_pkgdown.yml

title: SIMplyBee
url: http://www.simplybee.info
development:
  mode: auto
navbar:
  structure:
    left:
    - home
    - reference
    - articles
    - news
    right: github
  components:
    home:
      icon: fa-home
      href: index.html
    reference:
      icon: fa-question-circle
      text: Reference
      href: reference/index.html
    articles:
      icon: fa-book
      text: Articles
      menu:
      - text: Introduction to honeybee biology
        href: articles/A_Introduction_to_honeybee_biology.html
      - text: Colony Events
        href: articles/C_Colony_events.html
      - text: Multiple colonies
        href: articles/B_Multiple_colonies.html
      - text: Crossing
        href: articles/D_Crossing.html
      - text: Genomics
        href: articles/E_Genomics.html
      - text: Sampling functions
        href: articles/G_Sampling_functions.html
      - text: Quantitative Genetics
        href: articles/F_Quantitative_Genetics.html
      - text: FAQs
        href: articles/Z_FAQs.html
reference:
  - title: Class
    contents:
    - Colony-class
    - MultiColony-class
    - SimParamBee
    - c,NULLOrPop-method


  - title: Colony and MultiColony operations
  - subtitle: Utility
    contents:
    - createColony
    - setLocation
    - createMultiColony
    - selectColonies
    - pullColonies
    - removeColonies
    - getId
    - rcircle
  - subtitle: Events
    contents:
    - cross
    - buildUp
    - downsize
    - supersede
    - split
    - swarm
    - collapse
    - combine
    - resetEvents
  - subtitle: Event information
    contents:
    - getEvents
    - hasCollapsed
    - hasSplit
    - hasSuperseded
    - hasSwarmed
    - isProductive
  - subtitle: Caste specific events - Add
    contents:
    - addWorkers
    - addDrones
    - addVirginQueens
  - subtitle: Caste specific events - Replace
    contents:
    - reQueen
    - replaceWorkers
    - replaceDrones
    - replaceVirginQueens
  - subtitle:  Caste specific events - Remove
    contents:
    - removeQueen
    - removeWorkers
    - removeDrones
    - removeVirginQueens


  - title: Caste operations
  - subtitle: Create
    desc: (output is Population)
    contents:
    - createWorkers
    - createDrones
    - createVirginQueens
    - createDCA
  - subtitle: Get
    desc: (output is Population)
    contents:
    - getCastePop
    - getQueen
    - getFathers
    - getWorkers
    - getDrones
    - getVirginQueens
  - subtitle: Pull
    desc: (output is list of Populations)
    contents:
    - pullInd
    - pullCastePop
    - pullQueen
    - pullWorkers
    - pullDrones
    - pullVirginQueens
    - pullDroneGroupsFromDCA
  - subtitle: Get information
    contents:
    - getCaste
    - getQueenAge
    - getCasteId
    - getCasteSex
    - getLocation
  - subtitle: Queen's birth
    contents:
    - setQueensYearOfBirth
    - getQueenYearOfBirth


  - title: Is/are functions
  - subtitle: Individuals
    contents:
    - isCaste
    - isQueen
    - isFather
    - isWorker
    - isDrone
    - isVirginQueen
  - subtitle: Is caste present
    contents:
    - isQueenPresent
    - areFathersPresent
    - areWorkersPresent
    - areDronesPresent
    - isDronesPresent
    - areVirginQueensPresent
  - subtitle: Colony and MultiColony
    contents:
    - isColony
    - isEmpty
    - isMultiColony
    - isNULLColonies
  - subtitle: Other
    contents:
    - isSimParamBee


  - Title: Numbers functions
  - subtitle: Individuals
    contents:
    - nCaste
    - nQueens
    - nFathers
    - nWorkers
    - nDrones
    - nVirginQueens
    - nHomBrood
  - subtitle: Sampling individuals
    contents:
    - nFathersPoisson
    - nWorkersPoisson
    - nDronesPoisson
    - nVirginQueensPoisson
  - subtitle: Colony and MultiColony
    contents:
    - nColonies
    - nNULLColonies
    - nEmptyColonies
  - subtitle: Proportion functions
    contents:
    - downsizePUnif
    - splitPUnif
    - swarmPUnif



