Working group edits

_quarto.yml

@@ -5,7 +5,7 @@ project:
 book:
   title: IRA Passive Acoustic Monitoring Strategic Initiative Workshop Report
   subtitle: La Jolla, California 
-  date: March 2024
+  date: April 2024
   downloads: [pdf, docx]
   author:
   - name: Sofie Van Parijs
@@ -50,32 +50,47 @@ book:
       - name: NOAA Fisheries
         department: SEFSC
         address: 75 Virginia Beach Drive, Miami, FL 33149
+  - name: Rebecca Van Hoeck
+    email: [email protected]
+    affiliations:
+      - name: NOAA Fisheries 
+        department: NEFSC
+        address: 166 Water Street, Woods Hole, MA
   - name: Carrie Wall Bell
     email: [email protected]
     affiliations:
       - name: University of Colorado Boulder, Cooperative Institute for Research in Environmental Sciences
         department: NOAA National Centers for Environmental Information
         address: 325 Broadway, Boulder, CO 80305
-  - name: Rebecca Van Hoeck
-    email: [email protected]
-    affiliations:
-      - name: NOO Fisheries 
-        department: NEFSC
-        address: 166 Water Street, Woods Hole, MA
+  - name: Ann Allen
+  - name: Yvonne Barkley
+  - name: Kourtney Burger
+  - name: Manolo Castellote
+  - name: Genevieve Davis
+  - name: Annamaria DeAngelis
+  - name: Candice Emmons
+  - name: Samara Haver
+  - name: Cory Hom-Weaver
+  - name: Jennifer McCullough
+  - name: Megan McKenna
+  - name: Taiki Sakai
+  - name: Ludovic Tenorio
+  - name: Dan Woodrich
 
   chapters:
     - index.qmd
+    - text/ExecutiveSummary.qmd
     - text/Intro.qmd
   # - text/AttendeeIntros.qmd
     - text/Cloud.qmd
     - text/NCEI.qmd
     - text/Climate.qmd
     - text/StockAssess.qmd
     - text/Soundscape.qmd
-    - text/Detection.qmd
     - text/Github.qmd
+    - text/Detection.qmd
     - text/Management.qmd
-    - text/ListAttendees.qmd
+    #- text/ListAttendees.qmd
     - text/Acknowledgements.qmd
  #   - text/references.qmd
 

text/Acknowledgements.qmd

@@ -1,7 +1,7 @@
 # Acknowledgements
 
-The PAM SI working group acknowledges the support from the Inflation Reduction Act and NOAA's Climate Ready Fisheries investments for supporting the Essential Data Acquisition component that the PAM Strategic Initiative is a part of. Thank you to the Climate Ready Fisheries and Essential Data Acquisition staff for they administrative support of the the PAM Strategic initiative. The PAM SI working group especially acknowledges all participants of the March 2024 workshop whose valuable time, thoughtful engagement, and productive discussion made the success of this workshop possible.
+The PAM SI working group acknowledges the support from the Inflation Reduction Act and NOAA's Climate Ready Fisheries investments for supporting the Essential Data Acquisition component that the PAM Strategic Initiative is a part of. Thank you to the Climate Ready Fisheries and Essential Data Acquisition staff for their administrative support of the the PAM Strategic initiative. The PAM SI working group especially acknowledges all participants of the March 2024 workshop whose valuable time, thoughtful engagement, and productive discussion made the success of this workshop possible.
 
 Thank you to NOAA Fisheries Office of the Chief Information Officer for their support of the cloud computing projects and to Jeffrey Walker for his work on the PACM cloud transition. Thank you to the UxS Strategic Initiative for their collaboration on the Pacific Glider projects.
 
-Funding for participation of Taiki Sakai was provided by Bureau of Ocean Energy Management (G14 M20PG00013).
+Funding for participation of Taiki Sakai was provided by the Bureau of Ocean Energy Management (G14 M20PG00013).

text/Climate.qmd

@@ -8,15 +8,15 @@ To advance data integration in support of creating tools for climate change appl
 
 ### Project Team
 
-| Genevieve Davis   | Catherine Berchok |                    |
-|-------------------|-------------------|--------------------|
-| Candice Evans     | Ann Allen         | Melissa Soldevilla |
-| Manolo Castellote | Shannon Rankin    | Samara Haver       |
-| Taiki Sakai       |                   |                    |
+| Genevieve Davis (NEFSC)  | Catherine Berchok (AFSC) |                            |
+|--------------------------|--------------------------|----------------------------|
+| Candice Emmons (NWFSC)   | Ann Allen (PIFSC)        | Melissa Soldevilla (SEFSC) |
+| Manolo Castellote (AFSC) | Shannon Rankin (PIFSC)   | Samara Haver (OST)         |
+| Taiki Sakai (SWFSC)      |                          |                            |
 
