Added summaries/directions to each page

nmfs-ost · Sep 28, 2024 · b5bf9c3 · b5bf9c3
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diff --git a/_quarto.yml b/_quarto.yml
@@ -33,32 +33,28 @@ website:
     contents:
       - href: index.qmd
         text: Home
-      - href: content/SharedValues.qmd
-        text: Shared Values
-      - href: content/Onboarding.qmd
-        text: Onboarding
-      - href: content/Offboarding.qmd
-        text: Offboarding
       - href: content/LabManagement.qmd
         text: Lab Management
       - href: content/DataManagement.qmd
         text: Data Management
-      - href: content/Software.qmd
-        text: Software
       - href: content/Hardware.qmd
         text: Hardware
-      - href: content/FieldMethods.qmd
-        text: Field Methods
-      - href: content/AnalysisMethods.qmd
-        text: Analysis Methods
+      - section: "Software & Analysis"
+        contents: 
+          - content/Software.qmd
+          - content/AnalysisMethods.qmd
+
       - href: content/Reporting.qmd
         text: Reporting
-      - href: content/OpenScience.qmd
-        text: Open Science
-      - href: content/PublicationsPresentations.qmd
-        text: Publications and Presentations
-      - href: content/Resources.qmd
-        text: Resources
+      - section: "Optional Pages"
+        contents: 
+          - content/SharedValues.qmd
+          - content/Onboarding.qmd
+          - content/Offboarding.qmd
+          - content/FieldMethods.qmd
+          - content/OpenScience.qmd
+          - content/PublicationsPresentations.qmd
+          - content/Resources.qmd
       - section: "NMFS Open Science Directions"
         contents:
           - content/NMFS_OpenSciDirections/Intro.qmd

diff --git a/content/AnalysisMethods.qmd b/content/AnalysisMethods.qmd
@@ -5,21 +5,21 @@ title: Analysis Methods
 An analysis methods section is required and should include the following information;
 
 -   Data Prep and Archive
-
     -   Data prep (decompressing, creating LTSAs, decimating, etc.)
-
+        -   [SAEL example](https://sael-swfsc.github.io/adrift-analysis-methods/content/DataArchive/DataPrep.html)
     -   Data quality checks (QAQC scripts)
-
+        -   [SAEL example](https://sael-swfsc.github.io/adrift-analysis-methods/content/DataArchive/DataQualityCheck.html)
     -   Data upload steps
-
         -   If you have a internal storage include directions here on where data should be stored and in what format
 
         -   You can also include a data managment structure with standardized naming and storage/folder structures
 
+        -   [SAEL example](https://sael-swfsc.github.io/adrift-analysis-methods/content/DataArchive/DataUpload.html)
 -   Analysis methods for each species, group, or sound source
-
     -   You can break this down by baleen and toothed whales, soundscapes, etc.
 
-    -    Each section should include detailed and reproducible methods that anybody can recreate
+    -   Each section should include detailed and reproducible methods that anybody can recreate
+
+You can also link to a separate hardware repository if needed ([SAEL example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Analysis-adrift.html))
 
 This can be a section with subpages or a qmd
diff --git a/content/DataManagement.qmd b/content/DataManagement.qmd
@@ -6,14 +6,18 @@ A data management section is required and should include the following informati
 
 -   Data Archive Methods
     -   Information on where your data is archived (PACM, NCEI, Tethys, Internal databases, etc)
+    -   [SAEL Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Data-Archive.html)
 -   Permits and Permit Reporting Guidelines
     -   Include permit numbers and links to your centers/groups permits
     -   Include directions for permit reporting (Protected species, National Marine Sanctuaries, Navy, Fish and Wildlife, etc)
     -   You can include links to past permit reports (these can be private google drive folders if needed)
+    -   [SAEL example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Data-Archive.html)
 -   Species and Call Types in your region
     -   Develop a species and call type library for your region
     -   This can include spectrograms of calls and sound clips
+    -   [SAEL Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Data-SpeciesAndCallTypes.html)
 -   Media
-    -   links to sound archives, media archives, web sites, blogs, etc.
+    -   Links to sound archives, media archives, web sites, blogs, etc.
+    -   [SAEL Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/media.html)
 
 This can be a section with subpages or a qmd
diff --git a/content/FieldMethods.qmd b/content/FieldMethods.qmd
@@ -1,3 +1,7 @@
 ---
 title: Field Methods
 ---
+
+A field methods section is highly recommended to help your team keep track of all current and past fieldwork documentation. This can be a link to a separate repository that includes more detailed methods. Things to include here can include hardware specifications, checklists for fieldwork prep, deployment and recovery methods, etc.
+
+[ADRIFT example](https://sael-swfsc.github.io/adrift-field-methods/)
diff --git a/content/Hardware.qmd b/content/Hardware.qmd
@@ -5,13 +5,12 @@ title: Hardware
 A hardware section is required and should include the following information;
 
 -   Information on your recorders
-
 -   Array configurations and diagrams
-
 -   Platform information (towed, moored, drifting, etc.)
-
 -   Other sensors included (GPS devices, depth senors, etc.)
 
 This will be variable for each center and may change from project to project. You should list all hardware, present and past.
 
