Man pages for SIMplyBee
'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes
| addCastePop | Add caste individuals to the colony |
| buildUp | Build up Colony or MultiColony object by adding (raising)... |
| calcBeeGRMIbd | Calculate Genomic Relatedness Matrix (GRM) for honeybees from... |
| calcBeeGRMIbs | Calculate Genomic Relatedness Matrix (GRM) for honeybees from... |
| 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... |
| 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 |
| combineNULLAndPop | Combine a NULL and AlphaSimR population |
| 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) |
| createMatingStationDCA | Create a DCA of drones at a mating stations |
| createMultiColony | Create MultiColony object |
| cross | Cross (mate) virgin queen(s) as a population, of a colony, or... |
| downsize | Reduce number of workers and remove all drones and virgin... |
| downsizePFun | Sample the downsize proportion - proportion of removed... |
| editCsdLocus | Edit the csd locus |
| 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... |
| getCastePop | Access individuals of a caste |
| getCasteSex | Get sex of individuals of a caste, or sex of all members of... |
| getCsdAlleles | Get csd alleles |
| getCsdGeno | Get genotypes from the csd locus |
| getDd | Access dominance values of individuals in a caste |
| getEvents | Report which colony events have occurred |
| 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 |
| getQueenAge | Get (calculate) the queen's age |
| getQueenYearOfBirth | Access the queen's year of birth |
| getSegSiteGeno | Access genotypes for all segregating sites of individuals in... |
| getSegSiteHaplo | Access haplotypes for all segregating sites of individuals in... |
| getSnpGeno | Access SNP array genotypes of individuals in a caste |
| getSnpHaplo | Access SNP array haplotypes of individuals in a caste |
| hasCollapsed | Test if colony has collapsed |
| hasSplit | Test if colony has split |
| hasSuperseded | Test if colony has superseded |
| hasSwarmed | Test if colony has swarmed |
| isCaste | Is individual a member of a specific caste |
| isCsdActive | Is csd locus activated |
| isCsdHeterozygous | Test if individuals are heterozygous at the csd locus |
| isDronesPresent | Are drones present |
| isEmpty | Check whether a population, colony or a multicolony object... |
| isFathersPresent | Are fathers present (=queen mated) |
| isGenoHeterozygous | Test if a multilocus genotype is heterozygous |
| isNULLColonies | Check which of the colonies in a multicolony are NULL |
| isProductive | Test if colony is currently productive |
| isQueenPresent | Is the queen present |
| isSimParamBee | Test if x is a SimParamBee class object |
| isVirginQueensPresent | Are virgin queen(s) present |
| isWorkersPresent | Are workers present |
| 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 |
| nCaste | Level 0 function that returns the number of individuals of a... |
| nColonies | Number of colonies in a MultiColony object |
| nCsdAlleles | Report the number of distinct csd alleles |
| nDronesFun | Sample a number of drones |
| nFathersFun | Sample a number of fathers |
| nVirginQueensFun | Sample a number of virgin queens |
| nWorkersFun | Sample a number of workers |
| 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) |
| pullInd | Pull individuals from a population |
| 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 |
| replaceCastePop | Replace a proportion of caste individuals with new ones |
| reQueen | Re-queen |
| resetEvents | Reset colony events |
| 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 |
| SimParamBee | Honeybee simulation parameters |
| SIMplyBee-package | SIMplyBee: 'AlphaSimR' Extension for Simulating Honeybee... |
| simulateHoneyBeeGenomes | Simulate the Honey bee genome |
| split | Split colony in two MultiColony |
| splitPFun | Sample the split proportion - proportion of removed workers... |
| supersede | Supersede |
| swarm | Swarm |
| swarmPFun | Sample the swarm proportion - the proportion of workers that... |