  - title: Genome
  - subtitle: General
    contents:
    - simulateHoneyBeeGenomes
    - getPooledGeno
  - subtitle: Csd
    contents:
    - isCsdActive
    - nCsdAlleles
    - getCsdAlleles
    - getCsdGeno
    - isCsdHeterozygous
    - isGenoHeterozygous
    - calcQueensPHomBrood
    - nHomBrood
    - pHomBrood
    - editCsdLocus
  - subtitle: Haploid drone genome
    contents:
     - reduceDroneHaplo
     - reduceDroneGeno
  - subtitle: Get segregating sites' haplotypes or genotypes
    contents:
     - getSegSiteHaplo
     - getQueenSegSiteHaplo
     - getFathersSegSiteHaplo
     - getWorkersSegSiteHaplo
     - getDronesSegSiteHaplo
     - getVirginQueensSegSiteHaplo


     - getSegSiteGeno
     - getQueenSegSiteGeno
     - getFathersSegSiteGeno
     - getWorkersSegSiteGeno
     - getDronesSegSiteGeno
     - getVirginQueensSegSiteGeno
  - subtitle: Get QTL haplotypes or genotypes
    contents:
    - getQtlHaplo
    - getQueenQtlHaplo
    - getFathersQtlHaplo
    - getWorkersQtlHaplo
    - getDronesQtlHaplo
    - getVirginQueensQtlHaplo

    - getQtlGeno
    - getQueenQtlGeno
    - getFathersQtlGeno
    - getWorkersQtlGeno
    - getDronesQtlGeno
    - getVirginQueensQtlGeno
  - subtitle: Get SNP haplotypes or genotypes
    contents:
    - getSnpHaplo
    - getQueenSnpHaplo
    - getFathersSnpHaplo
    - getWorkersSnpHaplo
    - getDronesSnpHaplo
    - getVirginQueensSnpHaplo

    - getSnpGeno
    - getQueenSnpGeno
    - getFathersSnpGeno
    - getWorkersSnpGeno
    - getDronesSnpGeno
    - getVirginQueensSnpGeno
  - subtitle: Get IBD (Identity-By-Descent) haplotypes
    contents:
    - getIbdHaplo
    - getQueenIbdHaplo
    - getFathersIbdHaplo
    - getWorkersIbdHaplo
    - getDronesIbdHaplo
    - getVirginQueensIbdHaplo
  - subtitle: Calculate genomic information
    contents:
    - calcBeeGRMIbs
    - calcBeeGRMIbd
    - calcBeeAlleleFreq
  - subtitle: Calculate phenotypic information
    contents:
    - getPheno
  - subtitle: Calculate criterion
    contents:
    - calcColonyValue
    - calcInheritanceCriterion
    - calcPerformanceCriterion
    - calcSelectionCriterion

  - title: Planned mating
  - subtitile:
    contents:
    - createMatingStationDCA
    - createCrossPlan
    - mapCasteToColonyValue
    - cross

  - title: Quantitative Genetics
  - subtitle: Genetic values
    contents:
    - getQueenGv
    - getFathersGv
    - getWorkersGv
    - getDronesGv
    - getVirginQueensGv
    - getWorkersGv
  - subtitle: Breeding values
    contents:
    - getQueenBv
    - getFathersBv
    - getWorkersBv
    - getDronesBv
    - getVirginQueensBv
  - subtitle: Dominance deviations
    contents:
    - getQueenDd
    - getFathersDd
    - getWorkersDd
    - getDronesDd
    - getVirginQueensDd
  - subtitle: Epistatic devaitions
    contents:
    - getAa

  - title: Combine REMOVE EXPORT AND DELETE
    contents:
    - combineBeeGametesHaploDiploid
    - combineBeeGametes