+You can also link to a separate hardware repository if needed ([SAEL example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Hardware_ADRIFT.html))
+
 This can be a section with subpages or a qmd
diff --git a/content/LabManagement.qmd b/content/LabManagement.qmd
@@ -6,13 +6,19 @@ A lab management section is required and should include the following informatio
 
 -   Safety
     -   Both lab safety and field safety
+
     -   Link to your centers safety website
+
     -   Chemical inventory (if applicable)
+
     -   Lithium battery safety
-        -   This is an essential section to include if your lab uses these. Work with your lab safety manager to develop handling and storage instructions. See [SAEL lab manual lithium battery page](https://sael-swfsc.github.io/SAEL-lab-manual/content/Safety_Lithium-Batteries.html) for inspo
+
+        -   This is an essential section to include if your lab uses these. Work with your lab safety manager to develop handling and storage instructions. See [SAEL lab manual lithium battery page](https://sael-swfsc.github.io/SAEL-lab-manual/content/Safety_Lithium-Batteries.html)
+
+    -   [SAEL Lab Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Safety-Lab.html)
 -   Inventory
     -   Highly recommended to keep track of equipment, loans, and gear in the field
-
     -   This can be a link to a Google sheet or embedded in the website
+    -   [SAEL Lab Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Inventory.html)
 
 This can be a section with subpages or a qmd
diff --git a/content/Offboarding.qmd b/content/Offboarding.qmd
@@ -1,3 +1,7 @@
 ---
 title: Offboarding
 ---
+
+This page is optional but can be extremely beneficial when a member of your team is transitioning out of their current position. Things to include here are directions for project documentation, data and code storage/sharing, turning in equipment, etc.
+
+[Faylab example](https://thefaylab.github.io/lab-manual/06-offboarding.html)
diff --git a/content/Onboarding.qmd b/content/Onboarding.qmd
@@ -1,3 +1,7 @@
 ---
 title: Onboarding
 ---
+
+This page is optional but can be used as a landing page for new lab members. You can include introductory information, links to must read papers, new hire resources, goal setting information, etc.
+
+[Faylab example](https://thefaylab.github.io/lab-manual/04-onboarding.html)
diff --git a/content/OpenScience.qmd b/content/OpenScience.qmd
@@ -1,3 +1,7 @@
 ---
-title: Software
+title: Open Science
 ---
+
+This section is optional but is a great place for all of your open science related resources and tools. You can include information here for our Openscapes work, stack exchange, GitHub, co working guides, etc.
+
+[SAEL Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/OpenScience_Getting-Started.html)
diff --git a/content/PublicationsPresentations.qmd b/content/PublicationsPresentations.qmd
@@ -1,3 +1,4 @@
 ---
-title: Software
+title: Publications and Presentations
 ---
+This may fit in the reporting section
diff --git a/content/Reporting.qmd b/content/Reporting.qmd
@@ -1,3 +1,3 @@
 ---
-title: Software
+title: Reporting
 ---
diff --git a/content/Resources.qmd b/content/Resources.qmd
@@ -1,3 +1,5 @@
 ---
 title: Resources
 ---
+
+This page is optional but can be a good spot for any remaining resources or tools you want easy access to.
diff --git a/content/SharedValues.qmd b/content/SharedValues.qmd
@@ -1,3 +1,9 @@
 ---
 title: Shared Values
 ---
+
+A shared values / lab culture page is optional but is highly recommended. Establishing these values as a team can help create a positive and inclusive environment, foster a shared vision, promote collaboration, and build team cohesion while supporting individual growth.
+
+[SAEL example](https://sael-swfsc.github.io/SAEL-lab-manual/content/SharedValues-BestPractices.html)
+
+[Faylab example](https://thefaylab.github.io/lab-manual/02-lab-culture-philosophy.html)
diff --git a/content/Software.qmd b/content/Software.qmd
@@ -6,5 +6,6 @@ A software section is required and should include the following information;
 
 -   List of software you use and their applications (R, Matlab/Triton, Python, PAMGuard, Raven, etc.)
 -   Also include software packages or tools your team has built (PAMPal, PAMmisc, Banter, PAMscapes, Driftwatch, etc.)
+    -   [SAEL example](https://sael-swfsc.github.io/SAEL-lab-manual/content/Analysis-software.html)
 
 This can be a section with subpages or a qmd
diff --git a/index.qmd b/index.qmd
@@ -4,14 +4,10 @@ subtitle: "Template for development of regional lab manuals as part of the Passi
 page-layout: full
 ---
 
-## Template Intro
-
-This is a template for a simple Quarto website that looks like a "book". This is a common format for documentation. It includes a GitHub Action that will build the website automatically when you make changes to the files. The NOAA palette and fonts has been added to `theme.scss`. The webpage will be on the `gh-pages` branch. Serving the website files from this branch is a common way to keep all the website files from cluttering your main branch.
-
-The GitHub Action installs R so you can have R code in your qmd or Rmd files. Note, you do not need to make changes to your Rmd files unless your need Quarto features like cross-references.
-
 ## PAM SI Lab Manual Template
 
+Insert goals here
+
 ### Required Pages
 
 In order to keep consistency between science centers, the following sections/pages will be required in all lab manuals. These will be directly linked to the National PAM Repository. The links will direct you to the associated template page with more directions on what to include.
@@ -44,3 +40,9 @@ Here are two lab manuals to pull inspiration from
 -   [Faylab Manual](https://thefaylab.github.io/lab-manual/)
 
 ## How To Use This Template
+
+## Template Intro
+
+This is a template for a simple Quarto website that looks like a "book". This is a common format for documentation. It includes a GitHub Action that will build the website automatically when you make changes to the files. The NOAA palette and fonts has been added to `theme.scss`. The webpage will be on the `gh-pages` branch. Serving the website files from this branch is a common way to keep all the website files from cluttering your main branch.
+
+The GitHub Action installs R so you can have R code in your qmd or Rmd files. Note, you do not need to make changes to your Rmd files unless your need Quarto features like cross-references.