Scott's edits; this version to Council

SOE-MAFMC-2020.Rmd

@@ -133,7 +133,7 @@ ylims <- c(ymin, ymax)
 
 # Report Structure
 
-The major messages of the report are synthesized in the 2-page overview. The information in this report is organized around general ecosystem-level management objectives (Table \ref{tab:management-objectives}), and indicators related to these objectives are grouped into four general categories in the four sections below: economic and social, protected species, fish and invertebrates, and habitat quality and ecosystem productivity. Each section begins with a summary of main messages with links to other sections, including any new information added at the request of the Fishery Management Councils, and includes figures with brief descriptions of all current indicators. Detailed technical methods documentation^[https://NOAA-EDAB.github.io/tech-doc] and indicator data^[https://github.com/NOAA-EDAB/ecodata] are available online. The details of standard figure formatting (Fig. \ref{fig:docformat}a), categorization of fish and invertebrate species into feeding groups (Table \ref{tab:species-groupings}), and definitions of ecological production units (EPUs, including the Mid-Atlantic Bight, MAB; Fig. \ref{fig:docformat}b) are provided at the end of the document. 
+The major messages of the report are synthesized in the 2-page summary, above. The information in this report is organized around general ecosystem-level management objectives (Table \ref{tab:management-objectives}), and indicators related to these objectives are grouped into four general categories in the four sections below: economic and social, protected species, fish and invertebrates, and habitat quality and ecosystem productivity. Each section begins with a summary of main messages with links to other sections, including any new information added at the request of the Fishery Management Councils, and includes figures with brief descriptions of all current indicators. Detailed technical methods documentation^[https://NOAA-EDAB.github.io/tech-doc] and indicator data^[https://github.com/NOAA-EDAB/ecodata] are available online. The details of standard figure formatting (Fig. \ref{fig:docformat}a), categorization of fish and invertebrate species into feeding groups (Table \ref{tab:species-groupings}), and definitions of ecological production units (EPUs, including the Mid-Atlantic Bight, MAB; Fig. \ref{fig:docformat}b) are provided at the end of the document. 
 
 ```{r management-objectives}
 
@@ -199,7 +199,7 @@ ecodata::ppr %>%
   theme_ts()
 ```
 
-Total seafood landings and MAFMC managed species seafood landings have declined over the long term (Fig. \ref{fig:total-landings}). with a slight increase 2016-2018. Seafood landings for feeding guilds are also stable or declining overall (Fig. \ref{fig:comm-landings}), although landings of piscivores and planktivores increased in the MAB. Recent increased landings of *Illex* squid are apparent in the piscivores guild (attributed to the planktivores guild in previous reports). Landings of apex predators are available for 2016-2018 but trends are not detectable in this short time series.
+Total seafood landings and MAFMC managed species seafood landings have declined over the long term (Fig. \ref{fig:total-landings}) with a slight increase 2016-2018. Seafood landings for feeding guilds are also stable or declining overall (Fig. \ref{fig:comm-landings}), although landings of piscivores and planktivores increased in the MAB. Recent increased landings of *Illex* squid are apparent in the piscivores guild (attributed to the planktivores guild in previous reports). Landings of apex predators are available for 2016-2018 but trends are not detectable in this short time series.
 
 ```{r total-landings, fig.cap = paste0("Total commercial seafood landings (black) and ",region," managed seafood landings (red)."), fig.width = 4, fig.asp = 0.45}
 #Get data for plotting
@@ -437,7 +437,7 @@ ggplot(data = indicators)+
 
 Commercial fleet diversity indices were updated with 2018 data and remain near the long term average^[https://noaa-edab.github.io/ecodata/human_dimensions#mid-atlantic].
 
-The trend in the number of Mid-Atlantic fishing communities that were highly engaged (red bar) in commercial fishing has shown a decrease since 2004 (Fig. \ref{fig:MAB-comm-engagement-trend}). Some of the communities that were highly engaged have moved into the moderate (blue bar) or medium-high (green bar) category, and thus the number of moderately to medium-highly engaged communities have increased. Significant changes in engagement scores have also been observed in medium-highly engaged communities. The average engagement score has decreased since 2004. These changes may be driven by the decline in value landed by primary species such as sea scallops in this group of communities. 
+Commerical fishery engagement measures the number of permits, dealers, and landings in a community^[https://www.fisheries.noaa.gov/national/socioeconomics/social-indicator-definitions#fishing-engagement-and-reliance-indices]. The trend in the number of Mid-Atlantic fishing communities that were highly engaged (red bar) in commercial fishing has shown a decrease since 2004 (Fig. \ref{fig:MAB-comm-engagement-trend}). Some of the communities that were highly engaged have moved into the moderate (blue bar) or medium-high (green bar) category, and thus the number of moderately to medium-highly engaged communities have increased. Significant changes in engagement scores have also been observed in medium-highly engaged communities. The average engagement score has decreased since 2004. These changes may be driven by the decline in value landed by primary species such as sea scallops in this group of communities. 
 
