Initial Tech Doc 2025 Update

.github/ISSUE_TEMPLATE/page_edit.yml

@@ -1,6 +1,6 @@
 name: State of the Ecosystem - Edit Tech Doc Page
 description: Use this issue template to suggest an edit to a page in the State of the Ecosystem technical documentation.
-title: "[Tech DOc Page Edit]: "
+title: "[Tech Doc Page Edit]: "
 labels: ["page edit"]
 assignees: "BBeltz1"
 body:

_404.Rmd

@@ -0,0 +1,13 @@
+# Page not found
+## The page you are looking for has likely been moved or renamed. See below for details.
+
+**The following pages have been moved or renamed**
+
+- [Bottom Temperature - in situ](https://noaa-edab.github.io/catalog/bottom_temp_insitu.html)
+- [Bottom Temperature - Seasonal Anomaly](https://noaa-edab.github.io/catalog/bottom_temp_model_anom.html)
+- [Bottom Temperature - Seasonal Gridded](https://noaa-edab.github.io/catalog/bottom_temp_model_gridded.html)
+- [Cetacean Distribution Shifts](https://noaa-edab.github.io/catalog/cetacean_dist.html)
+- [Thermal Habitat Persistence](https://noaa-edab.github.io/catalog/thermal_habitat_gridded.html)
+- [Seasonal OISST Anomaly Map](https://noaa-edab.github.io/catalog/seasonal_oisst_anom_gridded.html)
+
+**If the page you are looking for is not listed above, please refer to the Table of Contents to the left. If you are having trouble finding something, please email Brandon Beltz ([email protected]) for assistance.**

_bookdown.yml

@@ -23,7 +23,8 @@ rmd_files:
     #-   "chapters/annual_chl_pp.Rmd" *Turned off in catalog
     -   "chapters/habs.Rmd"
     -   "chapters/SAV.Rmd"
-    #-   "chapters/calanus_variation.Rmd" *Missing tech doc page
+    -   "chapters/zooplankton_index.Rmd"
+    -   "chapters/calanus_variation.Rmd"
     -   "chapters/wbts_mesozooplankton.Rmd"
     -   "chapters/zoo_abundance_anom.Rmd"
     #-   "chapters/zoo_diversity.Rmd" *Missing tech doc page
@@ -37,33 +38,38 @@ rmd_files:
     #-   "chapters/ne_inshore_survey.Rmd" *Shares tech doc page with mab_inshore_survey
     #-   "chapters/osw_survey_impact.Rmd" *Missing tech doc page
     -   "chapters/condition.Rmd"
+    -   "chapters/finfish_traits.Rmd"
     -   "chapters/habitat_diversity.Rmd"
     -   "chapters/species_dist.Rmd"
     -   "chapters/energy_density.Rmd"
     -   "chapters/spawn_timing.Rmd"
     -   "chapters/exp_n.Rmd"
     -   "chapters/forage_index.Rmd"
+    -   "chapters/benthos_index.Rmd"
     -   "chapters/harborporpoise.Rmd"
     -   "chapters/hms_cpue.Rmd"
     -   "chapters/hms_landings.Rmd"
     -   "chapters/hms_stock_status.Rmd"
-    -   "chapters/HMS_species_distribution.Rmd"
+    -   "chapters/cetacean_dist.Rmd"
     -   "chapters/narw.rmd"
     -   "chapters/productivity_anomaly.Rmd"
     -   "chapters/seal_pups.Rmd"
     -   "chapters/gom_salmon.Rmd"
     -   "chapters/grayseal.Rmd"
     -   "chapters/seabird_ne.Rmd"
+    -   "chapters/cetacean_acoustic.Rmd"
+    -   "chapters/wea_sound.Rmd"
     -   "chapters/species_groupings.rmd"  
 #
 #
 # #################### OCEANOGRAPHIC ##################
     -   "chapters/sectionHeaders/oceanographic.rmd" 
-    -   "chapters/bottom_temp.Rmd"
-    #-   "chapters/bottom_temp_comp.Rmd" *Missing tech doc page
-    -   "chapters/bottom_temp_seasonal_gridded.Rmd"
-    -   "chapters/seasonal_sst_anomaly_gridded.Rmd"
+    -   "chapters/bottom_temp_insitu.Rmd"
+    #-   "chapters/bottom_temp_model_anom.Rmd" *Missing tech doc page
+    -   "chapters/bottom_temp_model_gridded.Rmd"
+    -   "chapters/seasonal_oisst_anom_gridded.Rmd"
     #-   "chapters/seasonal_oisst_anom.Rmd" *Missing tech doc page
+    #-   "chapters/surface_temp_mom6.Rmd"
     -   "chapters/trans_dates.Rmd"
     -   "chapters/long_term_sst.Rmd"
     -   "chapters/cold_pool.Rmd"
@@ -81,7 +87,8 @@ rmd_files:
     #-   "chapters/heatwave_year.Rmd" *Shares tech doc page with heatwave
     #-   "chapters/timing_shifts.Rmd" *Missing tech doc page
     #-   "chapters/observation_synthesis.Rmd" *Missing tech doc page
-    -   "chapters/ocean_acidification.Rmd"  
+    -   "chapters/ocean_acidification.Rmd"
+    -   "chapters/gom_acidification.Rmd"
 #
 #
 # ######################## ECONOMIC ##################
@@ -95,6 +102,7 @@ rmd_files:
     -   "chapters/bennet.Rmd"
     -   "chapters/stock_status.Rmd"
     -   "chapters/engagement.Rmd"
+    #-   "chapters/community_climate_vulnerability.Rmd" *Missing tech doc page
     -   "chapters/aquaculture.Rmd"
     -   "chapters/Wind_dev_speed.Rmd"
     -   "chapters/wind_port.Rmd"

