From 9715e2bab011b7fc1f7c4410190f206113cc0e02 Mon Sep 17 00:00:00 2001 From: Brandon Beltz - NOAA Affiliate <136381970+BBeltz1@users.noreply.github.com> Date: Thu, 29 Feb 2024 16:39:23 -0500 Subject: [PATCH 1/3] change catalog urls to match ecodata names adjusted make rmd function to set the url of each catalog page to its ecodata data name. built catalog with new urls. added catalog page for rec hms. --- R/make_rmd.R | 4 +- chapters/HMS_species_distribution.rmd | 10 +-- chapters/SAV.rmd | 2 +- chapters/abc_acl.rmd | 2 +- chapters/aggregate_biomass.rmd | 2 +- chapters/aquaculture.rmd | 2 +- chapters/bennet.rmd | 2 +- chapters/bottom_temp.rmd | 4 +- chapters/bottom_temp_comp.rmd | 4 +- chapters/bottom_temp_seasonal_gridded.rmd | 2 +- chapters/calanus_variation.rmd | 4 +- chapters/ch_bay_sal.rmd | 4 +- chapters/ch_bay_temp.rmd | 2 +- chapters/ches_bay_sst.rmd | 5 +- chapters/ches_bay_synthesis.rmd | 2 +- chapters/ches_bay_wq.rmd | 6 +- chapters/chl_pp.rmd | 20 +++-- chapters/cold_pool.rmd | 2 +- chapters/comdat.rmd | 2 +- chapters/commercial_div.rmd | 2 +- chapters/condition.rmd | 2 +- chapters/energy_density.rmd | 6 +- chapters/engagement.rmd | 6 +- chapters/exp_n.rmd | 2 +- chapters/forage_index.rmd | 4 +- chapters/gom_salmon.rmd | 4 +- chapters/grayseal.rmd | 2 +- chapters/gsi.rmd | 2 +- chapters/habitat_diversity.rmd | 2 +- chapters/habs.rmd | 2 +- chapters/harborporpoise.rmd | 2 +- chapters/heatwave.rmd | 2 +- chapters/heatwave_year.rmd | 2 +- chapters/hms_cpue.rmd | 2 +- chapters/hms_landings.rmd | 4 +- chapters/hms_stock_status.rmd | 2 +- chapters/long_term_sst.rmd | 2 +- chapters/mab_inshore_survey.rmd | 2 +- chapters/mass_inshore_survey.rmd | 2 +- chapters/narw.rmd | 12 +-- chapters/ne_inshore_survey.rmd | 2 +- chapters/observation_synthesis.rmd | 2 +- chapters/ocean_acidification.rmd | 8 +- chapters/osw_survey_impact.rmd | 4 +- chapters/persistent_hotspots.rmd | 2 +- chapters/phyto_size.rmd | 2 +- chapters/ppr.rmd | 2 +- chapters/productivity_anomaly.rmd | 5 +- chapters/rec_hms.rmd | 91 +++++++++++++++++++++++ chapters/recdat.rmd | 2 +- chapters/seabird_ne.rmd | 2 +- chapters/seal_pups.rmd | 2 +- chapters/seasonal_oisst_anom.rmd | 2 +- chapters/seasonal_sst_anomaly_gridded.rmd | 2 +- chapters/slopewater.rmd | 4 +- chapters/spawn_timing.rmd | 2 +- chapters/species_dist.rmd | 2 +- chapters/species_groupings.rmd | 2 +- chapters/stock_status.rmd | 2 +- chapters/thermal_habitat_area.rmd | 2 +- chapters/thermal_habitat_persistence.rmd | 2 +- chapters/timing_shifts.rmd | 2 +- chapters/trans_dates.rmd | 2 +- chapters/wbts_mesozooplankton.rmd | 4 +- chapters/wcr.rmd | 2 +- chapters/wind_dev_speed.rmd | 2 +- chapters/wind_port.rmd | 2 +- chapters/wind_revenue.rmd | 2 +- chapters/zoo_abundance_anom.rmd | 2 +- chapters/zoo_diversity.rmd | 2 +- 70 files changed, 202 insertions(+), 109 deletions(-) create mode 100644 chapters/rec_hms.rmd diff --git a/R/make_rmd.R b/R/make_rmd.R index b8471472..46147a56 100644 --- a/R/make_rmd.R +++ b/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$description),append=T,fill=T,file=con) cat("",append=T,fill=T,file=con) # add space diff --git a/chapters/HMS_species_distribution.rmd b/chapters/HMS_species_distribution.rmd index 1ab391b8..1841a343 100644 --- a/chapters/HMS_species_distribution.rmd +++ b/chapters/HMS_species_distribution.rmd @@ -1,6 +1,6 @@ -# Cetacean Distribution Shifts +# Cetacean Distribution Shifts {#HMS_species_distribution} -**Description**: The data presented here are the locations of the center of core habitat for cetacean by season as documented in 2010 versus 2017. +**Description**: The data presented here are the locations of the center of core habitat for cetaceans by season as documented in 2010 versus 2017. **Indicator family**: @@ -16,7 +16,7 @@ knitr::opts_chunk$set(echo = F) library(ecodata) ``` ## Introduction to Indicator -Marine species are being affected by global climate changes, where and in most cases the documented responses include distribution shifts from their historical habitat. In addition, human-caused drivers such as the noise and physical disturbances from oil and gas exploration, fishing, boat traffic and infrastructure such as offshore renewable energy developments, as well as other maritime activities could also result in shifts. [@chavez-rosales_detection_2022] used Northwest Atlantic cetacean location data collected in its changing environment to investigate if their habitats are changing, and if so, to what extent. +Marine species are being affected by global climate changes, and in most cases the documented responses include distribution shifts from their historical habitat. In addition, human-caused drivers such as the noise and physical disturbances from oil and gas exploration, fishing, boat traffic and infrastructure such as offshore renewable energy developments, as well as other maritime activities could also result in shifts. [@chavez-rosales_detection_2022] used Northwest Atlantic cetacean location data collected in its changing environment to investigate if their habitats are changing, and if so, to what extent. A climate vulnerability assessment is published for Atlantic and Gulf of Mexico marine mammal populations [@lettrich_vulnerability_2023]. @@ -57,8 +57,8 @@ Shifting species distributions alter both species interactions and fishery inter **Variable definitions** -1) Time=time period of centroid location. 2) species=cetacean species. 3) season. 4) wlat=latitude of centroid. -5) wlon=longitude of centroid. +1) Time=time period of centroid location. 2) species=cetacean species. 3) season. +4) wlat=latitude of centroid. 5) wlon=longitude of centroid. ```{r vars_HMS_species_distribution} # Pull all var names diff --git a/chapters/SAV.rmd b/chapters/SAV.rmd index f351c6cd..88f9a014 100644 --- a/chapters/SAV.rmd +++ b/chapters/SAV.rmd @@ -1,4 +1,4 @@ -# Submerged Aquatic Vegetation +# Submerged Aquatic Vegetation {#SAV} **Description**: The data provided here are the 1984-2022 area distribution and percent coverage of submerged aquatic vegetation in the Chesapeake Bay and its tributaries that area measured and calculated from photo-interpreted aerial imagery taken during surveys conducted in the growing season. diff --git a/chapters/abc_acl.rmd b/chapters/abc_acl.rmd index f73d7052..770e2560 100644 --- a/chapters/abc_acl.rmd +++ b/chapters/abc_acl.rmd @@ -1,4 +1,4 @@ -# ABC or ACL for Managed Stocks +# ABC or ACL for Managed Stocks {#abc_acl} **Description**: Mid-Atlantic Council catch limits (e.g., ABC or ACL) and associated total catch estimate by year for each species and sector (commercial or recreational, as appropriate). diff --git a/chapters/aggregate_biomass.rmd b/chapters/aggregate_biomass.rmd index b45b3565..4da76b6b 100644 --- a/chapters/aggregate_biomass.rmd +++ b/chapters/aggregate_biomass.rmd @@ -1,4 +1,4 @@ -# Aggregate Survey Biomass +# Aggregate Survey Biomass {#aggregate_biomass} **Description**: Aggregate biomass from Northeast Fisheries Science Center (NEFSC) bottom trawl survey. diff --git a/chapters/aquaculture.rmd b/chapters/aquaculture.rmd index 46d25d75..ff7a2731 100644 --- a/chapters/aquaculture.rmd +++ b/chapters/aquaculture.rmd @@ -1,4 +1,4 @@ -# Aquaculture Production +# Aquaculture Production {#aquaculture} **Description**: Oyster production: number of oysters harvested from aquaculture. diff --git a/chapters/bennet.rmd b/chapters/bennet.rmd index 4c38224b..94f17699 100644 --- a/chapters/bennet.rmd +++ b/chapters/bennet.rmd @@ -1,4 +1,4 @@ -# Bennet Indicator +# Bennet Indicator {#bennet} **Description**: The data presented here are changes in revenue ($ real) split into a price indicator and a volume indicator. The sum of the price and the volume indicator is equal to the revenue change relative to a base year, which is 1982. diff --git a/chapters/bottom_temp.rmd