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SIMplyBee README

SIMplyBee R package extends AlphaSimR for simulating honeybee populations and breeding programmes

Publication

Obšteter J., Strachan. L. K., Bubnič J., Prešern J., Gorjanc G. 2023. Genetics Selection Evolution, 55, 31. https://doi.org/10.1186/s12711-023-00798-y

Documentation

http://simplybee.info

Download

SIMplyBee is available on CRAN. You can install it with

install.packages(pkg = "SIMplyBee")

The development (and potentially unstable!) versions of SIMplyBee can be accessed from the main and devel GitHub branches using:

# New stable version of SIMplyBee before its submitted to CRAN
devtools::install_github(repo="HighlanderLab/SIMplyBee@main")

# Development version of SIMplyBee
devtools::install_github(repo="HighlanderLab/SIMplyBee@devel")

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Version

Install

install.packages('SIMplyBee')

Monthly Downloads

263

Version

0.4.1

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/HighlanderLab/SIMplyBee

Maintainer

Jana Obšteter

Last Published

September 20th, 2024

Functions in SIMplyBee (0.4.1)

SIMplyBee-package

SIMplyBee: 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes

Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By Descent genomic data

MultiColony-class

Honeybee multicolony object

calcColonyValue

Calculate colony value(s)

Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By State genomic data

calcInheritanceCriterion

Calculate the inheritance criterion

Honeybee simulation parameters

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

Honeybee colony

Add caste individuals to the colony

Combine two colony objects

calcPerformanceCriterion

Calculate the performance criterion

calcSelectionCriterion

Calculate the selection criterion

combineBeeGametes

Create diploid gametes from a mated queen

Creates caste population individuals from the colony

c,NULLOrPop-method

Combine a NULL and AlphaSimR population

combineBeeGametesHaploDiploid

Create diploid gametes from a mated queen

Create a new Colony

createMatingStationDCA

Create a DCA of drones at a mating stations

calcQueensPHomBrood

The expected proportion and a realised number of csd homozygous brood

createCrossPlan

Create a plan for crossing virgin queens

Access epistasis values of individuals in a caste

Cross (mate) virgin queen(s) as a population, of a colony, or of all given colonies

createMultiColony

Create MultiColony object

Reduce number of workers and remove all drones and virgin queens from a Colony or MultiColony object

Report caste of an individual

Edit the csd locus

Sample the downsize proportion - proportion of removed workers in downsizing

Get IDs of individuals of a caste, or ID of all members of colony

Report which colony events have occurred

Access breeding values of individuals in a caste

Access dominance values of individuals in a caste

Get sex of individuals of a caste, or sex of all members of colony

Create a drone congregation area (DCA)

Access individuals of a caste

getQueenYearOfBirth

Access the queen's year of birth

Access genetic values of individuals in a caste

Access IBD haplotypes of individuals in a caste

Access genotypes for all segregating sites of individuals in a caste

Get a pooled genotype from true genotypes

Access QTL genotypes of individuals in a caste

getSegSiteHaplo

Access haplotypes for all segregating sites of individuals in a caste

Access phenotype values of individuals in a caste

isCsdHeterozygous

Test if individuals are heterozygous at the csd locus

Get miscellaneous information in a population

Is csd locus activated

Get the colony ID

Is individual a member of a specific caste

Get the colony location

Test if colony has swarmed

Access SNP array genotypes of individuals in a caste

Test if colony is currently productive

Check which of the colonies in a multicolony are NULL

Test if x is a SimParamBee class object

Access SNP array haplotypes of individuals in a caste

Is the queen present

Test if colony has collapsed

Pull individuals from a caste in a colony

Sample a number of drones

isWorkersPresent

Are workers present

isVirginQueensPresent

Are virgin queen(s) present

Report the number of distinct csd alleles

nWorkersPoisson

Sample a number of workers

Number of colonies in a MultiColony object

Level 0 function that returns the number of individuals of a caste in a colony

Get csd alleles

Get (calculate) the queen's age

nFathersPoisson

Sample a number of fathers

isGenoHeterozygous

Test if a multilocus genotype is heterozygous

isFathersPresent

Are fathers present (=queen mated)

Pull out some colonies from the MultiColony object

nVirginQueensPoisson

Sample a number of virgin queens

pullDroneGroupsFromDCA

Pulls drone groups from a Drone Congregation Area (DCA)

Remove some colonies from the MultiColony object

replaceCastePop

Replace a proportion of caste individuals with new ones

reduceDroneHaplo

Reduce drone's double haplotypes to a single haplotype

Access QTL haplotypes of individuals in a caste

Get genotypes from the csd locus

Remove a proportion of caste individuals from a colony

setQueensYearOfBirth

Set the queen's year of birth

mapCasteToColonyValue

Map caste member (individual) values to a colony value

Sample the swarm proportion - the proportion of workers that swarm

Check whether a population, colony or a multicolony object has no individuals within

simulateHoneyBeeGenomes

Simulate the Honey bee genome

Split colony in two MultiColony

Sample the split proportion - proportion of removed workers in a managed split

Pull individuals from a population

Test if colony has superseded

Test if colony has split

Set colony location

isDronesPresent

Are drones present

reduceDroneGeno

Reduce drones' genotype to a single haplotype

Set miscellaneous information in a population

Finds loci on a genetic map and return a list of positions

Sample random points within a circle

Reset colony events

Select colonies from MultiColony object