chapters/benthos_index.Rmd

@@ -0,0 +1,52 @@
+# Benthic Invertebrate Indices {#benthos_index}
+
+**Description**: Aggregate macrobenthos and megabenthos invertebrate indices from fish stomach contents
+
+**Found in**: State of the Ecosystem - Indicator Catalog (2025) 
+
+**Indicator category**: Extensive analysis, not yet published
+
+**Contributor(s)**: Sarah Gaichas, James Gartland, Brian E. Smith, Sarah Weisberg, Sean Lucey
+
+**Data steward**: Sarah Gaichas <[email protected]>
+
+**Point of contact**: Sarah Gaichas <[email protected]>
+
+**Public availability statement**: Source data are publicly available. All data and code available on GitHub at <https://github.com/NOAA-EDAB/benthosindex>
+
+## Methods
+
+### Data Sources
+
+Data used to develop these indicators comes from multispecies diet data collected on the Northeast Fisheries Science Center (NEFSC) and NorthEast Area Monitoring and Assessment Program (NEAMAP) bottom trawl surveys. Bottom temperature data is described in [Bottom temperature - High Resolution](https://noaa-edab.github.io/tech-doc/bottom_temp_seasonal_gridded.html). 
+
+### Data Analysis
+
+VAST spatio-temporal modeling [@thorson_comparing_2017; @thorson_guidance_2019] is described here.
+
+The approach follows that used for the forage fish index [@gaichas_assessing_2023], which was in turn based on @ng_predator_2021.
+
+Two stages of model selection determined whether to include:
+
+1. spatial and spatio-temporal random effects, and
+2. vessel effects, and "catchability" covariates affecting the observation process: mean predator size, number of predators, and bottom temperature.
+Using REML in stage 1, models including spatial and spatio-temporal random effects as well as anisotropy were best supported by the data. This was true for the spring dataset and the fall dataset for both macrobenthos and megabenthos.
+
+In stage 2, combinations of catchability covariates were better supported by the data than vessel effects. Model comparisons led us to the best model fit using mean predator length, number of predator species, and bottom temperature at a survey station as catchability covariates.
+
+Model selection results are reported at [this link](https://noaa-edab.github.io/benthosindex/WorkflowDecisions.html).
+
+Scripts used to run the model selection and to produce the final bias corrected models are posted at <https://github.com/NOAA-EDAB/benthosindex/tree/main/VASTscripts>
+
+### Data Processing 
+
+The basic workflow is to develop a dataset of stomach contents data where fish predators act as samplers of the prey field, then fit a vector autoregressive spatio-temporal (VAST) model to this dataset to generate an index. Dataset development is described here.
+
+NEFSC survey food habits data were extracted and provided by Brian Smith (NEFSC). NEAMAP survey food habits data were extracted and processed by James Gartland (VIMS). Macrobenthos and Megabenthos categories were those used in Northeast US food web models. The Macrobenthos Rpath category has 833 food habits database species codes. The Megabenthos Rpath category has 105 food habits database species codes. All are listed at [this link](https://noaa-edab.github.io/benthosindex/WorkflowDecisions.html).
+
+Benthic predator/size combinations were selected using a cluster analysis of a diet similarity matrix provided by Brian Smith. Species categorized as pelagic or piscivorous feeders were eliminated, and all other species were retained as general benthivores. This resulted in 88 predator/size combinations used to "sample" benthic invertebrates. The predator/size list is available at [this link](https://noaa-edab.github.io/benthosindex/WorkflowDecisions.html).
+
+These input datasets were processed, aggregated, and combined with bottom temperature data to become VAST model input datasets using the script at [this link](https://github.com/NOAA-EDAB/benthosindex/blob/main/fhdata/VASTbenthos_ProcessInputDat.R).
+
+**catalog link**
+<https://noaa-edab.github.io/catalog/benthos_index.html>

