# 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes

## Documentation for package ‘SIMplyBee’ version 0.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G H I M N P R S misc

## -- A --

addCastePop | Add caste individuals to the colony
addDrones | Add caste individuals to the colony
addVirginQueens | Add caste individuals to the colony
addWorkers | Add caste individuals to the colony
areDronesPresent | Are workers present
areFathersPresent | Are fathers present (=queen mated)
areVirginQueensPresent | Are virgin queen(s) present
areWorkersPresent | Are workers present

## -- B --

buildUp | Build up Colony or MultiColony object by adding (raising) workers and drones

## -- C --

c-method | Honeybee colony
c-method | Honeybee multicolony object
c-method | Combine a NULL and AlphaSimR population
calcBeeAlleleFreq | Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By State genomic data
calcBeeGRMIbd | Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By Descent genomic data
calcBeeGRMIbs | Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By State genomic data
calcColonyAa | Calculate colony value(s)
calcColonyBv | Calculate colony value(s)
calcColonyDd | Calculate colony value(s)
calcColonyGv | Calculate colony value(s)
calcColonyPheno | Calculate colony value(s)
calcColonyValue | Calculate colony value(s)
calcInheritanceCriterion | Calculate the inheritance criterion
calcPerformanceCriterion | Calculate the performance criterion
calcQueensPHomBrood | The expected proportion and a realised number of csd homozygous brood
calcSelectionCriterion | Calculate the selection criterion
collapse | Collapse
Colony-class | Honeybee colony
combine | Combine two colony objects
combineBeeGametes | Create diploid gametes from a mated queen
combineBeeGametesHaploDiploid | Create diploid gametes from a mated queen
createCastePop | Creates caste population individuals from the colony
createColony | Create a new Colony
createDCA | Create a drone congregation area (DCA)
createDrones | Creates caste population individuals from the colony
createMatingStationDCA | Create a DCA of drones at a mating stations
createMultiColony | Create MultiColony object
createRandomCrossPlan | Create a cross plan by randomly sampling drones for each queen from a drone population
createVirginQueens | Creates caste population individuals from the colony
createWorkers | Creates caste population individuals from the colony
cross | Cross (mate) virgin queen(s) as a population, of a colony, or of all given colonies

## -- D --

downsize | Reduce number of workers and remove all drones and virgin queens from a Colony or MultiColony object
downsizePUnif | Sample the downsize proportion - proportion of removed workers in downsizing

