Merge pull request #116 from NOAA-EDAB/operation_phoenix

pull MA SSC version of catalog into master for versioning

DESCRIPTION

@@ -1,7 +1,9 @@
-Package: placeholder
+Package: catalog
 Type: Book
-Title: Synthetic Indicator Cataloque
+Title: Synthetic Indicator Catalogue
 Description: Catalogue containing indicator used in the State of the Ecosystem Report and Beyond...
+Authors@R: c(person("Brandon", "Beltz", email = "[email protected]", role = c("cre", "aut")),
+             person("Andy", "Beet", email = "[email protected]", role = "aut"))
 Version: 1.0.0
 License: file LICENSE
 Depends: 
@@ -13,5 +15,5 @@ Depends:
 Suggests:
   downlit
 Remotes: 
-  NOAA-EDAB/ecodata@dev
+  NOAA-EDAB/ecodata@5.0.1
 

R/make_rmd.R

@@ -21,8 +21,8 @@ make_rmd <- function(listobject){
   # start to create the Rmd
   #cat(paste0("# ",stringr::str_to_title(indicator_name)),append=T,fill=T,file=con)  
   ### DESCRIPTION, CONTRIBUTORS, AFFILIATION, FAMILY
-#  cat(paste0("# ",listobject$dataname," {#",listobject$indicatorname,"}"),append=T,fill=T,file=con)    
-  cat(paste0("# ",listobject$dataname),append=T,fill=T,file=con)    
+  cat(paste0("# ",listobject$dataname," {#",listobject$indicatorname,"}"),append=T,fill=T,file=con)    
+  #cat(paste0("# ",listobject$dataname),append=T,fill=T,file=con)    
   cat("",append=T,fill=T,file=con) # add space
   cat(paste0("**Description**: ",listobject$description),append=T,fill=T,file=con)
   cat("",append=T,fill=T,file=con) # add space

_bookdown.yml

@@ -79,6 +79,7 @@ rmd_files:
     -   "chapters/commercial_div.rmd"
     -   "chapters/ppr.rmd"
     -   "chapters/recdat.rmd"
+    -   "chapters/rec_hms.rmd"
     -   "chapters/abc_acl.rmd"
     -   "chapters/bennet.rmd"
     -   "chapters/stock_status.rmd"

