean and standard deviation of SST over the period of 1982-2012 for each EPU, as well as the daily mean for 2017. | ||
|
|
||
| R code used for analysis and plotting can be found [here](https://github.com/NOAA-EDAB/tech-doc/blob/master/R/stored_scripts/annual_sst_cycles_analysis_and_plotting.R) | ||
|
|
||
| ```{r , out.width="80%", fig.asp = 0.45, fig.cap = "Long-term mean SSTs for the Mid-Atlantic Bight (A), Georges Bank (B), and Gulf of Maine (C). Orange and cyan shading show where the 2017 daily SST values were above or below the long-term mean respectively; red and dark blue shades indicate days when the 2017 mean exceeded +/- 1 standard deviation from the long-term mean.", echo = F, fig.align="center", eval=T } | ||
| knitr::include_graphics(file.path(image.dir, "annual_SST_cycle_plot.png")) | ||
| ``` |
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