b/chapters/bottom_temp.rmd index b40fe514..5447647a 100644 --- a/chapters/bottom_temp.rmd +++ b/chapters/bottom_temp.rmd @@ -1,4 +1,4 @@ -# Bottom Temperature - in situ +# Bottom Temperature - in situ {#bottom_temp} **Description**: The data presented here are time series of regional average bottom temperature anomalies from ship-based measurements made on the Northeast Continental Shelf. @@ -45,7 +45,7 @@ Temporal scale: Annual **Synthesis Theme**: - +- [X] Multiple System Drivers ```{r autostats_bottom_temp} diff --git a/chapters/bottom_temp_comp.rmd b/chapters/bottom_temp_comp.rmd index 0aef2074..87b3cb2c 100644 --- a/chapters/bottom_temp_comp.rmd +++ b/chapters/bottom_temp_comp.rmd @@ -1,4 +1,4 @@ -# Bottom temperature - Seasonal Anomaly +# Bottom temperature - Seasonal Anomaly {#bottom_temp_comp} **Description**: The data are seasonal bottom temperature anomaly time series for each EPU @@ -7,7 +7,7 @@ - [X] Oceanographic -**Contributor(s)**: Joseph Caracappa, Hubert duPontavice, Vincent Saba, Zhuomin Chen +**Contributor(s)**: Joseph Caracappa, Hubert du Pontavice, Vincent Saba, Zhuomin Chen **Affiliations**: NEFSC diff --git a/chapters/bottom_temp_seasonal_gridded.rmd b/chapters/bottom_temp_seasonal_gridded.rmd index b699df01..074807aa 100644 --- a/chapters/bottom_temp_seasonal_gridded.rmd +++ b/chapters/bottom_temp_seasonal_gridded.rmd @@ -1,4 +1,4 @@ -# Bottom temperature - Seasonal Gridded +# Bottom temperature - Seasonal Gridded {#bottom_temp_seasonal_gridded} **Description**: Seasonal mean bottom temperatures on the Northeast Continental Shelf between 1959 and 2023 in a 1/12° grid. diff --git a/chapters/calanus_variation.rmd b/chapters/calanus_variation.rmd index eecf65c7..a3bb60db 100644 --- a/chapters/calanus_variation.rmd +++ b/chapters/calanus_variation.rmd @@ -1,4 +1,4 @@ -# Seasonal Variation of Calanus finmarchicus +# Seasonal Variation of Calanus finmarchicus {#calanus_variation} **Description**: Abundance of late copepodid stages of the planktonic copepod, Calanus finmarchicus, measured during seasonal surveys between 1977 and 2019. Data from NOAA EcoMon/MARMAP program @@ -26,8 +26,6 @@ Historically, the high abundance of C. finmarchicus in the GOM combined with the This phenology indicator shows the change in abundance of the planktonic copepod, Calanus finmarchicus over a mean annual cycle in Wilkinson Basin, the primary overwintering habitat of this species in the western Gulf of Maine. The data are provided by the NOAA EcoMon/MARMAP survey, which has sampled stations along the Northeast U.S. Shelf, including the Gulf of Maine, seasonally (2-6 times per year) in nearly all years since 1977. The 333 µm mesh plankton nets used by the survey quantitatively capture only the late copepodid stages (C3-adult) of C. finmarchicus, but these stages nevertheless are representative of the seasonal variation in abundance of the population. This indicator serves as a baseline that can be used to interpret future changes in wGoM C. finmarchicus abundance. ## Key Results and Visualizations -Calanus finmarchicus phenology figure (uploaded with data) here - Seasonal abundance (number m-3) of C. finmarchicus late copepodid stages (mostly stages CIII-CVI) in Wilkinson Basin. X-axis represents time of year, from 1 January (yearday 0) to 31 December (yearday 365). Background gray circles show individual MARMAP/EcoMon abundance data points in Wilkinson Basin between 1977-2019. Solid black line shows the seasonal pattern in mean abundance from the MARMAP/EcoMon data; dotted lines show 2x (top) and ½ (bottom) of the mean abundance. Colored horizontal lines show conceptual model of seasonally variable predominant drivers. Predominant drivers in winter (Jan-Mar: days 1-100) suggested to be a combination of predation mortality and advective loss. The abundance of late stage Calanus finmarchicus in the western Gulf of Maine is seasonally variable. The highest abundances are observed in May-June, the result of reproduction, the magnitude of which depends on the timing of food availability to females (Stage CVI) in late-winter through spring. By late summer, most of the C. finmarchicus population is present as Stage CV, which overwinters at depth in a dormant state. The number of stage CV and hence the overall population abundance dwindles depending on net losses from advection and vertebrate and invertebrate predators. The abundance reaches its nadir in February-March, when the population is in stage CV or newly molted adult females and males. Note the difference between the late winter and late spring mean abundances is about three orders of magnitude. diff --git a/chapters/ch_bay_sal.rmd b/chapters/ch_bay_sal.rmd index 4ddca77d..e87302a0 100644 --- a/chapters/ch_bay_sal.rmd +++ b/chapters/ch_bay_sal.rmd @@ -1,4 +1,4 @@ -# Chesapeake Bay Salinity +# Chesapeake Bay Salinity {#ch_bay_sal} **Description**: This data is collected from the CBIBS buoy system. @@ -49,7 +49,7 @@ The changes in the temperature and salinity have implications in the habitat ## Get the data -**Point of contact**: [Charles Pellerin (charles.pellerin@noaa.gov](mailto:Charles Pellerin (charles.pellerin@noaa.gov){.email} +**Point of contact**: [Charles Pellerin (charles.pellerin@noaa.gov)](mailto:Charles Pellerin (charles.pellerin@noaa.gov)){.email} **ecodata name**: `ecodata::ch_bay_sal` diff --git a/chapters/ch_bay_temp.rmd b/chapters/ch_bay_temp.rmd index a0cd3867..a9973420 100644 --- a/chapters/ch_bay_temp.rmd +++ b/chapters/ch_bay_temp.rmd @@ -1,4 +1,4 @@ -# Chesapeake Bay Temperature +# Chesapeake Bay Temperature {#ch_bay_temp} **Description**: This data is collected from the CBIBS buoy system. diff --git a/chapters/ches_bay_sst.rmd b/chapters/ches_bay_sst.rmd index 1acc9459..94887830 100644 --- a/chapters/ches_bay_sst.rmd +++ b/chapters/ches_bay_sst.rmd @@ -1,4 +1,4 @@ -# Chesapeake Bay Seasonal Sea Surface Temperature Anomaly +# Chesapeake Bay Seasonal Sea Surface Temperature Anomaly {#ches_bay_sst} **Description**: Chesapeake Bay Seasonal Sea Surface Temperature Anomaly @@ -61,7 +61,8 @@ In the fall season, there were warmer-than-average temperatures in the Western S **Variable definitions** -1) sst: sea surface temperature 2023, Celsius 2) sst_climatol: sea surface temperature climatology 2007-2022, Celsius +1) sst: sea surface temperature 2023, Celsius +2) sst_climatol: sea surface temperature climatology 2007-2022, Celsius 3) sst_anomaly: sea surface temperature anomaly 2023 minus 2007-2022, Celsius ```{r vars_ches_bay_sst} diff --git a/chapters/ches_bay_synthesis.rmd b/chapters/ches_bay_synthesis.rmd index 6013173e..3c3ea0b1 100644 --- a/chapters/ches_bay_synthesis.rmd +++ b/chapters/ches_bay_synthesis.rmd @@ -1,4 +1,4 @@ -# Chesapeake Bay 2023 Synthesis +# Chesapeake Bay 2023 Synthesis {#ches_bay_synthesis} **Description**: Synthesis of Chesapeake Bay 2023 habitat conditions with implications for managed species diff --git a/chapters/ches_bay_wq.rmd b/chapters/ches_bay_wq.rmd index 44c9ea36..25096ff0 100644 --- a/chapters/ches_bay_wq.rmd +++ b/chapters/ches_bay_wq.rmd @@ -1,4 +1,4 @@ -# Chesapeake Bay Water Quality Standards Attainment +# Chesapeake Bay Water Quality Standards Attainment {#ches_bay_wq} **Description**: Chesapeake Bay Water Quality Attainment Indicator @@ -61,8 +61,8 @@ Patterns of attainment of individual designated uses are variable (Figure 2). Ac **Variable definitions** -Period: Assessment period Year 1: Starting year of the assessment period Year 2: Ending year of the assessment period -Total: The overall attainment indicator +Period: Assessment period Year 1: Starting year of the assessment period +Year 2: Ending year of the assessment period Total: The overall attainment indicator MSN-DO: Estimated attainment of the dissolved oxygen criterion for the migratory spawning and nursery