_pkgdown.yml

template:
  params:
    ganalytics: UA-53797708-7
  includes:
    before_title: '<a href="https://www.usgs.gov/"><img src="logo.png" id="logo" alt="Home" style="padding: 0px 50px 0px 0px;"></a>'
  bootstrap: 5
  theme: atom-one-light
  bslib:
    bg: "white"
    fg: "#283140"
    navbar-brand-color: "white"
    navbar-light-color: "white"
    nav-link-color: "white"
    nav-link-hover-color: "#a9a9a9"
    navbar-light-brand-hover-color: "white"
    navbar-light-hover-color: "white"
    text-muted: "white"
    pkgdown-nav-height: 125px
    
navbar:
  left:
  - text: Overview and Updates
    href: articles/Overview.html
  - text: Introduction
    href: articles/EGRET.html
  - text: Function Help Pages
    href: reference/index.html
  - text: Articles
    menu:
    - text: Enhancements
      href: articles/Enhancements.html
    - text: WRTDS Kalman
      href: articles/WRTDSK.html
    - text: Running in Parallel
      href: articles/parallel.html
    - text: Random Residuals
      href: articles/rResid.html
    - text: Seasonal Analysis
      href: articles/SeasonalFraction.html
    - text: Daily Streamflow Trends
      href: articles/streamflow_trend.html
    - text: Trends by month
      href: articles/TrendsByMonth.html
    - text: Alternative Q Method
      href: articles/AlternativeQMethod.html
    - text: Annual_Hydrograph_Timing
      href: articles/Annual_Hydrograph_Timing.html
    - text: Join discrete and sensor data
      href: articles/Join_closest.html
    - text: Compare QW and UV
      href: articles/Compare_QW_and_UV.html
    - text: Custom Units
      href: articles/units.html
  - text: Bibliograpy
    href: articles/References_WRTDS.html
  right:
  - icon: fa-gitlab fa-lg
    href: https://code.usgs.gov/water/EGRET
reference:
  - title: Import Data
    desc:  Functions for user-generated or web retrieval data.
    contents:
      - readUserDaily
      - readUserSample
      - readNWISDaily
      - readNWISSample
      - readWQPSample
      - readNWISInfo
      - readWQPInfo
  - title: WRTDS
    desc: Functions working running and analyzing the WRTDS model
    contents:
      - modelEstimation
      - setUpEstimation
      - WRTDSKalman
      - runPairs
      - runGroups
      - runSeries
      - run_WRTDS
      - estCrossVal
      - estDailyFromSurfaces
      - estSurfaces
      - flexFN
      - getConcFluxFromSurface
      - getSurfaceEstimates
  - title: Plot Data
    desc: Functions for plotting eList objects
    contents:
      - multiPlotDataOverview
      - plotFlowSingle
      - plotFluxQ
      - plotFour
      - plotFourStats
      - plotQTimeDaily
      - plotSDLogQ
      - boxConcMonth
      - boxQTwice
      - plotConcTime
      - plotConcQ
      - boxConcThree
      - plot15
      - plot1of15
  - title: Plot Model Outputs
    desc: Functions for plotting modeled eList objects
    contents:
      - plotConcPred
      - plotFluxPred
      - plotResidPred
      - plotResidQ
      - plotResidTime
      - boxResidMonth
      - plotConcHist
      - plotFluxHist
      - plotFluxTimeDaily
      - plotConcTimeDaily
      - plotConcQSmooth
      - plotConcTimeSmooth
      - fluxBiasMulti
      - plotContours
      - plotDiffContours
      - plotWRTDSKalman
      - plotTimeSlice
      - plotMonthTrend
      - flexPlotAddOn
      - genericEGRETDotPlot 
      - generalAxis
      - logPretty1
      - logPretty3
  - title: Table
    desc: Functions for creating tables from eList objects
    contents:
      - printSeries
      - makeAnnualSeries
      - tableChange
      - tableFlowChange
      - tableResults
      - setupYears
      - calculateMonthlyResults
  - title: Utilities
    desc: Additional utility functions
    contents:
      - blankTime
      - cleanUp
      - compressData
      - cumQdate
      - dataOverview
      - decimalDate
      - errorStats
      - fixSampleFrame
      - flowDuration
      - fluxBiasStat
      - printPairs
      - printGroups
      - getDaily
      - getInfo
      - getSample
      - getSurfaces
      - jitterSam
      - makeAugmentedSample
      - mergeReport
      - nCensoredVals
      - nDischarge
      - nObservations
      - printFluxUnitCheatSheet
      - printqUnitCheatSheet
      - processQWData
      - randomSubset
      - removeDuplicates
      - saveResults
      - setPA
      - stitch
      - triCube
      - censoredSegments
      - checkStartEndDate
      - checkSurfaceSpan
      - Constants
      - dateFormatCheck
      - decimalHighLow
      - makeDateInfo
      - populateConcentrations
      - populateDaily
      - populateDailySamp
      - populateDateColumns
      - populateParameterINFO
      - populateSampleColumns
      - populateSiteINFO
      - qUnit-class
      - concUnit-class
      - readDataFromFile
      - Choptank_eList
      - selectDays
      - setSeasonLabel
      - setSeasonLabelByUser
      - startEnd
      - surfaceIndex
      - surfaceStartEnd
      - yPretty 
      - monthLabel-class
      - is.egret
      - as.egret 
      - EGRET-package
      - fluxUnit-class