 ```{r MAB-comm-engagement-trend, fig.width = 8, fig.asp = 0.4, fig.cap = "Commercial engagement scores (total pounds landed, value landed, commercial permits, and commercial dealers in a community) for Mid-Atlantic fishing communities, 2004-2018."}
 
@@ -687,7 +687,7 @@ Additional social indicators for Mid-Atlantic communities are available online^[
 
 ## Fish habitat overlap with offshore wind lease areas  (coastwide) 
 
-Habitat modeling [@friedland_changes_2020] indicates that summer flounder, butterfish, longfin squid, and spiny dogfish are among fish species highly likely to occupy wind energy lease areas (Fig. \ref{fig:wind-hab}). Habitat conditions for many of these species have become more favorable over time within wind lease areas (increasing trend in probability of occupancy). Table \ref{tab:wind-habitat-table} lists the top 5 species in each season most likely to occupy the wind lease areas in the northern, central, and southern portions of the MAB, along with observed trends in probability of occupancy.
+Fish habitat modeling based on NEFSC bottom trawl surveys [@friedland_changes_2020] indicates that summer flounder, butterfish, longfin squid, and spiny dogfish are among fish species highly likely to occupy wind energy lease areas (Fig. \ref{fig:wind-hab}). Habitat conditions for many of these species have become more favorable over time within wind lease areas (increasing trend in probability of occupancy). Table \ref{tab:wind-habitat-table} lists the top 5 species in each season most likely to occupy the wind lease areas in the northern, central, and southern portions of the MAB, along with observed trends in probability of occupancy.
 
 ```{r wind-habitat-table, eval = T, echo = F, fig.cap='', out.width='80%'}
 wind1 <- ecodata::wind_occupancy
@@ -797,7 +797,7 @@ ggplot() +
 
 Protected species include marine mammals (under the Marine Mammal Protection Act), endangered and threatened species (under the Endangered Species Act), and migratory birds (under the Migratory Bird Treaty Act). In the Northeast US, endangered/threatened species include Atlantic salmon, Atlantic and shortnose sturgeon, all sea turtle species, and 5 baleen whales. Fishery management objectives for protected species generally focus on reducing threats and on habitat conservation/restoration; here we report on the status of these actions as well as indicating the potential for future interactions driven by observed and predicted ecosystem changes in the Northeast US region. Also, a marine mammal climate vulnerability assessment is currently underway and for Atlantic and Gulf of Mexico populations and will be reported on in future versions of this report. 
 
-While Harbor porpoise bycatch continues to be quite low as reported previously, this year saw the continuation of four Unusual Mortality Events (UMEs) for three large whale species and four seal species, with several mortalities attributed to human interactions. Strong evidence exists to suggest that the level of interaction between right whales and the combination of offshore lobster fishery in the US and snow crab fishery in Canada is contributing substantially to the decline of the species.
+While harbor porpoise bycatch continues to be quite low as reported previously, this year saw the continuation of four Unusual Mortality Events (UMEs) for three large whale species and four seal species, with several mortalities attributed to human interactions. Strong evidence exists to suggest that the level of interaction between right whales and the combination of offshore lobster fishery in the US and snow crab fishery in Canada is contributing substantially to the decline of the species.
 
 ## Whales (coastwide)
 North Atlantic right whales are among the most endangered large whale populations in the world. Changes in right whale trends can have implications for fisheries management where fisheries interact with these whales. Additional management restrictions could have a large impact on fishing times, gears, etc. Although the population increased steadily from 1990 to 2011, it has decreased recently (Fig. \ref{fig:NARW-abundance}). Reduced survival rates of adult females and diverging abundance trends between sexes have also been observed. It is estimated that there are only about 100 reproductive adult females remaining in the population. In 2018 there were no  new calves observed, and a drop in annual calf production roughly mirrors the abundance decline (Fig. \ref{fig:NARW-calf-abundance}), however seven new calves were born in 2019. Right whale distribution has changed since 2010. New research suggests that recent climate driven changes in ocean circulation has resulted in right whale distribution changes driven by increased warm water influx through the Northeast Channel, which has reduced the primary right whale prey (*Calanus finmarchicus*) in the central and eastern portions of the Gulf of Maine.
@@ -964,10 +964,10 @@ ggplot(data = stock_status) +
 ```
 