designated use OW-DO: Estimated attainment of the dissolved oxygen criterion for the open water designated use DW-DO: Estimated attainment of the dissolved oxygen criterion for the deep water designated use diff --git a/chapters/chl_pp.rmd b/chapters/chl_pp.rmd index a6b98fd5..736be584 100644 --- a/chapters/chl_pp.rmd +++ b/chapters/chl_pp.rmd @@ -1,8 +1,6 @@ -# Chlorophyll and Primary Production +# Chlorophyll and Primary Production {#chl_pp} -**Description**: Satellite derived phytoplankton data including chlorophyll concentration, phytoplankton size class, and primary production for the Northeast Continental Shelf and ecological production units. - -(To be expanded) +**Description**: Satellite derived phytoplankton data including chlorophyll concentration, phytoplankton size class, and primary production for the Northeast Continental Shelf and ecological production units. **Indicator family**: @@ -18,12 +16,18 @@ knitr::opts_chunk$set(echo = F) library(ecodata) ``` ## Introduction to Indicator -Phytoplankton are the foundation of the marine food web and are the primary food source for zooplankton and filter feeders such as shellfish. Numerous environmental and oceanographic factors interact to drive the abundance, composition, spatial distribution, and productivity of phytoplankton. Satellite derived measurements of chlorophyll, the dominant photosynthetic pigment in phytoplankton, are used to estimate phytoplankton biomass. Phytoplankton growth depends on the availability of carbon dioxide, sunlight and nutrients and their growth rates can be influenced by water temperature, water depth, wind, and grazing pressure. Primary productivity is a measure of the amount of carbon produced by phytoplankton. The seasonal cycle of phytoplankton size distribution are typically dominated by larger-celled microplankton during the winter-spring and fall bloom periods, while smaller-celled nanoplankton dominate during the warmer summer months. +Phytoplankton are key biological regulators of the structure and function of most marine ecosystems. They are the foundation of the marine food web and are the primary food source for zooplankton and filter feeders such as shellfish. Numerous environmental and oceanographic factors interact to drive the abundance, composition, spatial distribution, seasonal timing and productivity of phytoplankton. Satellite derived measurements of chlorophyll, the dominant photosynthetic pigment in phytoplankton, are used to estimate total phytoplankton biomass. The size structure of the phytoplankton community influences important biogeochemical and ecological processes, including transfer of energy through the marine food web. Phytoplankton growth depends on the availability of carbon dioxide, sunlight and nutrients and their growth rates can be influenced by water temperature, water depth, wind, and grazing pressure. Primary productivity is a measure of the amount of carbon produced by phytoplankton. -(To be expanded) +The unique physical characteristics of the Northeast U.S. continental shelf help make it among the most productive continental shelf systems in the world influenced by both bottom-up (e.g. nutrient concentrations, light availability, and mixing/stratification) and top-down (e.g. grazing) controls. Phytoplankton biomass, composition, and productivity all have high spatial, seasonal and interannual variability. The most pronounced spatial pattern is the decrease in phytoplankton biomass from the coast to the shelf break. Georges Bank and Nantucket Shoals are shallow regions that are well mixed by tides. This mixing supplies sufficient nutrients to support phytoplankton growth throughout the year. In other regions, blooms of large diatom species occur on a seasonal cycle when growing conditions are ideal. ## Key Results and Visualizations -(In development) +The seasonal cycles of phytoplankton size distribution are typically dominated by larger-celled microplankton during the winter-spring and fall bloom periods, while smaller-celled nanoplankton dominate during the warmer summer months. In 2023, MAB total chlorophyll was below average in early spring, near average through the summer and above average throughout the fall. A peak in primary production occurred in summer, followed by an above average productivity associated with the early fall bloom. Phytoplankton size class distributions were near average for most of the year, except during the early fall bloom. + +Total chlorophyll concentrations on Georges Bank were above average for most of the year. The early winter bloom was most likely associated with diatoms, however the above average chlorophyll, primary production and microplankton fraction from April through August can be attributed to the dinoflagellate _Tripos muelleri_. + +Total chlorophyll concentrations in the Gulf of Maine were above average for most of the year. The early winter bloom was most likely associated with diatoms, however the record high chlorophyll, primary production and microplankton fraction from April through August can be attributed to the dinoflagellate _Tripos muelleri_. + +There is high interannual variability of the seasonal phytoplankton cycle. At the monthly scale, MAB chlorophyll and primary production are increasing during January and there has been a decrease in September chlorophyll, likely due to extension of the [summer stratification](https://noaa-edab.github.io/catalog/transition-dates.html) and delayed fall turnover. Fall and winter chlorophyll and primary production are increasing on Georges Bank and Gulf of Maine. ### MidAtlantic @@ -117,7 +121,7 @@ Temporal scale: Daily, weekly, monthly, annual, climatology (1998 to current yea ``` ## Implications -(In development) +Phytoplankton abundance, productivity, diversity, cell size, phenology, and carbon fluxes are regulated by the local physical and chemical environment and grazing. Interannual and climatological changes in temperature, freshwater inputs (due to ice sheet melting and/or enhanced river discharge), wind direction, and wind speed can alter the circulation patterns, upwelling conditions, and nutrient fluxes, directly affecting the timing, location, species composition of phytoplankton blooms in the NES. As the NES responds to warming, changing phenologies, changing chemistry, and changes in circulation patterns, we must understand how varying biophysical interactions control phytoplankton and subsequently affect fisheries, their habitats and the people, businesses and communities that depend on them. ## Get the data diff --git a/chapters/cold_pool.rmd b/chapters/cold_pool.rmd index 1e85d77c..3e50c09b 100644 --- a/chapters/cold_pool.rmd +++ b/chapters/cold_pool.rmd @@ -1,4 +1,4 @@ -# Cold Pool Index +# Cold Pool Index {#cold_pool} **Description**: Three annual cold pool indices (and standard error) for ss1959 through 2023 diff --git a/chapters/comdat.rmd b/chapters/comdat.rmd index bb00988e..0b7e58a3 100644 --- a/chapters/comdat.rmd +++ b/chapters/comdat.rmd @@ -1,4 +1,4 @@ -# Commercial Landings and Revenue +# Commercial Landings and Revenue {#comdat} **Description**: Commercial landings and revenue from dealer reports diff --git a/chapters/commercial_div.rmd b/chapters/commercial_div.rmd index 77cf2384..b3df79c4 100644 --- a/chapters/commercial_div.rmd +++ b/chapters/commercial_div.rmd @@ -1,4 +1,4 @@ -# Commercial Catch and Fleet Diversity +# Commercial Catch and Fleet Diversity {#commercial_div} **Description**: Permit-level species diversity and Council-level fleet diversity. diff --git a/chapters/condition.rmd b/chapters/condition.rmd index 9edd292f..6451817a 100644 --- a/chapters/condition.rmd +++ b/chapters/condition.rmd @@ -1,4 +1,4 @@ -# Relative condition +# Relative condition {#condition} **Description**: NEFSC fall bottom trawl