 ### Summary
 
-We will create a streamlined workflow to integrate PAM data with necessary ancillary datasets to address questions relevant to climate change and long-term species trends. This workflow will include: identifying PAM data to be included; identifying the climatological data to be included; creating tools for accessing, formatting, and integrating a subset of these data streams; and using these tools and approaches broadly across all regions and species of interest. The first goal of this project is a comparison of humpback whale occurrence trends nationwide. All regions will submit and format their humpback detection data into the Passive Acoustic Cetacean Map database.The second goal will be to identify and create tools to access and apply relevant climate data on the humpback whale dataset. This workflow will allow for a national comparison of one species to be able to identify and compare changes (or lack thereof) within and across regions. Once this structure has been established, these standardized data formats, tools, and environmental data needs can be applied across the range of project goals and regional needs, including regional-specific high-profile species. This project directly supports the PAM SI objective to advance PAM data analysis and integration approaches with an emphasis on addressing long-term trends.
+We will create a streamlined workflow to integrate PAM data with necessary ancillary datasets to address questions relevant to climate change and long-term species trends. This workflow will include: identifying PAM data to be included; identifying the climatological data to be included; creating tools for accessing, formatting, and integrating a subset of these data streams; and using these tools and approaches broadly across all regions and species of interest. The first goal of this project is to compare humpback whale occurrence trends nationwide. All regions will submit and format their humpback detection data into the Passive Acoustic Cetacean Map database. The second goal will be to identify and create tools to access and apply relevant climate data on the humpback whale dataset. This workflow will allow for a national comparison of one species to be able to identify and compare changes (or lack thereof) within and across regions. Once this structure has been established, these standardized data formats, tools, and environmental data streams can be applied across the range of project goals and regional needs, including regional-specific high-profile species. This project directly supports the PAM SI objective to advance PAM data analysis and integration approaches with an emphasis on addressing long-term trends.
 
 ### Action Items
 

text/Cloud.qmd

@@ -8,22 +8,21 @@ Developing a National PAM Cloud operational repository for data processing and s
 
 ### Project Team
 
-| Sofie Van Parijs | Daniel Woodrich  |              |
-|------------------|------------------|--------------|
-| Ann Allen        | Sofie Van Parijs | Ludo Tenorio |
-| Taiki Sakai      |                  |              |
+| Sofie Van Parijs (NEFSC) | Daniel Woodrich (AFSC) |                      |
+|--------------------------|------------------------|----------------------|
+| Ann Allen (PIFSC)        | Taiki Sakai (SWFSC)    | Ludo Tenorio (SEFSC) |
 
 ### Summary
 
-We will work collaboratively with NMFS OCIO to create our Google Cloud Project (GCP) architecture with data buckets for each FMC. We will have a phased approach to testing and growing the project depending on the hurdles, cost models and successes that we encounter. Once the GCP project is up and running we can have monthly check in calls. Along with our National PACM GCP project fulfills the PAM SI Operational Cloud objective. 
+We will work collaboratively with NMFS OCIO to create our Google Cloud Project (GCP) architecture with data buckets for each FMC. We will have a phased approach to testing and growing the project depending on the hurdles, cost models, and successes that we encounter. Once the GCP project is up and running we can have monthly check in calls. Along with our National PACM GCP project fulfills the PAM SI Operational Cloud objective. 
 
 ### Action Items
 
 1.  **Phase 1:** Stand up the GCP project (Dan/NMFS OCIO team). *Deadline: April 2024*
 
 2.  **Phase 2:**  Design performance evaluation metrics template (PAM SI GCP team). *Deadline: May 2024*
 
-3.  **Phase 3:** Upload 1 year long data sets for each of the following science centers: SEFSC, NEFSC, PIFSC, AKFCS (Dan w FMC data experts). *Deadline: June 2024*
+3.  **Phase 3:** Upload 1 year long data sets for each of the following science centers: SEFSC, NEFSC, PIFSC, AFCS (Dan w FMC data experts). *Deadline: June 2024*
 
 4.  **Phase 4:** Software phase I: Upload and test software that are ready for GCP transfer e.g. Google AI, PyPAM, PamGuard, Raven, INSTINCT  (NEFSC IT, Dan, Taiki). *Deadline: June - September 2024*
 

text/Detection.qmd

@@ -52,11 +52,10 @@ Create a cross FMC list of short term and long term software development needs.
 
