_pkgdown.yml

url: https://kevinsee.github.io/PITcleanr/
template:
  params:
    bootswatch: sandstone
navbar:
  title: ~
  type: default
  structure:
    left:
    - home
    - intro
    - reference
    - articles
    - tutorials
    - news
    right: github
  components:
    reference:
      text: Functions
      href: reference/index.html
    articles:
      text: Vignettes
      menu:
      - text: '---------'
      - text: Getting Started
      - text: Querying, Compressing, and Making Sense of PIT Tag Detection Data
        href: articles/Prep_PIT_data.html
      - text: '---------'
      - text: More...
        href: articles/index.html
    news:
      text: News
      href: news/index.html
reference:
- title: Compressing PTAGIS Data
  desc: |
    Functions for reading in complete capture histories and compressing them
- contents:
  - readCTH
  - compress
  - qcTagHistory
  - extractTagObs
- title: Querying Data
  desc: |
    Functions for querying data from PTAGIS or NHDPlus
- contents: starts_with("query")
- title: Building Configuration File
  desc: |
    Functions to help the user build a configuration file
- contents: buildConfig
- title: Parent-Child Table
  desc: |
    Functions to help the user build, edit and visualize a parent-child table
- contents:
  - extractSites
  - buildParentChild
  - addParentChildNodes
  - editParentChild
  - findDwnstrmHydroseg
  - findDwnstrmSite
  - listParents
  - buildNodeOrder
  - buildPaths
  - plotNodes
  - buildNodeGraph
- title: Manipulate Data
  desc: |
    Functions to help the user manipulate and summarize data
- contents:
  - addDirection
  - estimateSpawnLoc
  - estNodeEff
  - filterDetections
  - prepWrapper
  - summarizeTagData
  - compressDART
  - readTestTag
- title: Deprecated functions
  desc: |
    These functions have been superseded
- contents:
  - obsNetwork
  - defineRepGrps
  - filterLGRtrapDB
  - findDwnStrmSite_RKM
  - processCapHist_LGD
  - processCapHist_PRD
  - processCapHist_PRO
  - processCapHist_TUM
  - processDART_LGR
  - summariseValidTagsLGR
  - writeCapHistOutput
  - writeFishPaths
  - writeSpwnPaths
  - writeOldNetworks
  - writeLGRNodeNetwork
  - writePRDNodeNetwork
  - writePRONodeNetwork
  - writeTUMNodeNetwork
  - writeTUMNodeNetwork_noUWE
articles:
- title: Getting Started
  contents:
  - Prep_PIT_data
- title: Specific components
  contents:
  - read_in_data
  - configuration_files
  - compress_data
  - parent_child
- title: DABOM
  desc: |
    Vignettes aimed at preparing data for DABOM
  contents:
  # - DABOM_prep
  - quick_prep