survey relative condition diff --git a/chapters/energy_density.rmd b/chapters/energy_density.rmd index 5f96d5e2..82959e2b 100644 --- a/chapters/energy_density.rmd +++ b/chapters/energy_density.rmd @@ -1,6 +1,6 @@ -# Forage Fish Energy Density +# Forage Fish Energy Density {#energy_density} -**Description**: Energy density of alewife, butterfish, sand lance, and Atlantic mackerel varies seasonally, with seasonal estimates both higher and lower than estimates from previous decades. The data presented are the seasonal (Spring and Fall) energy density (kJ/g) for eight important forage species; Alewife, Atlantic Herring, Silver Hake, Northern Sand Lance, Atlantic Mackerel, Butterfish, Northern Shortfin Squid, and Inshore Longfin Squid. Samples are obtained from the NEFSC seasonal bottom trawl surveys and processed int he lab to estimate energy content. +**Description**: Energy density of alewife, butterfish, sand lance, and Atlantic mackerel varies seasonally, with seasonal estimates both higher and lower than estimates from previous decades. The data presented are the seasonal (Spring and Fall) energy density (kJ/g) for eight important forage species; Alewife, Atlantic Herring, Silver Hake, Northern Sand Lance, Atlantic Mackerel, Butterfish, Northern Shortfin Squid, and Inshore Longfin Squid. Samples are obtained from the NEFSC seasonal bottom trawl surveys and processed in the lab to estimate energy content. **Indicator family**: @@ -77,7 +77,7 @@ Source data are NOT publicly available. ## Accessibility and Constraints -Email mark.wuenschel@noaa.gov for further information. Data tables are beign created to make this readily available soon. +Email mark.wuenschel@noaa.gov for further information. Data tables are being created to make this readily available soon. **tech-doc link** diff --git a/chapters/engagement.rmd b/chapters/engagement.rmd index fcde7642..9a22cfaf 100644 --- a/chapters/engagement.rmd +++ b/chapters/engagement.rmd @@ -1,4 +1,4 @@ -# Engagement, Reliance, and Environmental Justice in Top Fishing Communities +# Engagement, Reliance, and Environmental Justice in Top Fishing Communities {#engagement} **Description**: The data presented here are 2021 environmental justice indicators in top commercial and top recreational communities in Mid-Atlantic and New England regions, respectively. @@ -16,7 +16,7 @@ knitr::opts_chunk$set(echo = F) library(ecodata) ``` ## Introduction to Indicator -We report the top ten communities most engaged in, and/or reliant upon, commercial and recreational fisheries and the degree to which these communities may be vulnerable to environmental justice issues (i.e., Poverty, Population Composition, and Personal Disruption). To select and present these communities we developed indicators (or indices that inform the importance of fishing and relative social conditions in each community. +We report the top ten communities most engaged in, and/or reliant upon, commercial and recreational fisheries and the degree to which these communities may be vulnerable to environmental justice issues (i.e., Poverty, Population Composition, and Personal Disruption). To select and present these communities we developed indicators (or indices) that inform the importance of fishing and relative social conditions in each community. The engagement and reliance indices demonstrate the importance of commercial and recreational fishing to a given community relative to other coastal communities in a region. Similarly, the environmental justice indices characterize different facets and levels of social vulnerability in a given community relative to other coastal communities in a region. @@ -145,7 +145,7 @@ It is also important to note that factor scores and their associated categorical ## Get the data -**Point of contact**: [Lisa Colburn (lisa.l.colburn@noaa.gov)](mailto:Lisa Colburn (lisa.l.colburn@noaa.gov)){.email} +**Point of contact**: [Lisa Colburn (lisa.l.colburn@noaa.gov); Changhua Weng (changhua.weng@noaa.gov)](mailto:Lisa Colburn (lisa.l.colburn@noaa.gov); Changhua Weng (changhua.weng@noaa.gov)){.email} **ecodata name**: `ecodata::engagement` diff --git a/chapters/exp_n.rmd b/chapters/exp_n.rmd index 133be309..7c00323b 100644 --- a/chapters/exp_n.rmd +++ b/chapters/exp_n.rmd @@ -1,4 +1,4 @@ -# Expected Number of Species +# Expected Number of Species {#exp_n} **Description**: Diversity metric from the Northeast Fisheries Science Center (NEFSC) Bottom Trawl Surveys. diff --git a/chapters/forage_index.rmd b/chapters/forage_index.rmd index 6cb9c44f..444fdb5e 100644 --- a/chapters/forage_index.rmd +++ b/chapters/forage_index.rmd @@ -1,4 +1,4 @@ -# Forage Fish Index +# Forage Fish Index {#forage_index} **Description**: Aggregate forage fish biomass index from fish stomach contents @@ -75,7 +75,7 @@ Changes in the distribution of forage biomass also affects predator distribution ## Get the data -**Point of contact**: [Sarah.Gaichas@noaa.gov](mailto:Sarah.Gaichas@noaa.gov){.email} +**Point of contact**: [Sarah Gaichas (Sarah.Gaichas@noaa.gov)](mailto:Sarah Gaichas (Sarah.Gaichas@noaa.gov)){.email} **ecodata name**: `ecodata::forage_index` diff --git a/chapters/gom_salmon.rmd b/chapters/gom_salmon.rmd index e1696cdd..bf11b9a0 100644 --- a/chapters/gom_salmon.rmd +++ b/chapters/gom_salmon.rmd @@ -1,6 +1,6 @@ -# Gulf of Maine Atlantic salmon +# Gulf of Maine Atlantic salmon {#gom_salmon} -**Description**: The data presented here are time series of documented Atlantic salmon returns to Gulf of Maine Rivers since 1972 and return rates for two sea winter returns from hatchery smolt stockings. +**Description**: The data presented here are time series of documented Atlantic salmon returns to Gulf of Maine rivers since 1972 and return rates for two sea winter returns from hatchery smolt stockings. **Indicator family**: diff --git a/chapters/grayseal.rmd b/chapters/grayseal.rmd index 6f7fdb2a..7664886e 100644 --- a/chapters/grayseal.rmd +++ b/chapters/grayseal.rmd @@ -1,4 +1,4 @@ -# Gray Seal Bycatch +# Gray Seal Bycatch {#grayseal} **Description**: The data presented here are time series of the species specific estimates of bycatch from U.S. North Atlantic commercial fisheries. diff --git a/chapters/gsi.rmd b/chapters/gsi.rmd index c9a4c10b..22db3f7d 100644 --- a/chapters/gsi.rmd +++ b/chapters/gsi.rmd @@ -1,4 +1,4 @@ -# Gulf Stream Index +# Gulf Stream Index {#gsi} **Description**: The monthly Gulf Stream North Wall Index presented here are based on the gridded EN.4.2.2 analyses dataset from 1954 to 2022 (https://www.metoffice.gov.uk/hadobs/en4/), calculated following @joyce_relationship_2009. diff --git a/chapters/habitat_diversity.rmd b/chapters/habitat_diversity.rmd index d899b5e5..58136898 100644 --- a/chapters/habitat_diversity.rmd +++ b/chapters/habitat_diversity.rmd @@ -1,4 +1,4 @@ -# Species Richness +# Species Richness {#habitat_diversity} **Description**: Abundance data were extracted from the NEFSC’s SVDBS database using Survdat for 55 fish species regularly sampled on spring and fall NEFSC bottom trawl surveys (see SOE Tech Doc for a list). Data were converted to presence/absence for species richness modeling. diff --git a/chapters/habs.rmd b/chapters/habs.rmd index 6a40d855..5a1b83c2 100644 --- a/chapters/habs.rmd +++ b/chapters/habs.rmd @@ -1,4 +1,4 @@ -# Harmful Algal Blooms +# Harmful Algal Blooms {#habs} **Description**: These data represent annual estimated abundance of Alexandrium catanella cysts in the Gulf of Maine and the presence of PSP toxins in blue mussels at coastal sites in the Gulf of Maine (MA, NH, ME), and shellfishery closures (MA). diff --git a/chapters/harborporpoise.rmd b/chapters/harborporpoise.rmd index 7ac0c754..5f912cbf 100644 --- a/chapters/harborporpoise.rmd +++ b/chapters/harborporpoise.rmd @@ -1,4 +1,4 @@ -# Harbor Porpoise Bycatch +# Harbor