bibliography/StateOftheEcosystem.bib

@@ -3275,3 +3275,109 @@ @article{de_lafontaine_pelagic_1991
 	year = {1991},
 	pages = {99--124.},
 }
+
+@article{colburn_indicators_2016,
+	title = {Indicators of climate change and social vulnerability in fishing dependent communities along the {Eastern} and {Gulf} {Coasts} of the {United} {States}},
+	volume = {74},
+	issn = {0308-597X},
+	url = {https://www.sciencedirect.com/science/article/pii/S0308597X16302123},
+	doi = {10.1016/j.marpol.2016.04.030},
+	abstract = {Changing climatic conditions are affecting the relationship between fishing communities and the marine resources they depend on. This shift will require an adaptive response on the part of policy makers and fishery managers. In the U.S., the National Oceanic and Atmospheric Administration (NOAA) established, in its fisheries agency (NOAA Fisheries), a set of social indicators of fishing community vulnerability and resilience to evaluate the impacts of changes in fishery management regimes. These indicators enhance the analytical capabilities within NOAA Fisheries for conducting fisheries social impact assessments and informing ecosystem-based fishery management. Building on the existing Community Social Vulnerability Indicators (CSVIs), new measures of climate change vulnerability are defined for the U.S. Eastern and Gulf coasts. These new indicators are used to assess the impact of sea level rise on critical commercial fishing infrastructure and the dependence of communities on species identified as vulnerable to the effects of climate change. Examples are provided in this article to demonstrate the utility of these new indicators to policy makers and the NOAA strategic goal for building resilient coastal communities that are environmentally and economically sustainable. Integration of CSVIs and the new climate change vulnerability indices highlight community needs for unique solutions in order to adapt to environmental and social changes and maintain their well-being.},
+	urldate = {2024-02-16},
+	journal = {Marine Policy},
+	author = {Colburn, Lisa L. and Jepson, Michael and Weng, Changhua and Seara, Tarsila and Weiss, Jeremy and Hare, Jonathan A.},
+	month = dec,
+	year = {2016},
+	keywords = {Climate change, Indicators, Fishing communities, Social vulnerability},
+	pages = {323--333},
+	file = {Full Text:C\:\\Users\\andrew.beet\\Zotero\\storage\\TU6U2J9P\\Colburn et al. - 2016 - Indicators of climate change and social vulnerabil.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\andrew.beet\\Zotero\\storage\\J6S2IF4Q\\S0308597X16302123.html:text/html},
+}
+
+@article{okeefe_forming_2013,
+	title = {Forming a {Partnership} to {Avoid} {Bycatch}},
+	volume = {38},
+	issn = {0363-2415},
+	url = {https://doi.org/10.1080/03632415.2013.838122},
+	doi = {10.1080/03632415.2013.838122},
+	abstract = {Bycatch of Yellowtail Flounder in the U.S. Sea Scallop Fishery is a constraint to achieving optimum yield of scallops. Between 2000 and 2009, in-season bycatch closures of prime scallop grounds resulted in economic losses over US{\textbackslash}100 million. To address this constraint, we collaborated with the scallop fishing industry to implement a bycatch avoidance program in the Nantucket Lightship harvest area in 2010. Vessels shared near real-time location information about bycatch amounts during fishing activities. We compiled the information, identified bycatch hotspots, and provided daily advisories to vessels on the fishing grounds. Catch per tow of Yellowtail and fishing effort in high bycatch regions significantly declined after the fleet received the advisories. The fleet harvested the target scallop allocation worth US{\textbackslash}40 million while catching only 32\% of the Yellowtail bycatch limit. This program continues as a collaborative, iterative approach to bycatch reduction that balances fleet objectives with conservation constraints.},
+	number = {10},
+	urldate = {2024-03-08},
+	journal = {Fisheries},
+	author = {O'Keefe, Catherine E. and DeCelles, Gregory R.},
+	month = nov,
+	year = {2013},
+	note = {Publisher: Taylor \& Francis
+\_eprint: https://doi.org/10.1080/03632415.2013.838122},
+	pages = {434--444},
+}
+
+@article{pdf,
+	title = {Trends and change points in surface and bottom thermal environments of the {US} {Northeast} {Continental} {Shelf} {Ecosystem}},
+	volume = {n/a},
+	issn = {1054-6006},
+	doi = {10.1111/fog.12485},
