'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes
Add caste individuals to the colony
Build up Colony or MultiColony object by adding (raising) workers and ...
Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identica...
Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identica...
Calculate colony value(s)
Calculate the inheritance criterion
Calculate the performance criterion
The expected proportion and a realised number of csd homozygous brood
Calculate the selection criterion
Collapse
Honeybee colony
Combine two colony objects
Create diploid gametes from a mated queen
Create diploid gametes from a mated queen
Combine a NULL and AlphaSimR population
Creates caste population individuals from the colony
Create a new Colony
Create a plan for crossing virgin queens
Create a drone congregation area (DCA)
Create a DCA of drones at a mating stations
Create MultiColony object
Cross (mate) virgin queen(s) as a population, of a colony, or of all g...
Reduce number of workers and remove all drones and virgin queens from ...
Sample the downsize proportion - proportion of removed workers in down...
Edit the csd locus
Access epistasis values of individuals in a caste
Access genetic values of individuals in a caste
Access breeding values of individuals in a caste
Report caste of an individual
Get IDs of individuals of a caste, or ID of all members of colony
Access individuals of a caste
Get sex of individuals of a caste, or sex of all members of colony
Test if colony has collapsed
Get csd alleles
Get genotypes from the csd locus
Access dominance values of individuals in a caste
Report which colony events have occurred
Access IBD haplotypes of individuals in a caste
Get the colony ID
Get the colony location
Get miscellaneous information in a population
Access phenotype values of individuals in a caste
Get a pooled genotype from true genotypes
Access QTL genotypes of individuals in a caste
Access QTL haplotypes of individuals in a caste
Get (calculate) the queen's age
Access the queen's year of birth
Access genotypes for all segregating sites of individuals in a caste
Access haplotypes for all segregating sites of individuals in a caste
Access SNP array genotypes of individuals in a caste
Access SNP array haplotypes of individuals in a caste
Test if colony has split
Test if colony has superseded
Test if colony has swarmed
Is individual a member of a specific caste
Is csd locus activated
Test if individuals are heterozygous at the csd locus
Are drones present
Check whether a population, colony or a multicolony object has no indi...
Are fathers present (=queen mated)
Test if a multilocus genotype is heterozygous
Check which of the colonies in a multicolony are NULL
Test if colony is currently productive
Is the queen present
Test if x is a SimParamBee class object
Are virgin queen(s) present
Are workers present
Map caste member (individual) values to a colony value
Finds loci on a genetic map and return a list of positions
Honeybee multicolony object
Level 0 function that returns the number of individuals of a caste in ...
Number of colonies in a MultiColony object
Report the number of distinct csd alleles
Pull out some colonies from the MultiColony object
Sample a number of drones
Sample a number of fathers
Sample a number of virgin queens
Sample a number of workers
Pull individuals from a caste in a colony
Pulls drone groups from a Drone Congregation Area (DCA)
Pull individuals from a population
Sample random points within a circle
Reduce drones' genotype to a single haplotype
Reduce drone's double haplotypes to a single haplotype
Remove a proportion of caste individuals from a colony
Remove some colonies from the MultiColony object
Replace a proportion of caste individuals with new ones
Re-queen
Reset colony events
Select colonies from MultiColony object
Set colony location
Set miscellaneous information in a population
Set the queen's year of birth
Honeybee simulation parameters
SIMplyBee: 'AlphaSimR' Extension for Simulating Honeybee Populations a...
Simulate the Honey bee genome
Split colony in two MultiColony
Sample the split proportion - proportion of removed workers in a manag...
Supersede
Swarm
Sample the swarm proportion - the proportion of workers that swarm
An extension of the 'AlphaSimR' package (<https://cran.r-project.org/package=AlphaSimR>) for stochastic simulations of honeybee populations and breeding programmes. 'SIMplyBee' enables simulation of individual bees that form a colony, which includes a queen, fathers (drones the queen mated with), virgin queens, workers, and drones. Multiple colony can be merged into a population of colonies, such as an apiary or a whole country of colonies. Functions enable operations on castes, colony, or colonies, to ease 'R' scripting of whole populations. All 'AlphaSimR' functionality with respect to genomes and genetic and phenotype values is available and further extended for honeybees, including haplo-diploidy, complementary sex determiner locus, colony events (swarming, supersedure, etc.), and colony phenotype values.