Porpoise Bycatch {#harborporpoise} **Description**: The data presented here are time series of the species specific estimates of bycatch from U.S. North Atlantic commercial fisheries. diff --git a/chapters/heatwave.rmd b/chapters/heatwave.rmd index 2b8b66a3..8b95f286 100644 --- a/chapters/heatwave.rmd +++ b/chapters/heatwave.rmd @@ -1,4 +1,4 @@ -# Annual Heatwave Intensity +# Annual Heatwave Intensity {#heatwave} **Description**: Surface and bottom MHWs for 2023. diff --git a/chapters/heatwave_year.rmd b/chapters/heatwave_year.rmd index 887cf8bc..c62c587d 100644 --- a/chapters/heatwave_year.rmd +++ b/chapters/heatwave_year.rmd @@ -1,4 +1,4 @@ -# Marine Heatwave Events +# Marine Heatwave Events {#heatwave_year} **Description**: Surface and bottom MHWs for 2023. diff --git a/chapters/hms_cpue.rmd b/chapters/hms_cpue.rmd index 40ffa20a..9a2979a6 100644 --- a/chapters/hms_cpue.rmd +++ b/chapters/hms_cpue.rmd @@ -1,4 +1,4 @@ -# Highly Migratory Species POP Catch Per Unit Effort +# Highly Migratory Species POP Catch Per Unit Effort {#hms_cpue} **Description**: CPUE from pelagic observer program (POP) observed hauls, presented as number of fish per haul, is provided for the northeast (i.e., the Northeast Coastal and Mid-Atlantic Bight fishing areas) by year/species from 1992-2022. diff --git a/chapters/hms_landings.rmd b/chapters/hms_landings.rmd index b618380d..2951c0bd 100644 --- a/chapters/hms_landings.rmd +++ b/chapters/hms_landings.rmd @@ -1,6 +1,6 @@ -# Highly Migratory Species Landings +# Highly Migratory Species Landings {#hms_landings} -**Description**: Aggregated Atlantic HMS landings data prepared for the Fisheries of the United States (FUS) report, spanning 2015-2022. +**Description**: Aggregated Atlantic highly migratory species landings data prepared for the Fisheries of the United States (FUS) report, spanning 2015-2022. **Indicator family**: diff --git a/chapters/hms_stock_status.rmd b/chapters/hms_stock_status.rmd index 52fffecf..8f1c0932 100644 --- a/chapters/hms_stock_status.rmd +++ b/chapters/hms_stock_status.rmd @@ -1,4 +1,4 @@ -# Highly Migratory Species Stock Status +# Highly Migratory Species Stock Status {#hms_stock_status} **Description**: Summary of the most recent stock assessment results for each assessed Highly Migratory Species. diff --git a/chapters/long_term_sst.rmd b/chapters/long_term_sst.rmd index 062e76ce..7ea1ebe3 100644 --- a/chapters/long_term_sst.rmd +++ b/chapters/long_term_sst.rmd @@ -1,4 +1,4 @@ -# NE Shelf Annual Sea Surface Temperature (SST) +# NE Shelf Annual Sea Surface Temperature (SST) {#long_term_sst} **Description**: Average annual sea-surface temperatures from the NOAA extended reconstructed sea surface temperature data set (ERSST V5) on the Northeast Continental Shelf. diff --git a/chapters/mab_inshore_survey.rmd b/chapters/mab_inshore_survey.rmd index 5865331a..bf00ede5 100644 --- a/chapters/mab_inshore_survey.rmd +++ b/chapters/mab_inshore_survey.rmd @@ -1,4 +1,4 @@ -# Inshore Survey (Mid Atlantic) +# Inshore Survey (Mid Atlantic) {#mab_inshore_survey} **Description**: Biomass time series for aggregate species groups from *three* inshore bottom trawl surveys conducted throughout the NE US: diff --git a/chapters/mass_inshore_survey.rmd b/chapters/mass_inshore_survey.rmd index b4ab517c..e5cdd184 100644 --- a/chapters/mass_inshore_survey.rmd +++ b/chapters/mass_inshore_survey.rmd @@ -1,4 +1,4 @@ -# Inshore Survey (Massachusetts) +# Inshore Survey (Massachusetts) {#mass_inshore_survey} **Description**: Biomass time series for aggregate species groups from *three* inshore bottom trawl surveys conducted throughout the NE US: diff --git a/chapters/narw.rmd b/chapters/narw.rmd index 70215fa9..7b89df1d 100644 --- a/chapters/narw.rmd +++ b/chapters/narw.rmd @@ -1,4 +1,4 @@ -# Right Whale Abundance +# Right Whale Abundance {#narw} **Description**: The data presented here are time series of the North Atlantic right whale population abundance estimates and calf abundance estimates. @@ -73,7 +73,7 @@ Temporal scale: Annual 1990 - 2022 ``` ## Implications -Strong evidence exists to suggest that interactions between right whales and both the fixed gear fisheries in the U.S. and Canada and vessel strikes in the U.S. are contributing substantially to the decline of the species [@hayes_north_2018]. Further, right whale distribution has changed since 2010. New research suggests that recent climate driven changes in ocean circulation have 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 fnmarchicus) in the central and eastern portions of the Gulf of Maine [@hayes_north_2018; @record_rapid_2019; @sorochan_north_2019]. Additional potential stressors include offshore wind development, which overlaps with important habitat areas used year-round by right whales, including mother and calf migration corridors and foraging habitat [@quintana-rizzo_residency_2021; @schick_striking_2009]. This area is also a primary right whale winter foraging habitat. Additional information can be found in the offshore wind section. Turbine presence and extraction of energy from the system could alter local oceanography @christiansen_emergence_2022. persistent foraging hotspots of right whales and seabirds overlap on Nantucket Shoals, where unique hydrography aggregates enhanced prey densities @white_spatial_2020 ; @sorochan_north_2019. +Strong evidence exists to suggest that interactions between right whales and both the fixed gear fisheries in the U.S. and Canada and vessel strikes in the U.S. are contributing substantially to the decline of the species [@hayes_north_2018]. Further, right whale distribution has changed since 2010. New research suggests that recent climate driven changes in ocean circulation have 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 [@hayes_north_2018; @record_rapid_2019; @sorochan_north_2019]. Additional potential stressors include offshore wind development, which overlaps with important habitat areas used year-round by right whales, including mother and calf migration corridors and foraging habitat [@quintana-rizzo_residency_2021; @schick_striking_2009]. This area is also a primary right whale winter foraging habitat. Additional information can be found in the offshore wind section. Turbine presence and extraction of energy from the system could alter local oceanography @christiansen_emergence_2022. Persistent foraging hotspots of right whales and seabirds overlap on Nantucket Shoals, where unique hydrography aggregates enhanced prey densities @white_spatial_2020 ; @sorochan_north_2019. The UMEs are under investigation and are likely the result of multiple drivers. For all large whale UMEs, human interaction appears to have contributed to increased mortalities, although investigations are not complete. @@ -85,12 +85,14 @@ The UMEs are under investigation and are likely the result of multiple drivers. **Variable definitions** -"Palka_NARW_abundance_2023_10_02.csv 1) Year. 2) lower95 = lower 95% confidence interval value in number of animals. +"Palka_NARW_abundance_2023_10_02.csv 1) Year. +2) lower95 = lower 95% confidence interval value in number of animals. 3) Median=median estimate of right whale abundance in number of animals. 4) Upper95= upper 95% confidence interval value in number of animals. 