chapters/bottom_temp.Rmd → chapters/bottom_temp_insitu.Rmd

@@ -1,4 +1,4 @@
-# Bottom temperature - in situ {#bottom_temp}
+# Bottom temperature - in situ {#bottom_temp_insitu}
 
 **Description**: Time series of annual in situ bottom temperatures on the Northeast Continental Shelf.
 
@@ -36,4 +36,4 @@ All temperature observations are subject to rigorous quality control protocols f
 Derived bottom temperature data were formatted for inclusion in the `ecodata` R package using the R code found [here](https://github.com/NOAA-EDAB/ecodata/blob/master/data-raw/get_bottom_temp.R).
 
 **catalog link**
-<https://noaa-edab.github.io/catalog/bottom_temp.html>
+<https://noaa-edab.github.io/catalog/bottom_temp_insitu.html>

chapters/bottom_temp_seasonal_gridded.Rmd → chapters/bottom_temp_model_gridded.Rmd

@@ -1,4 +1,4 @@
-# Bottom temperature - High Resolution {#bottom_temp_seasonal_gridded}
+# Bottom temperature - High Resolution {#bottom_temp_model_gridded}
 
 **Description**: Seasonal bottom temperatures on the Northeast Continental Shelf between 1959 and 2022 in a 1/12° grid. 
 
@@ -51,4 +51,4 @@ We used the methodology presented in du Pontavice et al. (2023) based on the Nor
 Derived bottom temperature data were formatted for inclusion in the `ecodata` R package using the R code found [here](https://github.com/NOAA-EDAB/ecodata/blob/master/data-raw/get_bottom_temp_comp.R).
 
 **catalog link**
-<https://noaa-edab.github.io/catalog/bottom_temp_seasonal_gridded.html>
+<https://noaa-edab.github.io/catalog/bottom_temp_model_gridded.html>

