Added a working document for the WGSAM report

vignettes/.gitignore

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+*.html
+*.R

vignettes/WGSAM/GBRpathBib.bib

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+@techreport{aydin_alaska_2007,
+	type = {{US} {Department} of {Commerce}, {NOAA} {Technical} {Memo}},
+	title = {A comparison of the {Bering} {Sea}, {Gulf} of {Alaska}, and {Aleutian} {Islands} large marine ecosystems through food web modeling},
+	number = {NMFS-AFSC-178},
+	author = {Aydin, KY and Gaichas, S. and Ortiz, I and Kinzey, D and Friday, N},
+	year = {2007},
+	pages = {298}
+}
+
+@techreport{buchheister_NWACS_2017,
+	type = {University of {Maryland} {Center} for {Environmental} {Sciences}  {Report}},
+	title = {Technical {Documentation} of the {Northwest} {Atlantic} {Continental} {Shelf} ({NWACS}) {Ecosystem} {Model}. {Report} to the {Lenfest} {Ocean} {Program}, {Washington}, {D}.{C}},
+	number = {TS -694 -17},
+	author = {Buchheister, Andre and Miller, Thomas J and Houde, Edward D and Loewensteiner, David A},
+	month = apr,
+	year = {2017},
+	pages = {58},
+}
+
+@article{colleter_ecobase_2015,
+	title = {Global overview of the applications of the {Ecopath} with {Ecosim} modeling approach using the {EcoBase} models repository},
+	volume = {302},
+	issn = {0304-3800},
+	url = {http://www.sciencedirect.com/science/article/pii/S0304380015000447},
+	doi = {10.1016/j.ecolmodel.2015.01.025},
+	urldate = {2019-08-06},
+	journal = {Ecological Modelling},
+	author = {Colléter, Mathieu and Valls, Audrey and Guitton, Jérôme and Gascuel, Didier and Pauly, Daniel and Christensen, Villy},
+	month = apr,
+	year = {2015},
+	pages = {42--53},
+}
+
+@article{christensen_ecopath_1992,
+	title = {{ECOPATH} {II} - a software for balancing steady-state ecosystem models and calculating network characteristics},
+	volume = {61},
+	journal = {Ecological Modelling},
+	author = {Christensen, Villy and Pauly, Daniel},
+	year = {1992},
+	pages = {169--185}
+}
+
+@article{christensen_ecopath_2004,
+	series = {Placing {Fisheries} in their {Ecosystem} {Context}},
+	title = {Ecopath with {Ecosim}: methods, capabilities and limitations},
+	volume = {172},
+	issn = {0304-3800},
+	doi = {10.1016/j.ecolmodel.2003.09.003},
+	number = {2–4},
+	urldate = {2016-02-02},
+	journal = {Ecological Modelling},
+	author = {Christensen, Villy and Walters, Carl J},
+	month = mar,
+	year = {2004},
+	pages = {109--139},
+}
+
+@article{fulton_complexity_2003,
+	title = {Effect of complexity on marine ecosystem models},
+	volume = {253},
+	issn = {0171-8630},
+	url = {://000183487200001},
+	journal = {Marine Ecology-Progress Series},
+	author = {Fulton, E. A. and Smith, A. D. M. and Johnson, C. R.},
+	year = {2003},
+	pages = {1--16}
+}
+
+@article{fulton_EBFM_MSE_2014,
+	title = {An {Integrated} {Approach} {Is} {Needed} for {Ecosystem} {Based} {Fisheries} {Management}: {Insights} from {Ecosystem}-{Level} {Management} {Strategy} {Evaluation}},
+	volume = {9},
+	issn = {1932-6203},
+	shorttitle = {An {Integrated} {Approach} {Is} {Needed} for {Ecosystem} {Based} {Fisheries} {Management}},
+	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084242},
+	doi = {10.1371/journal.pone.0084242},
+	number = {1},
+	urldate = {2019-06-28},
+	journal = {PLOS ONE},
+	author = {Fulton, Elizabeth A. and Smith, Anthony D. M. and Smith, David C. and Johnson, Penelope},
+	month = jan,
+	year = {2014},
+	pages = {e84242},
+}
+
+@article{gaichas_beer_2015,
+	title = {Wasp waist or beer belly? {Modeling} food web structure and energetic control in {Alaskan} marine ecosystems, with implications for fishing and environmental forcing},
+	volume = {138},
+	issn = {0079-6611},
+	shorttitle = {Wasp waist or beer belly?},
+	doi = {10.1016/j.pocean.2015.09.010},
+	journal = {Progress in Oceanography},
+	author = {Gaichas, Sarah and Aydin, Kerim and Francis, Robert C.},