 ### Project Team
 
-| Canidce Emmons (NWFSC)      |                             |                             |
+| Canidce Emmons (NWFSC)      |                             |                         |
 |-------------------------|-----------------------|-------------------------|
-| Jennifer McCullough (PIFSC) | Annamaria DeAngelis (NEFSC) | Jennifer McCullough (PIFSC) |
-| Sofie Van Parijs (NEFSC)    | Taiki Sakai (SWFSC/NEFSC)   | Ludovic Tenorio (SEFSC)     |
-| Cory Hom-Weaver (SWFSC)     |                             |                             |
+| Jennifer McCullough (PIFSC) | Annamaria DeAngelis (NEFSC) | Cory Hom-Weaver (SWFSC) |
+| Sofie Van Parijs (NEFSC)    | Taiki Sakai (SWFSC/NEFSC)   | Ludovic Tenorio (SEFSC) |
 
 ### Summary
 

text/ExecutiveSummary.qmd

@@ -0,0 +1,27 @@
+---
+title: Executive Summary
+---
+
+The NOAA Fisheries Passive Acoustic Monitoring Strategic Initiative (PAM SI) is an Inflation Reduction Act (IRA) funded effort as part of NOAA Fisheries’ \$349 million Climate Ready Fisheries initiative to build a dynamically managed fisheries system that accounts for climate change and supports science-based management and conservation. The PAM SI is one of seven Strategic Initiatives within the Essential Data Acquisition and Management component of Climate Ready Fisheries that focuses on development of advanced technologies in support of expanding and modernizing stock assessments, data systems, and infrastructure. In March 2024 the PAM SI team held a three-day workshop to identify specific priority projects that address common barriers and challenges across all PAM programs. 
+
+This report provides a brief background and situational context for the needs of the NOAA Fisheries PAM programs and lays out a target action plan to address each priority project identified. These priority projects represent an ambitious, collaborative effort to make transformational progress towards a modern National PAM enterprise that provides valuable scientific information about stock assessments, long-term species trends, and climate impacts on marine ecosystems.Any progress towards these  PAM SI projects will provide the critical infrastructure - including human capital, hardware, and software - for continued success and expansion of the applications of PAM to the NOAA Fisheries protected species mission and mandates beyond the lifetime of the IRA funding. This is especially important because some components included here are unfunded.
+
+NOAA Fisheries’ PAM programs collect underwater sound recordings of the marine environment. Identification of the sounds produced by protected marine mammal species, fishes, humans, or the  environment allows for an understanding of marine soundscapes and provides information on changes in species distribution, behavior and/or density. The technological revolution in PAM over the past decade has allowed both acoustic recorders and analytical approaches to increasingly become an integral part of NOAA Fisheries core science mission. PAM’s capacity for creating long term time series makes it an ideal approach for evaluating changes in species stocks, ecosystem interactions, and climate change. There are currently 7 NMFS PAM programs including each NMFS Science Center and the S&T’s Ocean Acoustic Program (OAP). The success and advancement of the Fisheries PAM programs also relies on close collaboration with the NOAA National Centers for Environmental Information (NCEI) and the NOAA Office of the National Marine Sanctuaries (ONMS). The transformational value of the PAM SI lies in bringing together representatives from each of these programs to work collaboratively on common high priority infrastructure and analytical needs. 
+
+The PAM SI working groups has identified four key objectives: 1) Accelerate Pacific-wide PAM-glider operations; 2) Establishing National PAM Operational and Archival Cloud Storage solutions; 3) Developing a National PAM Decision Support Tool; and 4) Advancing National PAM Analytical and Integration Approaches. Progress towards these objectives will implement transformational activities that will significantly change the way in which we collect, analyze, and make PAM data accessible for answering mission critical questions. Because PAM SI Objectives 1 and 3 are collaborations with the UxS SI and IRA North Atlantic Right Whale projects, respectively, they are not further detailed in this report. More information about those objectives can be found in the [PAM SI Proposal](https://docs.google.com/document/d/1BPkv6vRO97T9Vitud8Ng5ws7tudbtD-IF2NwzX4oRmU/edit?usp=sharing). 
+
+During the March 2024 workshop, the PAM SI team engaged in a series of eight Round Table Discussions focused on a common barrier or need for all PAM programs, each resulting in one or more priority projects. 
+
+Priority projects supporting Objective 2 include:
+
+-   a Google Cloud Project to establish national operational cloud storage and processing capabilities; and
+-   an NCEI archiving project to build a more streamlined archive workflow. 
+
+Priority projects supporting Objective 4 include:
+
+-   a pilot project to evaluate long-term trends in nationwide humpback whale spatio-temporal distribution that will develop data integration tools that can be applied to any region or species of interest; 
+-   three project options that would expand the applications of PAM data for stock assessments through density estimation and species distribution models; 
+-   two projects to expand the applications of soundscape metrics and visualizations; and
+-   multiple projects focused on establishing an open science approach for information sharing to support collaborative analytical approaches across the regions. 
+
+Lastly, the PAM SI discussed the target management tools, metrics, and strategies relevant to stock assessments and climate that we strive to achieve through the SI. This report details the expected outcome, project leads, project team, action items, and target timeline for each of these priority projects.