 
-Trends for a suite of 48 commercially or ecologically important species along the entire Northeast Shelf continue to show movement towards the northeast and generally into deeper water (Fig. \ref{fig:spec-dist}). Marine mammal distribution maps are available online^[https://www.nefsc.noaa.gov/AMAPPSviewer/]; updated maps and trends are currently being developed.
+Trends for a suite of 48 commercially or ecologically important fish species along the entire Northeast Shelf continue to show movement towards the northeast and generally into deeper water (Fig. \ref{fig:spec-dist}). We hope to expand analysis beyond fish. Marine mammal distribution maps are available online^[https://www.nefsc.noaa.gov/AMAPPSviewer/]; updated maps and trends are currently being developed.
 
 
-```{r spec-dist,fig.width = 4, fig.asp = 1.0, fig.cap = "Aggregate species distribution metrics for species in the Northeast Large Marine Ecosystem. Along-shelf distance measures the center of biomass along an axis oriented from the southwest to the northwest generally following the slope of coastline."}
+```{r spec-dist,fig.width = 4, fig.asp = 1.0, fig.cap = "Aggregate species distribution metrics for fish in the Northeast Large Marine Ecosystem. Along-shelf distance measures the center of biomass along an axis oriented from the southwest to the northwest generally following the slope of coastline."}
 
 spec_dist <- ecodata::species_dist %>% 
   group_by(Var) %>% 
@@ -1353,7 +1353,7 @@ knitr::include_graphics(file.path(image.dir, "MABcondition_2019_viridis_final.jp
 ```
 
 ## Fish productivity (MAB)
-We describe patterns of aggregate fish productivity in the Mid-Atlantic with the small fish per large fish anomaly indicator derived from NEFSC bottom trawl survey data (Fig. \ref{fig:MAB-recruitment}). The indicator shows that fish productivity has been relatively low in this region since 2010, although productivity across all species is trending back up towards average. Species with above average 2018 productivity in the Mid-Atlantic include witch flounder, silver hake and red hake. As for MAFMC managed species in other regions, in 2017 Summer flounder had above average production in the Gulf of Maine while butterfish had above average production on Georges Bank based on this indicator^[https://noaa-edab.github.io/ecodata/TestInteractive]. However, for 2018, it was mainly New England managed species with above average productivity in the New England systems.
+We describe patterns of aggregate fish productivity in the Mid-Atlantic with the small fish per large fish anomaly indicator derived from NEFSC bottom trawl survey data (Fig. \ref{fig:MAB-recruitment}). The indicator shows that fish productivity has been relatively low in this region since 2010, although productivity across all species is trending back up towards average. Species with above average 2018 productivity in the Mid-Atlantic include witch flounder, silver hake and red hake. As for MAFMC managed species in other regions, in 2017 Summer flounder had above average production in the Gulf of Maine while butterfish had above average production on Georges Bank based on this indicator^[https://noaa-edab.github.io/ecodata/InteractiveSOE]. However, for 2018, it was mainly New England managed species with above average productivity in the New England systems.
 