chapters/calanus_variation.Rmd

@@ -0,0 +1,40 @@
+# Seasonal and multiannual variation in abundance of Calanus finmarchicus in the western Gulf of Maine {#calanus_variation}
+
+**Description**: The data presented here are abundance estimates (no./m2) of the planktonic copepod, Calanus finmarchicus, collected at the NERACOOS-MBON Wilkinson Basin Time Series (WBTS) station between 2005-2023.
+
+**Found in**: State of the Ecosystem - Indicator Catalog (2024+) 
+
+**Indicator category**: Published methods
+
+**Contributor(s)**: Jeffrey A. Runge, Cameron R.S. Thompson, Shawn Shellito, Emma C. Dullaert, Isabel A. Honda, Douglas Vandemark, Dylan Pugh, Riley Young-Morse, Jackie Motyka, Rebecca J. Jones, Lee Karp Boss, Rubao Ji
+
+**Data steward**: Jeffrey Runge <[email protected]>
+
+**Point of contact**: Jeffrey Runge <[email protected]>
+
+**Public availability statement**: Source data are publicly available.
+
+## Methods
+
+### Data Sources
+
+Observations from 2004 - 2017: https://data.neracoos.org/erddap/tabledap/WBTS_CFIN_2004_2017.html
+
+Observations beginning in 2020: https://data.neracoos.org/erddap/tabledap/WBTS_CFIN_start_2020.html
+
+### Data Analysis
+
+All analyses were conducted using the R programming software (R Core Team, 2023), utilizing the mgcv package for GAMs (Wood, 2023). Model estimation was conducted using Restricted Maximum Likelihood (REML) and to ensure the robustness of the model, we utilized DHARMa (Hartig, 2023) residual diagnostics to perform a Kolmogorov-Smirnov test for scaled residuals, assess dispersion, and detect outliers. The GAMs that passed the significance and diagnostic tests were then visualized using ggplot2 in R to graphically display the model outputs and trends. The GAMs of seasonal trends in a time series measurement were only depicted if the day of year smoother was significant, while the GAMs of annual climatologies were only depicted if the year smoother was significant. 
+
+Time series indices of C. finmarchicus  abundance of copepodid stages and total mesozooplankton biomassare presented in the following format: the accepted GAM of each time series variable is used to estimate the expected average value and confidence interval  to depict climatology over an annual time period, or to depict the  trend in each season over multiple years. These estimated expected average values are the indices for each variable and can be calculated for any combination of year and day of year. For depicting the annual climatology , the year is set to 2012 while days range from 1 to 365. For depicting interannual trends, a single day is set within each season (see figure captions for which day) while years vary from 2023 to 2005. A transformation by the square root was applied  to achieve a normal distribution for the analysis, and in the depicted figure these values are displayed by their untransformed number.
+
+### Data Processing 
+
+The Wilkinson Basin Time Series (WBTS) Station (42°51.7ʹN, -69°51.8ʹW, previously Station WB-7) is located 60 km from Portsmouth, New Hampshire, in the northwest corner of Wilkinson Basin at an average station depth of 257 m.  Since the start of the time series in December, 2004, it has been accessed by day trips using the University of New Hampshire research vessel, R/V Gulf Challenger. Contingent on funding support, the station was sampled at approximately monthly intervals between January, 2005- August, 2008, April, 2012-May, 2013, October, 2015-July, 2017, January, 2021- March, 2024 and at less frequent intervals in other years, for a total of 142 visits for CTD casts, 116 of which also include net tows. It continues to be sampled at approximately monthly intervals since 2020 as part of the U.S. MBON.
+
+Sampling at the WBTS and CMTS stations generally follow guidelines established by the Atlantic Zone Monitoring Program (AZMP) operated in Canadian Maritime waters by Fisheries and Oceans Canada (Mitchell et al., 2002). All samples were taken during daytime hours, typically mid-morning to mid-afternoon. 
+
+To measure zooplankton abundance and biomass, two net two casts were made using a 0.75 meter diameter single ring (CMTS and WBTS stations) or a SEA-GEAR Model 9600 twin-ring 200 µm mesh net (WBTS station). The nets were towed vertically at approx. 40 m/min with the ring starting at  5-7 meters from the bottom. The samples were preserved in 4% buffered formaldehyde. In the laboratory, samples were split with a Folsom Splitter with half of the sample designated for measurement of total zooplankton biomass and the other for taxonomic enumeration. The biomass sample split was filtered onto one or more 47 mm diameter glass fiber filters or 100-200 µm mesh nitex screens preweighed in a plastic petri dish. The split sample was poured through the filter or screen mounted in a filter holder assisted with gentle vacuum pumping, rinsed with 100 ml of tap water, dried in an oven 65°C for 24-48 h and then collectively weighed on a Mettler Toledo PG403-S microbalance (1 mg precision). The half sample for enumeration was drained of formaldehyde solution on a fine mesh screen, the contents of which were then placed in a 4 l beaker containing a known quantity of filtered seawater (typically 2500-3000 ml).  Subsamples were taken while randomly stirring with either a 25 ml Hensen-Stempel pipette or a large-mouth pipette (we used a modified turkey baster)  emptied into graduated cylinder to measure subsample volume. Multiple subsamples were taken to ensure at least 50 Calanus copepodid stages were enumerated (typically about 3% of the total half-sample) under a Leica MZ 12.5 Zoom stereo microscope. While all copepodid stages in the subsamples were enumerated, an index of C. finmarchicus abundance is calculated as the total abundance of stage C3 to adult stage C6. Water column (i.e. to net depth) biomass (g dry weight m-2) and abundance (number of individuals m-2) were calculated by dividing the measurement in the total sample (taking into account split and aliquot of subsamples) by the area of the ring net (0.4418 m2).  Net volume filtered was also determined by a General Oceanics flowmeter installed in the mouth of the net, but the geometrically determined volumes were chosen as the standard because reliable flowmeter data was not available for every cast.
+
+**catalog link**
+<https://noaa-edab.github.io/catalog/calanus_variation.html>