+	month = nov,
+	year = {2015},
+	pages = {1--17}
+}
+
+@article{goethel_stakeholders_2018,
+	title = {Closing the feedback loop: on stakeholder participation in management strategy evaluation},
+	issn = {0706-652X, 1205-7533},
+	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfas-2018-0162},
+	doi = {10.1139/cjfas-2018-0162},
+	urldate = {2019-08-07},
+	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
+	author = {Goethel, Daniel R. and Lucey, Sean M. and Berger, Aaron M. and Gaichas, Sarah K. and Karp, Melissa A. and Lynch, Patrick D. and Walter, John F. and Deroba, Jonathan J. and Miller, Shana and Wilberg, Michael J.},
+	month = dec,
+	year = {2018},
+	pages = {1--19},
+}
+
+@techreport{ices_WGSAM_2016,
+	type = {{ICES} {CM}},
+	title = {Report of the {Working} {Group} on {Multispecies} {Assessment} {Methods} ({WGSAM}),  9–13 {November} 2015, {Woods} {Hole}, {USA}.},
+	number = {2015/SSGEPI:20},
+	author = {ICES},
+	year = {2016},
+	pages = {206}
+}
+
+@misc{link_EMAX_2006,
+	title = {Documentation for the {Energy} {Modeling} and {Analysis} {eXercise} ({EMAX})},
+	publisher = {US Department of Commerce},
+	author = {Link, Jason S. and Griswold, Carolyn A. and Methratta, Elizabeth T. and Gunnard, Jessie},
+	year = {2006}
+}
+
+@online{fishbase,
+	title = {FishBase},
+	url = {https://www.fishbase.org},
+	urldate = {2019-08-06},
+	author = {{FishBase}},
+	month = August,
+	year = {2019}
+}
+
+@online{garfo_small_mesh_nodate,
+	title = {Northeast ({NE}) multispecies small  mesh fishery exemptions},
+	url = {https://www.greateratlantic.fisheries.noaa.gov/regs/infodocs/small_mesh_exemption.pdf},
+	urldate = {2019-08-06},
+	author = {{GARFO}},
+	month = August,
+	year = {2019}
+}
+
+@techreport{jacobson_clams_2019,
+	type = {Northeast {Fisheries} {Science} {Center} {Reference} {Document}},
+	title = {Improving the {NEFSC} {Clam} {Survey} for {Atlantic} {Surfclams} and {Ocean} {Quahogs}},
+	number = {19-06},
+	author = {Jacobson, Larry and Hennen, Daniel},
+	year = {2019}
+}
+
+@techreport{link_food_habits_2000,
+	type = {{NOAA} {Technical} {Memorandum}},
+	title = {An {Overview} and {History} of the {Food} {Web} {Dynamics} {Program} of the {Northeast} {Fisheries} {Science} {Center}, {Woods} {Hole}, {Massachusetts}},
+	number = {NMFS-NE-159},
+	author = {Link, J. S. and Almeida, F. P.},
+	year = {2000},
+}
+
+@article{link_gom_2008,
+title = {Response of balanced network models to large-scale perturbation: Implications for evaluating the role of small pelagics in the Gulf of Maine},
+journal = {Ecological Modelling},
+volume = {220},
+number = {3},
+pages = {351-369},
+year = {2009},
+issn = {0304-3800},
+doi = {https://doi.org/10.1016/j.ecolmodel.2008.10.009},
+url = {https://www.sciencedirect.com/science/article/pii/S0304380008004973},
+author = {Jason Link and Laurel Col and Vincent Guida and David Dow and John O’Reilly and Jack Green and William Overholtz and Debra Palka and Chris Legault and Joseph Vitaliano and Carolyn Griswold and Michael Fogarty and Kevin Friedland},
+}
+
+@article{link_prebal_2010,
+	title = {Adding rigor to ecological network models by evaluating a set of pre-balance diagnostics: {A} plea for {PREBAL}},
+	volume = {221},
+	issn = {0304-3800},
+	doi = {10.1016/j.ecolmodel.2010.03.012},
+	number = {12},
+	urldate = {2019-06-07},
+	journal = {Ecological Modelling},
+	author = {Link, Jason S.},
+	month = jun,
+	year = {2010},
+	pages = {1580--1591},
+}
+
+@article{lucey_rpath_2020,
+	author = {Lucey, SM and Gaichas, SK and Aydin, KY},
+	title = {Conducting reproducible ecosystem modeling using the open source mass balance model Rpath},
+	journal = {Ecological Modelling},
+	volume = {427},
+    doi = {10.1016/j.ecolmodel.2020.109057},
+	year = {2020}
+}
+
+@article{lucey_mse_2021,
+    author = {Lucey, SM and Aydin, KY and Gaichas, SK and Cadrin, SX and Fay, G and Fogarty, MJ and Punt, A},