+	abstract = {Abstract Temperature is an important factor in defining the habitats of marine resource species. While satellite sensors operationally measure ocean surface temperatures, we depend on in situ measurements to characterize benthic habitats. Ship-based measurements were interpolated to develop a time series of gridded spring and fall, surface and bottom temperature fields for the US Northeast Shelf. Surface and bottom temperatures have increased over the study period (1968?2018) at rates between 0.18?0.31°C per decade and over a shorter time period (2004?2018) at rates between 0.26?1.49°C per decade. A change point analysis suggests that a warming regime began in the surface waters in 2011 centered on Georges Bank and the Nantucket Shoals; in following years, most of the Northeast Shelf had experienced a shift in surface temperature. A similar analysis of bottom temperature suggests a warming regime began in 2008 in the eastern Gulf of Maine; in following years, change points in temperature occurred further to the west in the Gulf of Maine, finally reaching the Middle Atlantic Bight by 2010. The spatial pattern in bottom water warming is consistent with well-known oceanographic patterns that advect warming North Atlantic waters into the Gulf of Maine. The varying spatial and temporal progression of warming in the two layers suggests they were actuated by different sets of forcing factors. We then compared these trends and change points to responses of lower and higher trophic level organisms and identified a number of coincident shifts in distribution and biomass of key forage and fisheries species.},
+	number = {n/a},
+	journal = {Fisheries Oceanography},
+	author = {Friedland, Kevin D. and Morse, Ryan E. and Manning, James P. and Melrose, Donald Christopher and Miles, Travis and Goode, Andrew G. and Brady, Damian C. and Kohut, Josh T. and Powell, Eric N.},
+	month = jun,
+	year = {2020},
+	keywords = {climate change, ecosystem, regime shift, temperature, resource species},
+	annote = {The following values have no corresponding Zotero field:publisher: John Wiley \& Sons, Ltd},
+	file = {Friedland_etal-FO_2020 Trends and change point:C\:\\Users\\andrew.beet\\Zotero\\storage\\VZ2TCJK6\\Friedland_etal-FO_2020 Trends and change point.pdf:application/pdf},
+}
+
+@article{cohen_global_2018,
+	title = {A global synthesis of animal phenological responses to climate change},
+	volume = {8},
+	copyright = {2018 The Author(s)},
+	issn = {1758-6798},
+	url = {https://www.nature.com/articles/s41558-018-0067-3},
+	doi = {10.1038/s41558-018-0067-3},
+	abstract = {Shifts in phenology are already resulting in disruptions to the timing of migration and breeding, and asynchronies between interacting species1–5. Recent syntheses have concluded that trophic level1, latitude6and how phenological responses are measured7are key to determining the strength of phenological responses to climate change. However, researchers still lack a comprehensive framework that can predict responses to climate change globally and across diverse taxa. Here, we synthesize hundreds of published time series of animal phenology from across the planet to show that temperature primarily drives phenological responses at mid-latitudes, with precipitation becoming important at lower latitudes, probably reflecting factors that drive seasonality in each region. Phylogeny and body size are associated with the strength of phenological shifts, suggesting emerging asynchronies between interacting species that differ in body size, such as hosts and parasites and predators and prey. Finally, although there are many compelling biological explanations for spring phenological delays, some examples of delays are associated with short annual records that are prone to sampling error. Our findings arm biologists with predictions concerning which climatic variables and organismal traits drive phenological shifts.},
+	language = {en},
+	number = {3},
+	urldate = {2024-03-08},
+	journal = {Nature Climate Change},
+	author = {Cohen, Jeremy M. and Lajeunesse, Marc J. and Rohr, Jason R.},
+	month = mar,
+	year = {2018},
+	note = {Publisher: Nature Publishing Group},
+	keywords = {Animal migration, Phenology},
+	pages = {224--228},
+	file = {Full Text PDF:C\:\\Users\\andrew.beet\\Zotero\\storage\\4YQTZII8\\Cohen et al. - 2018 - A global synthesis of animal phenological response.pdf:application/pdf},
+}
+
+@article{thomas_seasonal_2017,
+	title = {Seasonal trends and phenology shifts in sea surface temperature on the {North} {American} northeastern continental shelf},
+	volume = {5},
+	issn = {2325-1026},
+	url = {https://doi.org/10.1525/elementa.240},
+	doi = {10.1525/elementa.240},