 ```{r MAB-recruitment, fig.cap = "Small fish per large fish biomass anomaly in the Mid-Atlantic Bight. The summed anomaly across species is shown by the black line.", fig.width = 8, fig.asp = .55}
 
@@ -1542,9 +1542,9 @@ kable(d, booktabs = T, linesep = "",
 
 # Habitat Quality and Ecosystem Productivity
 
-Productivity of harvested fish and protected species, and therefore sustainability of fisheries, depends on adequate habitat, which encompasses physical and chemical conditions and biological productivity at the base of the food web. Many harvested and protected species on the Northeast US shelf occupy several distinct habitats throughout their life cycle, including estuaries, nearshore coastal, and offshore environments. The indicators in this section provide information on the changing conditions encountered by managed species in different seasons and across habitats, which may explain observed changes in species distribution and productivity. New for this year, offshore habitat models were used to determine which species are most likely to occupy offshore wind energy development lease areas. Ultimately, a better understanding of these ecological drivers may permit proactive management in a changing system. 
+Productivity of harvested fish and protected species, and therefore sustainability of fisheries, depends on adequate habitat, which encompasses physical and chemical conditions and biological productivity at the base of the food web. Many harvested and protected species on the Northeast US shelf occupy several distinct habitats throughout their life cycle, including estuaries, nearshore coastal, and offshore environments. The indicators in this section provide information on the changing conditions encountered by managed species in different seasons and across habitats, which may explain observed changes in species distribution and productivity. New for this year, habitat models were used to determine which species are most likely to occupy offshore wind energy development lease areas. Ultimately, a better understanding of these ecological drivers may permit proactive management in a changing system. 
 
-While management limiting nutrient inputs has significantly improved water quality in Chesapeake Bay (@zhang_chesapeake_2018), extremely high precipitation in late 2018-early 2019 led to reduced water quality. Temperature in coastal and offshore habitats continues to trend towards unprecedented levels, accompanied by alterations in ocean circulation patterns. Observed changes at the base of the food web, including timing of production and plankton community composition, affect productivity of protected and managed species in ways we do not yet fully understand. 
+While management limiting nutrient inputs has significantly improved water quality in Chesapeake Bay [@zhang_chesapeake_2018], extremely high precipitation in late 2018-early 2019 led to reduced water quality. Temperature in coastal and offshore habitats continues to trend towards unprecedented levels, accompanied by alterations in ocean circulation patterns. Observed changes at the base of the food web, including timing of production and plankton community composition, affect productivity of protected and managed species in ways we do not yet fully understand. 
 
 ## Estuarine habitat quality (Chesapeake Bay)
 Many important MAFMC managed species use estuarine habitats as nurseries or are considered estuarine and nearshore coastal-dependent (summer flounder, scup, black sea bass, and bluefish), and interact with other important estuarine-dependent species (e.g., striped bass and menhaden).
@@ -1581,7 +1581,7 @@ Estuarine water quality is measured in many other locations coastwide. Work is i
 ## Oceanographic conditions (coastwide) 
 Globally, 2019 was the 2nd warmest year on record and the last five years have been the warmest in the last 140 years^[https://www.nasa.gov/press-release/nasa-noaa-analyses-reveal-2019-second-warmest-year-on-record]. 
 
-Since the 1860’s, the Northeast US shelf sea surface temperature (SST) has exhibited an overall warming trend, with the past decade measuring well above the long term average (and the trendline; Fig. \ref{fig:long-term-sst}). Changes in the Gulf Stream, increases in the number of warm core ring formations and anomalous onshore intrusions of warm salty water are affecting the coastal ocean dynamics with important implications for commercial fisheries (@gawarkiewicz_changing_2018).
+Since the 1860’s, the Northeast US shelf sea surface temperature (SST) has exhibited an overall warming trend, with the past decade measuring well above the long term average (and the trendline; Fig. \ref{fig:long-term-sst}). Changes in the Gulf Stream, increases in the number of warm core ring formations and anomalous onshore intrusions of warm salty water are affecting the coastal ocean dynamics with important implications for commercial fisheries [@gawarkiewicz_changing_2018].
 
 ```{r long-term-sst, fig.width = 8, fig.asp = 0.25, fig.cap = "Average annual sea surface temperature (SST) over the Northeast US Shelf"}
 lt_sst <- ecodata::long_term_sst %>%