_pkgdown.yml

title: FSA

url: https://fishr-core-team.github.io/FSA/

authors:
  Derek H. Ogle:
    href: http://derekogle.com
  Jason Doll:
  Powell Wheeler:
  Alexis Dinno:
    
template:
  bootstrap: 5
  bootswatch: flatly
  
development:
  mode: release
  
reference:
  - title: Age Comparisons
    desc: Summarize and visualize bias and precision among multiple estimates of age for individual fish.
    contents:
      - ageBias
      - agePrecision
      - plotAB
  - title: Age-Length Keys
    desc: Process age-length keys including assigning ages to indvidual fish and visualizing a key.
    contents:
      - alkIndivAge
      - alkPlot
      - alkAgeDist
      - alkMeanVar
  - title: Size Structure
    desc: Efficiently calculate and summarize proportional size distribution (PSD) data.
    contents:
      - PSDlit
      - psdVal
      - psdPlot
      - psdCalc
      - psdCI
      - psdAdd
      - tictactoe
  - title: Condition and Weight-Length
    desc: Efficiently calculate and summarize relative weight and visualize weight-length data among groups with different slopes.
    contents:
      - WSlit
      - wsVal
      - wrAdd
      - lwCompPreds
  - title: Abundance (Capture-Recapture)
    desc: Estimate abundance with capture-recapture data, including handling and summarizing data in a capture history format.
    contents:
      - mrClosed
      - mrOpen
      - capHistConvert
      - capHistSum
  - title: Abundance (Depletion)
    desc: Estimate abundance with depletion and removal data.
    contents:
      - depletion
      - removal
  - title: Individual Growth
    desc: Fit various growth models (von Bertalanffy, Gompertz, logistic, Richards, Schnute) to individual fish.
    contents:
      - makeGrowthFun
      - showGrowthFun
      - findGrowthStarts
  - title: Mortality Rates
    desc: Estimate mortality rates from catch curve data and empirical models.
    contents:
      - catchCurve
      - chapmanRobson
      - metaM
  - title: Stock-Recruiment
    desc: Fit various (Beverton-Holt, Ricker, Shepherd) stock-recruitment functions.
    contents:
      - srFuns
      - srStarts
  - title: Utilities (Fisheries-Specific)
    desc: Utilities that are likely useful only to fisheries scientists.
    contents:
      - addZeroCatch
      - expandCounts
      - expandLenFreq
      - lencat
  - title: Utilities (General Statistics)
    desc: Utilities of a statistical nature that are likely to be useful to a fisheries scientist.
    contents:
      - binCI
      - hyperCI
      - poiCI
      - boot
      - dunnTest
      - extraSS
      - geomean
      - hist.formula
      - histFromSum
      - htest
      - ksTest
      - logbtcf
      - lrt
      - nlsBoot
      - nlsTracePlot
      - pcumsum
      - rSquared
      - se
      - Summarize
      - sumTable
  - title: Utilities (Other)
    desc: Miscellaneous utilities.
    contents:
      - FSA
      - capFirst
      - col2rgbt
      - fact2num
      - fishR
      - headtail
      - is.even
      - kCounts
      - lagratio
      - perc
      - peek
      - repeatedRows2Keep
      - validn
  - title: Data
    desc: Data files.
    contents:
      - BluegillJL
      - BrookTroutTH
      - ChinookArg
      - CodNorwegian
      - CutthroatAL
      - Ecoli
      - GrowthData1
      - GrowthData2
      - GrowthData3
      - Mirex
      - PikeNY
      - PikeNYPartial1
      - PSDlit
      - PSDWRtest
      - SMBassLS
      - SMBassWB
      - SpotVA1
      - WhitefishLC
      - WR79
      - WSlit

  - title: Defunct
    desc: Defunct functions.
    contents:
      - FSA-defunct

  - title: Deprecated
    desc: Deprecated functions.
    contents:
      - growthModels
      - vbStarts

navbar:
  left:
    - text: Reference
      href: reference/index.html
    - text: Demonstrations
      menu:
      - text: Computing Proportional Size Distribution Metrics
        href: articles/Computing_PSDs.html
      - text: Computing Relative Weights
        href: articles/Computing_Relative_Weights.html
      - text: Fitting Growth Functions
        href: articles/Fitting_Growth_Functions.html
    - text: Explanations
      menu:
      - text: Growth Function Equations
        href: articles/Growth_Function_Parameterizations.html
      - text: Explaining Starting Values for Growth Functions
        href: articles/Growth_Starting_Values.html
  right:
    - icon: fa-newspaper
      href: news/index.html
      aria-label: See package news
    - icon: fa-home fa
      href: index.html
      aria-label: Goto FSA home
    - icon: fa-github fa
      href: https://github.com/fishR-Core-Team/FSA
      aria-label: Goto FSA github page