## -- E --

editCsdLocus | Edit the csd locus

## -- G --

getAa | Access epistasis values of individuals in a caste
getBv | Access breeding values of individuals in a caste
getCaste | Report caste of an individual
getCasteId | Get IDs of individuals of a caste, or ID of all members of colony
getCastePop | Access individuals of a caste
getCasteSex | Get sex of individuals of a caste, or sex of all members of colony
getCsdAlleles | Get csd alleles
getCsdGeno | Get genotypes from the csd locus
getDd | Access dominance values of individuals in a caste
getDrones | Access individuals of a caste
getDronesAa | Access epistasis values of individuals in a caste
getDronesBv | Access breeding values of individuals in a caste
getDronesCsdAlleles | Get csd alleles
getDronesCsdGeno | Get genotypes from the csd locus
getDronesDd | Access dominance values of individuals in a caste
getDronesGv | Access genetic values of individuals in a caste
getDronesIbdHaplo | Access IBD haplotypes of individuals in a caste
getDronesPheno | Access phenotype values of individuals in a caste
getDronesQtlGeno | Access QTL genotypes of individuals in a caste
getDronesQtlHaplo | Access QTL haplotypes of individuals in a caste
getDronesSegSiteGeno | Access genotypes for all segregating sites of individuals in a caste
getDronesSegSiteHaplo | Access haplotypes for all segregating sites of individuals in a caste
getDronesSnpGeno | Access SNP array genotypes of individuals in a caste
getDronesSnpHaplo | Access SNP array haplotypes of individuals in a caste
getEvents | Report which colony events have occurred
getFathers | Access individuals of a caste
getFathersAa | Access epistasis values of individuals in a caste
getFathersBv | Access breeding values of individuals in a caste
getFathersCsdAlleles | Get csd alleles
getFathersCsdGeno | Get genotypes from the csd locus
getFathersDd | Access dominance values of individuals in a caste
getFathersGv | Access genetic values of individuals in a caste
getFathersIbdHaplo | Access IBD haplotypes of individuals in a caste
getFathersPheno | Access phenotype values of individuals in a caste
getFathersQtlGeno | Access QTL genotypes of individuals in a caste
getFathersQtlHaplo | Access QTL haplotypes of individuals in a caste
getFathersSegSiteGeno | Access genotypes for all segregating sites of individuals in a caste
getFathersSegSiteHaplo | Access haplotypes for all segregating sites of individuals in a caste
getFathersSnpGeno | Access SNP array genotypes of individuals in a caste
getFathersSnpHaplo | Access SNP array haplotypes of individuals in a caste
getGv | Access genetic values of individuals in a caste
getIbdHaplo | Access IBD haplotypes of individuals in a caste
getId | Get the colony ID
getLocation | Get the colony location
getPheno | Access phenotype values of individuals in a caste
getPooledGeno | Get a pooled genotype from true genotypes
getQtlGeno | Access QTL genotypes of individuals in a caste
getQtlHaplo | Access QTL haplotypes of individuals in a caste
getQueen | Access individuals of a caste
getQueenAa | Access epistasis values of individuals in a caste
getQueenAge | Get (calculate) the queen's age
getQueenBv | Access breeding values of individuals in a caste
getQueenCsdAlleles | Get csd alleles
getQueenCsdGeno | Get genotypes from the csd locus
getQueenDd | Access dominance values of individuals in a caste
getQueenGv | Access genetic values of individuals in a caste
getQueenIbdHaplo | Access IBD haplotypes of individuals in a caste
getQueenPheno | Access phenotype values of individuals in a caste
getQueenQtlGeno | Access QTL genotypes of individuals in a caste
getQueenQtlHaplo | Access QTL haplotypes of individuals in a caste
getQueenSegSiteGeno | Access genotypes for all segregating sites of individuals in a caste
getQueenSegSiteHaplo | Access haplotypes for all segregating sites of individuals in a caste
getQueenSnpGeno | Access SNP array genotypes of individuals in a caste
getQueenSnpHaplo | Access SNP array haplotypes of individuals in a caste
getQueenYearOfBirth | Access the queen's year of birth
getSegSiteGeno | Access genotypes for all segregating sites of individuals in a caste
getSegSiteHaplo | Access haplotypes for all segregating sites of individuals in a caste
getSnpGeno | Access SNP array genotypes of individuals in a caste
getSnpHaplo | Access SNP array haplotypes of individuals in a caste
getVirginQueens | Access individuals of a caste
getVirginQueensAa | Access epistasis values of individuals in a caste
getVirginQueensBv | Access breeding values of individuals in a caste
getVirginQueensCsdAlleles | Get csd alleles
getVirginQueensCsdGeno | Get genotypes from the csd locus
getVirginQueensDd | Access dominance values of individuals in a caste
getVirginQueensGv | Access genetic values of individuals in a caste
getVirginQueensIbdHaplo | Access IBD haplotypes of individuals in a caste
getVirginQueensPheno | Access phenotype values of individuals in a caste
getVirginQueensQtlGeno | Access QTL genotypes of individuals in a caste
getVirginQueensQtlHaplo | Access QTL haplotypes of individuals in a caste
getVirginQueensSegSiteGeno | Access genotypes for all segregating sites of individuals in a caste
getVirginQueensSegSiteHaplo | Access haplotypes for all segregating sites of individuals in a caste
getVirginQueensSnpGeno | Access SNP array genotypes of individuals in a caste
getVirginQueensSnpHaplo | Access SNP array haplotypes of individuals in a caste
getWorkers | Access individuals of a caste
getWorkersAa | Access epistasis values of individuals in a caste
getWorkersBv | Access breeding values of individuals in a caste
getWorkersCsdAlleles | Get csd alleles
getWorkersCsdGeno | Get genotypes from the csd locus
getWorkersDd | Access dominance values of individuals in a caste
getWorkersGv | Access genetic values of individuals in a caste
getWorkersIbdHaplo | Access IBD haplotypes of individuals in a caste
getWorkersPheno | Access phenotype values of individuals in a caste
getWorkersQtlGeno | Access QTL genotypes of individuals in a caste
getWorkersQtlHaplo | Access QTL haplotypes of individuals in a caste
getWorkersSegSiteGeno | Access genotypes for all segregating sites of individuals in a caste
getWorkersSegSiteHaplo | Access haplotypes for all segregating sites of individuals in a caste
getWorkersSnpGeno | Access SNP array genotypes of individuals in a caste
getWorkersSnpHaplo | Access SNP array haplotypes of individuals in a caste

## -- H --

hasCollapsed | Test if colony has collapsed
hasSplit | Test if colony has split
hasSuperseded | Test if colony has superseded
hasSwarmed | Test if colony has swarmed

