_pkgdown.yml

home:
  links:
    - text: PlantCV source code
      href: https://github.com/danforthcenter/PlantCV

url: https://danforthcenter.github.io/pcvr/
template:
  bootstrap: 5

footer:
  structure: 
    right: built_with
    left: [maintained_by, developed_in, logo_credit]
  components:
    maintained_by: Maintained by Josh Sumner
    developed_in: <br> Developed in DDPSC Datascience Core Facility
    logo_credit: <br> Logo design by <a href="https://twitter.com/Kerri_Gilbert">Kerri Gilbert</a>

navbar:
  title: "pcvr"
  left:
    - icon: fa-home fa-lg
      href: index.html
    - text: "Vignettes"
      menu:
        - text: "Bellwether"
          href: articles/bellwether.html
        - text: "Longitudinal Modeling"
          href: articles/longitudinal.html
        - text: "Root Phenotyping"
          href: articles/roots.html
        - text: "Directional Statistics"
          href: articles/directional.html
        - text: "Installation Tutorial"
          href: articles/installation.html
        - text: "Conjugate Tutorial"
          href: articles/pcvrTutorial_conjugate.html
        - text: "Intermediate Growth Modeling Tutorial"
          href: articles/pcvrTutorial_igm.html
        - text: "Advanced Growth Modeling Tutorial"
          href: articles/pcvrTutorial_agm.html
        - text: "Multi-Value Traits Tutorial"
          href: articles/pcvrTutorial_mvt.html
        - text: "Using online PlantCV Output"
          href: articles/reading_pcv_data.html
    - text: "Functions"
      href: reference/index.html
    - text: "News"
      href: news/index.html
    - text: "Quarto Tutorials"
      menu:
        - text: "Installation"
          href: https://github.com/danforthcenter/pcvr/tree/main/tutorials/pcvrInstallation
        - text: "Intro"
          href: https://github.com/danforthcenter/pcvr/tree/main/tutorials/pcvrTutorial_intro
        - text: "Growth Modeling"
          href: https://github.com/danforthcenter/pcvr/tree/main/tutorials/pcvrTutorial_intermediateGrowthModeling
        - text: "Advanced Growth Modeling"
          href: https://github.com/danforthcenter/pcvr/tree/main/tutorials/pcvrTutorial_advancedGrowthModeling
        - text: "Bayesian Conjugate Priors"
          href: https://github.com/danforthcenter/pcvr/tree/main/tutorials/pcvrTutorial_conjugate
        - text: "Multi-Value Traits"
          href: https://github.com/danforthcenter/pcvr/tree/crop_reporter/tutorials/pcvrTutorial_multiValueTraits
    - text: "PlantCV"
      href: https://plantcv.org/
  right:
   - icon: fa-github
     href: https://github.com/danforthcenter/pcvr
   - icon: fa-leaf
     href: https://github.com/danforthcenter/PlantCV
    
reference:
  - title: "Bayesian Statistics"
    desc: >
      Functions for Bayesian statistics.
    contents:
      - conjugate
      - growthSS
      - fitGrowth
      - growthPlot
      - testGrowth
      - barg
      - combineDraws
      - plotPrior
      - distributionPlot
      - brmViolin
  - title: "Modeling"
    desc: >
      Functions for Bayesian or Frequentist Longitudinal (and other) Modeling
    contents:
      - growthSim
      - growthSS
      - fitGrowth
      - growthPlot
      - testGrowth
  - title: "Lemnatech System Support"
    desc: >
      Functions for use with Lemnatech style data.
    contents:
      - bw.outliers
      - bw.time
      - bw.water
      - pwue
  - title: "Single-Value Traits"
    desc: >
      Functions suited for use with single-value trait data
      (Height, Area, etc)
    contents:
    - conjugate
    - growthSS
    - frem
    - relativeTolerance
    - cumulativePheno
  - title: "Multi-Value Traits"
    desc: >
      Functions suited for use with multi-value trait data
      (spectral indices, colorspaces, CropReporter, etc)
    contents:
      - conjugate
      - mv_ag
      - pcv.emd
      - pcv.joyplot
      - pcadf
      - mvSS
      - pcv.net
      - pcv.plsr
  - title: "Reading PlantCV output"
    desc: >
      Functions for reading different formats of PlantCV output (note for PlantCV >= 4.1)
      data.table::fread or utils::read.csv are perfectly adequate.
    contents:
      - read.pcv.3
      - read.pcv
  - title: "internal"
    contents:
      - awkHelper
      - brmPlot
      - brmSurvPlot
      - checkGroups
      - fitGrowthbrms
      - fitGrowthflexsurv
      - fitGrowthmgcvgam
      - fitGrowthnlme
      - fitGrowthnlmegam
      - fitGrowthnlrq
      - fitGrowthnlrqgam
      - fitGrowthnls
      - fitGrowthnlsgam
      - fitGrowthsurvreg
      - flexsurvregPlot
      - gam_diff
      - net.plot
      - nlmePlot
      - nlrqPlot
      - nlsPlot
      - mvSim
      - pcv_theme
      - plotVIP
      - rqPlot
      - fitGrowthlm
      - fitGrowthrq
      - survregPlot
      - summary.pcvrss
      - print.pcvrss
      - pcvrss-class
      - print.pcvrsssummary