+    title = {Evaluating fishery management strategies using an ecosystem model as an operating model},
+    journal = {Fisheries Research},
+    year = {2021},
+    volume = {234},
+    doi = {https://doi.org/10.1016/j.fishres.2020.105780}
+}
+
+@techreport{nefsc_SAW_2007,
+	type = {Northeast {Fisheries} {Science} {Center} {Reference} {Document}},
+	title = {44th {SAW} {Assessment} {Summary} {Report}},
+	number = {07-03},
+	author = {NEFSC},
+	year = {2007},
+	pages = {58}
+}
+
+@techreport{nefsc_scallop_2018,
+	type = {Northeast {Fisheries} {Science} {Center} {Reference} {Document}},
+	title = {65th {Northeast} {Regional} {Stock} {Assessment} {Workshop} (65th {SAW}) {Assessment} {Report}},
+	number = {18-11},
+	author = {NEFSC},
+	year = {2018},
+	pages = {659}
+}
+
+@article{nelson_cluster_2014,
+	title = {Cluster {Sampling}: {A} {Pervasive}, {Yet} {Little} {Recognized} {Survey} {Design} in {Fisheries} {Research}},
+	volume = {143},
+	issn = {0002-8487},
+	doi = {10.1080/00028487.2014.901252},
+	number = {4},
+	journal = {Transactions of the American Fisheries Society},
+	author = {Nelson, Gary A.},
+	month = jul,
+	year = {2014},
+	pages = {926--938},
+}
+
+@techreport{plaganyi_models_2007,
+	address = {Rome},
+	title = {Models for an ecosystem approach to fisheries},
+	type = {FAO Fisheries Technical Paper},
+	shorttitle = {Models for an ecosystem approach to fisheries},
+	number = {477},
+	institution = {FAO},
+	author = {Plaganyi, E. E.},
+	year = {2007}
+}
+
+@techreport{politis_bts_2014,
+	type = {Northeast {Fisheries} {Science} {Center} {Reference} {Document}},
+	title = {Northeast {Fisheries} {Science} {Center} bottom trawl survey protocols for the {NOAA} {Ship} {Henry} {B}. {Bigelow}.},
+	copyright = {Public Domain},
+	url = {https://repository.library.noaa.gov/view/noaa/4825},
+	number = {14-06},
+	urldate = {2019-08-06},
+	author = {Politis, Philip J. and Galbraith, John K. and Kostovick, Paul and Brown, Russell W.},
+	month = apr,
+	year = {2014},
+	keywords = {Henry B. Bigelow (Ship)--Cruise., Trawls and trawling--Equipment and supplies--Calibration--Atlantic Coast (New England).},
+	pages = {138}
+}
+
+@article{polovina_ecopath_1984,
+	title = {Model of a {Coral}-{Reef} {Ecosystem} .1. {The} {Ecopath} {Model} and {Its} {Application} to {French} {Frigate} {Shoals}},
+	volume = {3},
+	issn = {0722-4028},
+	doi = {10.1007/Bf00306135},
+	number = {1},
+	journal = {Coral Reefs},
+	author = {Polovina, J. J.},
+	year = {1984},
+	pages = {1--11},
+}
+
+@article{trites_mammal_size_1998,
+	title = {Estimating mean body masses of marine mammals from maximum body lengths},
+	volume = {76},
+	author = {Trites, Andrew W and Pauly, Daniel},
+	year = {1998},
+	pages = {11},
+}
+
+@article{walters_ecosim_1997,
+	title = {Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments},
+	volume = {7},
+	issn = {0960-3166},
+	number = {2},
+	journal = {Reviews in Fish Biology and Fisheries},
+	author = {Walters, C. and Christensen, V. and Pauly, D.},
+	year = {1997},
+	pages = {139--172}
+}
+
+@article{walters_ecospace_2000,
+  title = {Ecospace: prediction of mesoscale spatial patterns in trophic relationships of exploited ecosystems, with emphasis on the impacts of marine protected areas},
+  author = {Walters, C. and Pauly, D. and Christensen, V.},
+  year = {2000},
+  journal = {Ecosystems},
+  volume = {2},
+  pages = {539-–554}
+}
+
+@article{ulanowicz_econetwrk_1991,
+	title = {A package for the analysis of ecosystem flow networks},
+	volume = {6},
+	issn = {0266-9838},
+	url = {http://www.sciencedirect.com/science/article/pii/026698389190024K},
+	doi = {10.1016/0266-9838(91)90024-K},
+	number = {3},
+	journal = {Environmental Software},
+	author = {Ulanowicz, Robert E. and Kay, James J.},
+	month = sep,
+	year = {1991},
+	pages = {131--142},
+}