+	abstract = {The northeastern North American continental shelf from Cape Hatteras to the Scotian Shelf is a region of globally extreme positive trends in sea surface temperature (SST). Here, a 33-year (1982–2014) time series of daily satellite SST data was used to quantify and map spatial patterns in SST trends and phenology over this shelf. Strongest trends are over the Scotian Shelf (\>0.6°C decade–1) and Gulf of Maine (\>0.4°C decade–1) with weaker trends over the inner Mid-Atlantic Bight ({\textasciitilde}0.3°C decade–1). Winter (January–April) trends are relatively weak, and even negative in some areas; early summer (May–June) trends are positive everywhere, and later summer (July–September) trends are strongest ({\textasciitilde}1.0°C decade–1). These seasonal differences shift the phenology of many metrics of the SST cycle. The yearday on which specific temperature thresholds (8° and 12°C) are reached in spring trends earlier, most strongly over the Scotian Shelf and Gulf of Maine ({\textasciitilde} –0.5 days year–1). Three metrics defining the warmest summer period show significant trends towards earlier summer starts, later summer ends and longer summer duration over the entire study region. Trends in start and end dates are strongest ({\textasciitilde}1 day year–1) over the Gulf of Maine and Scotian Shelf. Trends in increased summer duration are \>2.0 days year–1 in parts of the Gulf of Maine. Regression analyses show that phenology trends have regionally varying links to the North Atlantic Oscillation, to local spring and summer atmospheric pressure and air temperature and to Gulf Stream position. For effective monitoring and management of dynamically heterogeneous shelf regions, the results highlight the need to quantify spatial and seasonal differences in SST trends as well as trends in SST phenology, each of which likely has implications for the ecological functioning of the shelf.},
+	urldate = {2024-03-08},
+	journal = {Elementa: Science of the Anthropocene},
+	author = {Thomas, Andrew C. and Pershing, Andrew J. and Friedland, Kevin D. and Nye, Janet A. and Mills, Katherine E. and Alexander, Michael A. and Record, Nicholas R. and Weatherbee, Ryan and Henderson, M. Elisabeth},
+	editor = {Deming, Jody W. and Drinkwater, Ken},
+	month = aug,
+	year = {2017},
+	pages = {48},
+	file = {Full Text PDF:C\:\\Users\\andrew.beet\\Zotero\\storage\\SGJABFQW\\Thomas et al. - 2017 - Seasonal trends and phenology shifts in sea surfac.pdf:application/pdf;Snapshot:C\:\\Users\\andrew.beet\\Zotero\\storage\\JRMK8DUH\\Seasonal-trends-and-phenology-shifts-in-sea.html:text/html},
+}
+
+@article{weiskopf_climate_2020,
+	title = {Climate change effects on biodiversity, ecosystems, ecosystem services, and natural resource management in the {United} {States}},
+	volume = {733},
+	issn = {0048-9697},
+	url = {https://www.sciencedirect.com/science/article/pii/S0048969720312948},
+	doi = {10.1016/j.scitotenv.2020.137782},
+	abstract = {Climate change is a pervasive and growing global threat to biodiversity and ecosystems. Here, we present the most up-to-date assessment of climate change impacts on biodiversity, ecosystems, and ecosystem services in the U.S. and implications for natural resource management. We draw from the 4th National Climate Assessment to summarize observed and projected changes to ecosystems and biodiversity, explore linkages to important ecosystem services, and discuss associated challenges and opportunities for natural resource management. We find that species are responding to climate change through changes in morphology and behavior, phenology, and geographic range shifts, and these changes are mediated by plastic and evolutionary responses. Responses by species and populations, combined with direct effects of climate change on ecosystems (including more extreme events), are resulting in widespread changes in productivity, species interactions, vulnerability to biological invasions, and other emergent properties. Collectively, these impacts alter the benefits and services that natural ecosystems can provide to society. Although not all impacts are negative, even positive changes can require costly societal adjustments. Natural resource managers need proactive, flexible adaptation strategies that consider historical and future outlooks to minimize costs over the long term. Many organizations are beginning to explore these approaches, but implementation is not yet prevalent or systematic across the nation.},
+	urldate = {2024-03-08},
+	journal = {Science of The Total Environment},
+	author = {Weiskopf, Sarah R. and Rubenstein, Madeleine A. and Crozier, Lisa G. and Gaichas, Sarah and Griffis, Roger and Halofsky, Jessica E. and Hyde, Kimberly J. W. and Morelli, Toni Lyn and Morisette, Jeffrey T. and Muñoz, Roldan C. and Pershing, Andrew J. and Peterson, David L. and Poudel, Rajendra and Staudinger, Michelle D. and Sutton-Grier, Ariana E. and Thompson, Laura and Vose, James and Weltzin, Jake F. and Whyte, Kyle Powys},
+	month = sep,
+	year = {2020},
+	keywords = {Biodiversity, Ecosystem services, Ecosystems, Global change, Natural resource management},
+	pages = {137782},
+	file = {ScienceDirect Snapshot:C\:\\Users\\andrew.beet\\Zotero\\storage\\DYF6TMSH\\S0048969720312948.html:text/html},
+}