## -- I --

isCaste | Is individual a member of a specific caste
isColony | Honeybee colony
isCsdActive | Is csd locus activated
isCsdHeterozygous | Test if individuals are heterozygous at the csd locus
isDrone | Is individual a member of a specific caste
isDronesPresent | Are drones present
isEmpty | Check whether a population, colony or a multicolony object has no individuals within
isFather | Is individual a member of a specific caste
isFathersPresent | Are fathers present (=queen mated)
isGenoHeterozygous | Test if a multilocus genotype is heterozygous
isMultiColony | Honeybee multicolony object
isNULLColonies | Check which of the colonies in a multicolony are NULL
isProductive | Test if colony is currently productive
isQueen | Is individual a member of a specific caste
isQueenPresent | Is the queen present
isSimParamBee | Test if x is a SimParamBee class object
isVirginQueen | Is individual a member of a specific caste
isVirginQueensPresent | Are virgin queen(s) present
isWorker | Is individual a member of a specific caste
isWorkersPresent | Are workers present

## -- M --

mapCasteToColonyAa | Map caste member (individual) values to a colony value
mapCasteToColonyBv | Map caste member (individual) values to a colony value
mapCasteToColonyDd | Map caste member (individual) values to a colony value
mapCasteToColonyGv | Map caste member (individual) values to a colony value
mapCasteToColonyPheno | Map caste member (individual) values to a colony value
mapCasteToColonyValue | Map caste member (individual) values to a colony value
MultiColony-class | Honeybee multicolony object

## -- N --

nCaste | Level 0 function that returns the number of individuals of a caste in a colony
nColonies | Number of colonies in a MultiColony object
nCsdAlleles | Report the number of distinct csd alleles
nDrones | Level 0 function that returns the number of individuals of a caste in a colony
nDronesColonyPhenotype | Sample a number of drones
nDronesPoisson | Sample a number of drones
nDronesTruncPoisson | Sample a number of drones
nEmptyColonies | Number of colonies in a MultiColony object
nFathers | Level 0 function that returns the number of individuals of a caste in a colony
nFathersPoisson | Sample a number of fathers
nFathersTruncPoisson | Sample a number of fathers
nHomBrood | The expected proportion and a realised number of csd homozygous brood
nNULLColonies | Number of colonies in a MultiColony object
nQueens | Level 0 function that returns the number of individuals of a caste in a colony
nVirginQueens | Level 0 function that returns the number of individuals of a caste in a colony
nVirginQueensColonyPhenotype | Sample a number of virgin queens
nVirginQueensPoisson | Sample a number of virgin queens
nVirginQueensTruncPoisson | Sample a number of virgin queens
nWorkers | Level 0 function that returns the number of individuals of a caste in a colony
nWorkersColonyPhenotype | Sample a number of workers
nWorkersPoisson | Sample a number of workers
nWorkersTruncPoisson | Sample a number of workers

## -- P --

pHomBrood | The expected proportion and a realised number of csd homozygous brood
pullCastePop | Pull individuals from a caste in a colony
pullColonies | Pull out some colonies from the MultiColony object
pullDroneGroupsFromDCA | Pulls drone groups from a Drone Congregation Area (DCA)
pullDrones | Pull individuals from a caste in a colony
pullInd | Pull individuals from a population
pullQueen | Pull individuals from a caste in a colony
pullVirginQueens | Pull individuals from a caste in a colony
pullWorkers | Pull individuals from a caste in a colony

## -- R --

reduceDroneGeno | Reduce drones' genotype to a single haplotype
reduceDroneHaplo | Reduce drone's double haplotypes to a single haplotype
removeCastePop | Remove a proportion of caste individuals from a colony
removeColonies | Remove some colonies from the MultiColony object
removeDrones | Remove a proportion of caste individuals from a colony
removeQueen | Remove a proportion of caste individuals from a colony
removeVirginQueens | Remove a proportion of caste individuals from a colony
removeWorkers | Remove a proportion of caste individuals from a colony
replaceCastePop | Replace a proportion of caste individuals with new ones
replaceDrones | Replace a proportion of caste individuals with new ones
replaceVirginQueens | Replace a proportion of caste individuals with new ones
replaceWorkers | Replace a proportion of caste individuals with new ones
reQueen | Re-queen
resetEvents | Reset colony events

## -- S --

selectColonies | Select colonies from MultiColony object
setLocation | Set colony location
setQueensYearOfBirth | Set the queen's year of birth
show-method | Honeybee colony
show-method | Honeybee multicolony object
SimParamBee | Honeybee simulation parameters
simulateHoneyBeeGenomes | Simulate the Honey bee genome
split | Split colony in two MultiColony
splitPColonyStrength | Sample the split proportion - proportion of removed workers in a managed split
splitPUnif | Sample the split proportion - proportion of removed workers in a managed split
supersede | Supersede
swarm | Swarm
swarmPUnif | Sample the swarm proportion - the proportion of workers that swarm

## -- misc --

[-method | Honeybee multicolony object
[<--method | Honeybee multicolony object
[[-method | Honeybee multicolony object
[[<--method | Honeybee multicolony object