chapters/cetacean_acoustic.Rmd

@@ -0,0 +1,32 @@
+# Cetacean Weekly Acoustic Presence {#cetacean_acoustic}
+
+**Description**: This figure shows a summary of weekly acoustic presence of eight cetacean species summarized across two years at four recording sites in southern New England.
+
+**Found in**: State of the Ecosystem - Indicator Catalog (2025) 
+
+**Indicator category**: Published methods
+
+**Contributor(s)**: Sofie Van Parijs, Annamaria DeAngelis, Tyler Aldrich, Rochelle Gordon, Amanda Holdman, Jessica McCordic, Xavier Mouy, Tim Rowell, Sara Tennant, Annabel Westell, and Genevieve Davis
+
+**Data steward**: Rebecca Van Hoeck <[email protected]>
+
+**Point of contact**: Rebecca Van Hoeck <[email protected]>; Genevieve Davis <[email protected]>
+
+**Public availability statement**: Source data are publicly available.
+
+## Methods
+
+### Data Sources
+
+Data collected by the NEFSC Passive Acoustic Branch from four recording sites in and around the southern New England Wind Energy areas. 
+
+### Data Analysis
+
+Manual verification of the automated detections was conducted to confirm daily acoustic presence for each species. Weekly acoustic presence was summarized as the median number of days of acoustic presence per calendar week across all data. Horizontal lines within the boxes indicate the median, box boundaries indicate the 25th (lower quartile) and 75th (upper quartile) percentiles, vertical lines indicate the largest (upper whisker) and smallest (lower whisker) values no further than 1.5 times the interquartile range, and black dots represent outliers. Further details of the analysis can be found in Van Parijs et al (2023).
+
+### Data Processing 
+
+Species-specific vocalizations of eight cetacean were identified in the acoustic data using multiple automated detectors following the methodology described in Van Parijs et al (2023).
+
+**catalog link**
+<https://noaa-edab.github.io/catalog/cetacean_acoustic.html>

chapters/HMS_species_distribution.Rmd → chapters/cetacean_dist.Rmd

@@ -1,4 +1,4 @@
-# Cetacean Distribution Shifts {#HMS_species_distribution}
+# Cetacean Distribution Shifts {#cetacean_dist}
 
 **Description**: The data presented here are the locations of the center of core habitat for cetaceans by season as documented in 2010 versus 2017.
 
@@ -28,7 +28,7 @@ Centroid of spatial density distribution map from each season and species in 201
 ### Data processing
 Line transect data were processed using standard 2-team Distance sampling analysis methods, then used in generalized additive models to describe the spatiotemporal habitat-density relationships (Chavez-Rosales et al. 2022).
 
-The Cetacean distribution shifts indicator was formatted for inclusion in the `ecodata` R package using the R script  found [here](https://github.com/NOAA-EDAB/ecodata/blob/master/data-raw/get_hms_species_distribution.R).
+The Cetacean distribution shifts indicator was formatted for inclusion in the `ecodata` R package using the R script  found [here](https://github.com/NOAA-EDAB/ecodata/blob/master/data-raw/get_cetacean_dist.R).
 
 **catalog link**
-<https://noaa-edab.github.io/catalog/HMS_species_distribution.html>
+<https://noaa-edab.github.io/catalog/cetacean_dist.html>