_quarto.yml

project: 
  type: website
  
website: 
  page-navigation: true
  title: "Data Management & Storage Best Practices for Long-term and Archival Passive Acoustic Monitoring (PAM) Data" 
  site-url: "https://rwscollab.github.io/pam-data-mgmt/" 
  repo-url: https://github.com/RWSCollab/pam-data-mgmt 
  
  navbar:
    search: true
    logo: "RWSC_Logo_notext.png"
  
  page-footer:
    left: "© CC-By RWSC Marine Mammal Subcommittee, 2022"
    right: 🐋
  
  search:
    location: sidebar
    type: textbox
    
  sidebar:
    title: PAM Data Management Best Practices
    logo: "images/MM.png"
    pinned: true
    align: "center"
    tools: 
      - icon: globe
        href: https://rwsc.org
        text: "rwsc.org"
      - icon: github
        href: https://github.com/RWSCollab/pam-data-mgmt
        text: "github"
      - icon: cloud-download
        href: https://rwsc.org/wp-content/uploads/2022/12/RWSC-PAM-Data-Management-Storage-Best-Practices.pdf
        text: "download pdf"

    style: "floating"
    search: true
    collapse-level: 1
    
    contents:
      - href: index.qmd
        text: Introduction
      
      - text: "---"
        
      - section: 1. Planning Steps
        href: index.qmd#planning
        contents:
          - href: index.qmd#engage
            text: I. Engage with the RWSC Marine Mammal Subcommittee
            
          - href: index.qmd#codeploy
            text: II. Codeployment of other sensors
            
          - href: index.qmd#bottom
            text: III. Best practices to minimize bottom disturbance from underwater mooring systems
            
          - href: index.qmd#noise
            text: IV. Best practices to minimize self-noise from underwater mooring systems
            
          - href: index.qmd#navy
            text: V. Navy awareness of PAM deployments on the Atlantic OCS
            
      - text: "---"
      
      - section: 2. Deployment & Data Collection
        href: index.qmd#deploy
        contents: 
          - href: index.qmd#define
            text: VI. Definitions for raw, processed, cleaned, and analyzed data
            
          - href: index.qmd#hardware
            text: VII. PAM hardware calibration best practices and minimum specifications
            
          - href: index.qmd#qa
            text: VIII. Best practices for PAM data QA/QC
      
      - text: "---"
      
      - section: 3. Analysis, Reporting, & Visualization
        href: index.qmd#arv
        contents:
          - href: index.qmd#analysis
            text: IX. Analysis of species detections and ambient noise metrics
            
          - href: index.qmd#nefsc
            text: X. Reporting to NOAA NEFSC Passive Acoustics Research Group
            
          - href: index.qmd#archive
            text: XI. Archiving and access at NCEI Passive Acoustic Data Archive
            
          - href: index.qmd#visual
            text: XII. Visualizing species detection data
      
      - text: "---"      
      
      - href: index.qmd#appendixa
        text: Appendix A
      
      - text: "---"
      
      - href: index.qmd#appendixb
        text: Appendix B

format:
  html:
    theme: 
      - cosmo
      - rwsc.scss
    code-copy: true
    code-overflow: wrap
    toc: true
    link-external-newwindow: true

filters:
  - include-files.lua
  - quarto