5) Mean= mean estimate of right whale abundance in number of animals. -6) SD=standard deviation of estimate of right whale abundance in number of animals. Palka_NARW_Calves_1980_2023.csv -1) Year. 2) Tot.Calves = total number of right whale calves born that year in number of animals. " +6) SD=standard deviation of estimate of right whale abundance in number of animals. +Palka_NARW_Calves_1980_2023.csv 1) Year. +2) Tot.Calves = total number of right whale calves born that year in number of animals. " ```{r vars_narw} # Pull all var names diff --git a/chapters/ne_inshore_survey.rmd b/chapters/ne_inshore_survey.rmd index abf1fd5f..16359d22 100644 --- a/chapters/ne_inshore_survey.rmd +++ b/chapters/ne_inshore_survey.rmd @@ -1,4 +1,4 @@ -# Inshore Survey (New England) +# Inshore Survey (New England) {#ne_inshore_survey} **Description**: Biomass time series for aggregate species groups from *three* inshore bottom trawl surveys conducted throughout the NE US: diff --git a/chapters/observation_synthesis.rmd b/chapters/observation_synthesis.rmd index 6a54e411..1b0d084a 100644 --- a/chapters/observation_synthesis.rmd +++ b/chapters/observation_synthesis.rmd @@ -1,4 +1,4 @@ -# 2023 Observation Synthesis +# 2023 Observation Synthesis {#observation_synthesis} **Description**: Synthesis of multiple anomalous and extreme conditions observed in 2023 that should be noted and considered in future analyses. diff --git a/chapters/ocean_acidification.rmd b/chapters/ocean_acidification.rmd index dd9b665b..3f15769a 100644 --- a/chapters/ocean_acidification.rmd +++ b/chapters/ocean_acidification.rmd @@ -1,4 +1,4 @@ -# Ocean Acidification and Other Stressors +# Ocean Acidification and Other Stressors {#ocean_acidification} **Description**: Maps and variability of regional carbonate chemistry and other oceanographic properties @@ -102,10 +102,8 @@ The seasonal level resolution of data collected in the Mid-Atlantic Bight in 202 **Variable definitions** -1) depth_interpolated meters -2) temperature degrees Celsius 3) chlorophyll_a µg L-1 -4) oxygen_concentration_shifted_mgL mg L-1 5) pH_shifted -6) aragonite_saturation_state +1) depth_interpolated meters 2) temperature degrees Celsius 3) chlorophyll_a µg L-1 +4) oxygen_concentration_shifted_mgL mg L-1 5) pH_shifted 6) aragonite_saturation_state No Data diff --git a/chapters/osw_survey_impact.rmd b/chapters/osw_survey_impact.rmd index dc0d48c9..c6cc76bd 100644 --- a/chapters/osw_survey_impact.rmd +++ b/chapters/osw_survey_impact.rmd @@ -1,4 +1,4 @@ -# Survey Impacts from Offshore Wind Development +# Survey Impacts from Offshore Wind Development {#osw_survey_impact} **Description**: Offshore wind development is expected to have several impacts on federal and state surveys. @@ -43,7 +43,7 @@ Proposed wind development areas interact with the region’s federal scientific 3) Alteration of benthic and pelagic habitats, and airspace in and around the wind energy development, requiring new designs and methods to sample new habitats; and, 4) Reduced sampling productivity through navigation impacts of wind energy infrastructure on aerial and vessel survey operations. -Increased vessel transit between stations may decrease data collections that are already limited by annual days-at-sea day allocations. The total survey area overlap ranges from 1-70% for all Greater Atlantic federal surveys. The Gulf of Maine Cooperative Research Bottom Longline Survey (41%) and the Shrimp Survey (70%) have the largest percent overlap with the draft Gulf of Maine Wind Energy Areas. The remaining surveys range from 1-16% overlap. Individual survey strata have significant interaction with wind, including the sea scallop survey (up to 96% of individual strata) and the bottom trawl survey (BTS, up to 60% strata overlap). Additionally, up to 50% of the southern New England North Atlantic right whale survey’s area overlaps with proposed project areas and A region-wide survey mitigation program is underway @northeast_fisheries_science_center_us_fall_2022 +Increased vessel transit between stations may decrease data collections that are already limited by annual days-at-sea day allocations. The total survey area overlap ranges from 1-70% for all Greater Atlantic federal surveys. The Gulf of Maine Cooperative Research Bottom Longline Survey (41%) and the Shrimp Survey (70%) have the largest percent overlap with the draft Gulf of Maine Wind Energy Areas. The remaining surveys range from 1-16% overlap. Individual survey strata have significant interaction with wind, including the sea scallop survey (up to 96% of individual strata) and the bottom trawl survey (BTS, up to 60% strata overlap). Additionally, up to 50% of the southern New England North Atlantic right whale survey’s area overlaps with proposed project areas and a region-wide survey mitigation program is underway @northeast_fisheries_science_center_us_fall_2022 ## Get the data diff --git a/chapters/persistent_hotspots.rmd b/chapters/persistent_hotspots.rmd index edb24428..1460b43f 100644 --- a/chapters/persistent_hotspots.rmd +++ b/chapters/persistent_hotspots.rmd @@ -1,4 +1,4 @@ -# Persistent annual hotspots +# Persistent annual hotspots {#persistent_hotspots} **Description**: Integrated persistent annual hotspots derived from at-sea observations of seabirds, cetaceans and sea turtles collected on systematic ship and aerial surveys diff --git a/chapters/phyto_size.rmd b/chapters/phyto_size.rmd index d056526f..4ac108e1 100644 --- a/chapters/phyto_size.rmd +++ b/chapters/phyto_size.rmd @@ -1,4 +1,4 @@ -# Phytoplankton Size Class +# Phytoplankton Size Class {#phyto_size} **Description**: Satellite derived phytoplankton data including chlorophyll concentration, phytoplankton size class, and primary production for the Northeast Continental Shelf and ecological production units. diff --git a/chapters/ppr.rmd b/chapters/ppr.rmd index 5537367d..56d03e89 100644 --- a/chapters/ppr.rmd +++ b/chapters/ppr.rmd @@ -1,4 +1,4 @@ -# Ecosytem overfishing +# Ecosytem overfishing {#ppr} **Description**: Ecosystem overfishing is an ecological, and not legal, term that ultimately evaluates how much fish are caught in an ecosystem relative to how much can be produced. Several indices are used to evaluate ecosystem overfishing, the Ryther index, the Fogarty index, and primary production required. diff --git a/chapters/productivity_anomaly.rmd b/chapters/productivity_anomaly.rmd index 3db53874..b3b56c2d 100644 --- a/chapters/productivity_anomaly.rmd +++ b/chapters/productivity_anomaly.rmd @@ -1,4 +1,4 @@ -# Fish Productivity Indicators +# Fish Productivity Indicators {#productivity_anomaly} **Description**: Amount of small fish produced per large fish biomass over time @@ -92,7 +92,8 @@ The apparent decline in productivity across multiple managed species in the MAB, Variable names are organized using this format: [region] stock name - variable type and source Variables ending with "_Survey" are survey derived recruits/spawner anomalies Variables ending with "-Assessment" are assessment derived quantities Survey stock names are in ALL CAPS -NE LME prepended to a survey stock name means the anomalies are coastwide Assessment stock names are in Sentence case +NE LME prepended to a survey stock name means the anomalies are coastwide +Assessment stock names are in Sentence case Units for survey variables are the Z score of (number of recruits in year+1/biomass of adults in year) Units for plotted assessment variables are the Z score of (numbers of recruits per kg spawning biomass with recruits aligned to spawning biomass year using age at recruitment) Other variables are available in the assessment derived dataset but are not plotted. To be added later. diff --git a/chapters/rec_hms.rmd b/chapters/rec_hms.rmd new file mode 100644 index 00000000..a9a74ff3 --- /dev/null +++ b/chapters/rec_hms.rmd @@ -0,0 +1,91 @@ +# Recreational HMS {#rec_hms} + +**Description**: Recreational shark landings pulled from the Marine Recreational Information Program (MRIP). + +**Indicator family**: + +- [X] Megafauna + + +**Contributor(s)**: Brandon Beltz; Kim Bastille + +**Affiliations**: NEFSC + +```{r echo=FALSE} +knitr::opts_chunk$set(echo = F) +library(ecodata) +``` +## Introduction to Indicator +Recreational shark landings pulled from the MRIP database + +## Key Results and Visualizations +Recreational landings of sharks are