'AlphaSimR' Extension for Simulating Honeybee Populations and
Breeding Programmes
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Documentation for package ‘SIMplyBee’ version 0.4.1
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 |
| createCrossPlan | Create a plan for crossing virgin queens |
| 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 |
| 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 |
| getMisc | Get miscellaneous information in a population |
| 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 |
| isVirginQueenPresent | Are virgin queen(s) present |
| isVirginQueens | 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 |
| mapLoci | Finds loci on a genetic map and return a list of positions |
| 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 --
| rcircle | Sample random points within a circle |
| 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 |
| setMisc | Set miscellaneous information in a population |
| 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 |