plotted. Sharks are categorized as large coastal, pelagic, prohibited and small coastal. + +### MAB + +```{r plot_rec_hmsMAB} +# Plot indicator +ggplotObject <- ecodata::plot_rec_hms(report='MidAtlantic') +ggplotObject +``` + +### NE + +```{r plot_rec_hmsNE} +# Plot indicator +ggplotObject <- ecodata::plot_rec_hms(report='NewEngland') +ggplotObject +``` + + +## Indicator statistics +Spatial scale: by EPU + +Temporal scale: annually from 1981 to 2022 + +**Synthesis Theme**: + +- [X] Multiple System Drivers + + +```{r autostats_rec_hms} +# Either from Contributor or ecodata +``` + +## Implications +Sharks are landed recreationally in quantities that are relevant to fisheries management. These landings should be considered when assessing the populations of sharks. + +## Get the data + +**Point of contact**: [Brandon Beltz (brandon.beltz@noaa.gov)](mailto:Brandon Beltz (brandon.beltz@noaa.gov)){.email} + +**ecodata name**: `ecodata::rec_hms` + +**Variable definitions** + +See variables below + +```{r vars_rec_hms} +# Pull all var names +vars <- ecodata::rec_hms |> + dplyr::select(Var) |> + dplyr::distinct() + +DT::datatable(vars) +``` +**Indicator Category**: + +- [X] Database pull + + +## Public Availability + +Source data are publicly available. + +## Accessibility and Constraints + +_No response_ + +**tech-doc link** + + diff --git a/chapters/recdat.rmd b/chapters/recdat.rmd index c49d70b9..9d939830 100644 --- a/chapters/recdat.rmd +++ b/chapters/recdat.rmd @@ -1,4 +1,4 @@ -# Recreational Fishing Indicators +# Recreational Fishing Indicators {#recdat} **Description**: A variety of indicators derived from MRIP Recreational Fisheries Statistics, including total recreational catch, total angler trips by region, annual diversity of recreational fleet effort, and annual diversity of managed species. diff --git a/chapters/seabird_ne.rmd b/chapters/seabird_ne.rmd index 693a70a5..703be0bf 100644 --- a/chapters/seabird_ne.rmd +++ b/chapters/seabird_ne.rmd @@ -1,4 +1,4 @@ -# Seabird diet and productivity - New England +# Seabird diet and productivity - New England {#seabird_ne} **Description**: Common tern annual diet and productivity at seven Gulf of Maine colonies managed by the National Audubon Society’s Seabird Restoration Program diff --git a/chapters/seal_pups.rmd b/chapters/seal_pups.rmd index 63964fde..5757eab4 100644 --- a/chapters/seal_pups.rmd +++ b/chapters/seal_pups.rmd @@ -1,4 +1,4 @@ -# Gray Seal Pups +# Gray Seal Pups {#seal_pups} **Description**: The data presented here are counts of gray seal pups at 4 U.S. haulout sites from 1988 to 2021. diff --git a/chapters/seasonal_oisst_anom.rmd b/chapters/seasonal_oisst_anom.rmd index 77a64aa5..29da4a45 100644 --- a/chapters/seasonal_oisst_anom.rmd +++ b/chapters/seasonal_oisst_anom.rmd @@ -1,4 +1,4 @@ -# Sea-surface temperature anomaly +# Sea-surface temperature anomaly {#seasonal_oisst_anom} **Description**: Seasonal sea surface temperature anomaly diff --git a/chapters/seasonal_sst_anomaly_gridded.rmd b/chapters/seasonal_sst_anomaly_gridded.rmd index f7400da1..9a5e80c5 100644 --- a/chapters/seasonal_sst_anomaly_gridded.rmd +++ b/chapters/seasonal_sst_anomaly_gridded.rmd @@ -1,4 +1,4 @@ -# Seasonal OISST Anomaly Map +# Seasonal OISST Anomaly Map {#seasonal_sst_anomaly_gridded} **Description**: Mapped seasonal sea surface temperature anomaly diff --git a/chapters/slopewater.rmd b/chapters/slopewater.rmd index 58b91b59..f7ef256c 100644 --- a/chapters/slopewater.rmd +++ b/chapters/slopewater.rmd @@ -1,4 +1,4 @@ -# Slopewater Proportions +# Slopewater Proportions {#slopewater} **Description**: This index gives the relative proportions of watermass type observed in the deep Northeast Channel (150-200 m water depth). @@ -37,7 +37,7 @@ Temporal scale: Annual **Synthesis Theme**: - +- [X] Multiple System Drivers ```{r autostats_slopewater} diff --git a/chapters/spawn_timing.rmd b/chapters/spawn_timing.rmd index 36918550..0a8a778b 100644 --- a/chapters/spawn_timing.rmd +++ b/chapters/spawn_timing.rmd @@ -1,4 +1,4 @@ -# Spawning Timing +# Spawning Timing {#spawn_timing} **Description**: Maturity information for groundfish is used to evaluate changes in spawning seasonality. diff --git a/chapters/species_dist.rmd b/chapters/species_dist.rmd index ca51163a..241c8825 100644 --- a/chapters/species_dist.rmd +++ b/chapters/species_dist.rmd @@ -1,4 +1,4 @@ -# Species Distribution Indicators +# Species Distribution Indicators {#species_dist} **Description**: Species mean depth, along-shelf distance, and distance to coastline diff --git a/chapters/species_groupings.rmd b/chapters/species_groupings.rmd index b7673922..50b5823b 100644 --- a/chapters/species_groupings.rmd +++ b/chapters/species_groupings.rmd @@ -1,4 +1,4 @@ -# Feeding guilds by management bodies +# Feeding guilds by management bodies {#species_groupings} **Description**: Classification of species guild membership by management bodies. diff --git a/chapters/stock_status.rmd b/chapters/stock_status.rmd index b56ce3f8..54029ca8 100644 --- a/chapters/stock_status.rmd +++ b/chapters/stock_status.rmd @@ -1,4 +1,4 @@ -# Stock Status +# Stock Status {#stock_status} **Description**: Summary of the most recent stock status results for each assessed species diff --git a/chapters/thermal_habitat_area.rmd b/chapters/thermal_habitat_area.rmd index 7794bd4f..9f807c08 100644 --- a/chapters/thermal_habitat_area.rmd +++ b/chapters/thermal_habitat_area.rmd @@ -1,4 +1,4 @@ -# Thermal Habitat Area +# Thermal Habitat Area {#thermal_habitat_area} **Description**: Calculates the proportion of each EPU that exceeds temperature thresholds as a daily time series from 1993 – 2023 diff --git a/chapters/thermal_habitat_persistence.rmd b/chapters/thermal_habitat_persistence.rmd index dce5b829..96bbc5c9 100644 --- a/chapters/thermal_habitat_persistence.rmd +++ b/chapters/thermal_habitat_persistence.rmd @@ -1,4 +1,4 @@ -# Thermal Habitat Persistence +# Thermal Habitat Persistence {#thermal_habitat_persistence} **Description**: The number of days per year per 1/12 degree cell that exceeds a temperature threshold. diff --git a/chapters/timing_shifts.rmd b/chapters/timing_shifts.rmd index f117d103..85341857 100644 --- a/chapters/timing_shifts.rmd +++ b/chapters/timing_shifts.rmd @@ -1,4 +1,4 @@ -# Timing shifts: Risks to Seasonal Management +# Timing shifts: Risks to Seasonal Management {#timing_shifts} **Description**: Shifts in the timing of life-cycle events are a risk to meeting seasonal and temporal management objectives. diff --git a/chapters/trans_dates.rmd b/chapters/trans_dates.rmd index c108d8f7..c67e6bf7 100644 --- a/chapters/trans_dates.rmd +++ b/chapters/trans_dates.rmd @@ -1,4 +1,4 @@ -# Transition Dates +# Transition Dates {#trans_dates} **Description**: The date that cool winter conditions transition to warm stratified summer conditions. diff --git a/chapters/wbts_mesozooplankton.rmd b/chapters/wbts_mesozooplankton.rmd index 0db7a14f..2fa0bb4f 100644 --- a/chapters/wbts_mesozooplankton.rmd +++ b/chapters/wbts_mesozooplankton.rmd @@ -1,4 +1,4 @@ -# Mesozooplankton Biomass at Wilkinson Basin +# Mesozooplankton Biomass at Wilkinson Basin {#wbts_mesozooplankton} **Description**: Mesozooplankton biomass at the Wilkinson Basin Time Series Station (WBTS): 2005-2022 @@ -21,8 +21,6 @@ The Wilkinson Basin Time Series Station (WBTS: 257 m depth), located in the nort Data collected at the WBTS station include CTD- rosette measurements of salinity, temperature and chlorophyll a concentration, microscopic enumeration of phytoplankton species, bacterial and microplankton measurements using flow cytometer, eDNA measurements, measurement of total mesozooplankton biomass and microscopic enumeration of zooplankton species collected with a 0.75 m, 200µm ring net towed from near bottom to the surface. Only the mesozooplankton biomass data are reported for the 2024 SOE; a fuller reporting of the time series data awaits further vetting and publication of the data in the primary literature. ## Key Results and Visualizations -Note: mesozooplankton biomass figure uploaded in data folder (not sure where to upload it) - Planktonic copepods typically constituted the great majority of catch of the vertically integrated ring net tow. Larger microzooplankton, like euphausids and jellyfish, are underrepresented. Chaetognaths, round tentaculate ctenophores, notably Pleurobrachia, and salps were captured, although the latter tend to degrade in formaldehyde over time and are likely underrepresented. Given these limitations, the mesozooplankton dry mass data allow comparison of biomass across pelagic ecosystems where similar measurements have been taken. Notably, at WBTS, the copepodid stages of Calanus finmarchicus typically make up 50% or more of the total mesozooplankton biomass in spring through fall. Following the seasonal life cycle of C. finmarchicus, mesozooplankton biomass is lowest in late winter and highest in summer. Biomass levels of 10-20 g m-2 observed in 2005-2008 in summer and winter were among the highest observed across the subarctic North Atlantic Ocean, including the Gulf of St. Lawrence (@de_lafontaine_pelagic_1991; @sorochan_north_2019), Scotian Shelf (@casault_optical_2022) and the Norwegian and Barents Seas (@melle_north_2014; @skjoldal_size-fractioned_2022). The mesozooplankton biomass collected at WBTS in late summer (Aug-Oct) and winter (Nov-Mar) has since declined significantly, by about 50%, between the start of the time series in 2005-2008 and 2021-2022 (see figure). The summer and winter biomass levels reflect the predominance of the larger, lipid rich late stage C. finmarchicus (CIV-CVI) as compared to spring, which is dominated by younger C. finmarchicus stages CI-CIV. diff --git a/chapters/wcr.rmd b/chapters/wcr.rmd index 360dd4d7..d3867f21 100644 --- a/chapters/wcr.rmd +++ b/chapters/wcr.rmd @@ -1,4 +1,4 @@ -# Warm Core Rings +# Warm Core Rings {#wcr} **Description**: Number of warm core rings produced annually by the Gulf Stream off the Northeast US diff --git a/chapters/wind_dev_speed.rmd b/chapters/wind_dev_speed.rmd index b5ea7f29..da782ad9 100644 --- a/chapters/wind_dev_speed.rmd +++ b/chapters/wind_dev_speed.rmd @@ -1,4 +1,4 @@ -# Speed and Scale of Offshore Wind Development in the Northeast +# Speed and Scale of Offshore Wind Development in the Northeast {#wind_dev_speed} **Description**: The footprint and timeline of offshore wind development in the Northeast by 2030 diff --git a/chapters/wind_port.rmd b/chapters/wind_port.rmd index e208f139..f47dbb11 100644 --- a/chapters/wind_port.rmd +++ b/chapters/wind_port.rmd @@ -1,4 +1,4 @@ -# Community Port Landings and Revenue from Wind Energy Areas (WEAs) +# Community Port Landings and Revenue from Wind Energy Areas (WEAs) {#wind_port} **Description**: NA diff --git a/chapters/wind_revenue.rmd b/chapters/wind_revenue.rmd index 5a034e6b..b3a46860 100644 --- a/chapters/wind_revenue.rmd +++ b/chapters/wind_revenue.rmd @@ -1,4 +1,4 @@ -# Fishery Impacts from Offshore Wind Development +# Fishery Impacts from Offshore Wind Development {#wind_revenue} **Description**: The data presented here include landings and revenue of managed species within existing offshore wind lease areas, Central Atlantic Bight final wind energy areas, and the Gulf of Maine draft wind energy area. diff --git a/chapters/zoo_abundance_anom.rmd b/chapters/zoo_abundance_anom.rmd index 008a4b9f..04858f06 100644 --- a/chapters/zoo_abundance_anom.rmd +++ b/chapters/zoo_abundance_anom.rmd @@ -1,4 +1,4 @@ -# Zooplankton Abundance Anomalies +# Zooplankton Abundance Anomalies {#zoo_abundance_anom} **Description**: Abundance anomalies for 20 zooplankton taxa diff --git a/chapters/zoo_diversity.rmd b/chapters/zoo_diversity.rmd index 4339873d..53208e9a 100644 --- a/chapters/zoo_diversity.rmd +++ b/chapters/zoo_diversity.rmd @@ -1,4 +1,4 @@ -# Zooplankton Diversity +# Zooplankton Diversity {#zoo_diversity} **Description**: Effective Shannon diversity calculated using 42 zooplankton taxa collected from EcoMon cruises From 5d52a6f88e58e3cdef674c29dec219e44f672055 Mon Sep 17 00:00:00 2001 From: Brandon Beltz - NOAA Affiliate <136381970+BBeltz1@users.noreply.github.com> Date: Fri, 1 Mar 2024 10:39:54 -0500 Subject: [PATCH 2/3] turned on rec_hms page in bookdown yml added rec_hms to the bookdown yml file to activate the page. --- _bookdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/_bookdown.yml b/_bookdown.yml index ff49595e..72f9044f 100644 --- a/_bookdown.yml +++ b/_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" From c5d692b74d3ec3107b878166a1237c2d65879653 Mon Sep 17 00:00:00 2001 From: Brandon Beltz - NOAA Affiliate <136381970+BBeltz1@users.noreply.github.com> Date: Mon, 4 Mar 2024 10:31:42 -0500 Subject: [PATCH 3/3] build engagement edits pulled edits from engagement github issues for inclusion in catalog --- chapters/engagement.rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/chapters/engagement.rmd b/chapters/engagement.rmd index 9a22cfaf..a8056ed4 100644 --- a/chapters/engagement.rmd +++ b/chapters/engagement.rmd @@ -33,9 +33,9 @@ In the 2023 report, we presented environmental justice vulnerability as a dichot ##### Commercial -Barnegat Light, NJ, is the only community that scored high for both commercial engagement and reliance based on 2021 data. Cape May, NJ ranked high for both commercial engagement and commercial reliance based on 2020 data but decreased to medium-high for its commercial reliance in 2021. Reedville, VA ranked high for both commercial engagement and commercial reliance based on 2020 data but decreased to medium-high and medium, respectively, in 2021. Reedville, VA; Hatteras and Hobucken, NC are no longer listed as top ten commercial fishing communities, replaced by Hampton, VA; Swan Quarter, NC; Bowers and Little Creek, DE. +Barnegat Light, NJ, and Reedville, VA are the only communities that scored high for both commercial engagement and reliance based on 2021 data. Cape May, NJ ranked high for both commercial engagement and commercial reliance based on 2020 data but decreased to medium-high for its commercial reliance in 2021. Hatteras and Hobucken, NC are no longer listed as top ten commercial fishing communities, replaced by Hampton, VA; Swan Quarter, NC; Bowers and Little Creek, DE. -Communities that ranked medium-high or above for one or more of the environmental justice indicators are highlighted in bright orange, including Hampton Bays/Shinnecock, NY; Atlantic City, NJ; Newport News, VA; Swan Quarter and Columbia, NC; Bower and Little Creek, DE. Communities that ranked medium for one or more of the environmental justice indicators are highlighted in purple, including Point Pleasant Beach, NJ; Hampton, VA; Beaufort and Wilmington, NC. +Communities that ranked medium-high or above for one or more of the environmental justice indicators are highlighted in bright orange, including Hampton Bays/Shinnecock, NY; Atlantic City, NJ; Swan Quarter and Columbia, NC; Bower and Little Creek, DE. Communities that ranked medium for one or more of the environmental justice indicators are highlighted in purple, including Point Pleasant Beach, NJ; Hampton, VA; Beaufort and Wilmington, NC. Detailed scores of the three environmental justice indicators for the same communities plotted in spider plots. Communities are plotted clockwise in a descending order of commercial engagement scores from high to low, with the most highly engaged community, Cape May, NJ, listed on the top. Among these communities, ranked medium-high or above for environmental justice vulnerability, Atlantic City, NJ scored high for all of the three environmental justice indicators.