Package: SIMplyBee 0.4.1

Jana Obšteter

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

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.

Authors:Jana Obšteter [aut, cre], Laura Strachan [aut], Jernej Bubnič [aut], Gregor Gorjanc [aut]

SIMplyBee_0.4.1.tar.gz
SIMplyBee_0.4.1.zip(r-4.7)SIMplyBee_0.4.1.zip(r-4.6)SIMplyBee_0.4.1.zip(r-4.5)
SIMplyBee_0.4.1.tgz(r-4.6-x86_64)SIMplyBee_0.4.1.tgz(r-4.6-arm64)SIMplyBee_0.4.1.tgz(r-4.5-x86_64)SIMplyBee_0.4.1.tgz(r-4.5-arm64)
SIMplyBee_0.4.1.tar.gz(r-4.7-arm64)SIMplyBee_0.4.1.tar.gz(r-4.7-x86_64)SIMplyBee_0.4.1.tar.gz(r-4.6-arm64)SIMplyBee_0.4.1.tar.gz(r-4.6-x86_64)
SIMplyBee_0.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SIMplyBee/json (API)

# Install 'SIMplyBee' in R:

install.packages('SIMplyBee', repos = c('https://highlanderlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/highlanderlab/simplybee/issues

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

cpp openmp

6.13 score 3 stars 28 scripts 287 downloads 201 exports 9 dependencies

Last updated from:01a56eebb9. Checks:12 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	170
linux-devel-x86_64	OK	173
source / vignettes	OK	218
linux-release-arm64	OK	172
linux-release-x86_64	OK	183
macos-release-arm64	OK	126
macos-release-x86_64	OK	231
macos-oldrel-arm64	OK	100
macos-oldrel-x86_64	OK	329
windows-devel	OK	206
windows-release	OK	184
windows-oldrel	ERROR	234
wasm-release	OK	124

Exports:addCastePop addDrones addVirginQueens addWorkers areDronesPresent areFathersPresent areVirginQueensPresent areWorkersPresent buildUp calcBeeAlleleFreq calcBeeGRMIbd calcBeeGRMIbs calcColonyGv calcColonyPheno calcColonyValue calcInheritanceCriterion calcPerformanceCriterion calcQueensPHomBrood calcSelectionCriterion collapse combine createCastePop createColony createCrossPlan createDCA createDrones createMatingStationDCA createMultiColony createVirginQueens createWorkers cross downsize downsizePUnif getCaste getCasteId getCastePop getCasteSex getCsdAlleles getCsdGeno getDrones getDronesCsdAlleles getDronesCsdGeno getDronesGv getDronesIbdHaplo getDronesPheno getDronesQtlGeno getDronesQtlHaplo getDronesSegSiteGeno getDronesSegSiteHaplo getDronesSnpGeno getDronesSnpHaplo getEvents getFathers getFathersCsdAlleles getFathersCsdGeno getFathersGv getFathersIbdHaplo getFathersPheno getFathersQtlGeno getFathersQtlHaplo getFathersSegSiteGeno getFathersSegSiteHaplo getFathersSnpGeno getFathersSnpHaplo getGv getIbdHaplo getId getLocation getMisc getPheno getPooledGeno getQtlGeno getQtlHaplo getQueen getQueenAge getQueenCsdAlleles getQueenCsdGeno getQueenGv getQueenIbdHaplo getQueenPheno getQueenQtlGeno getQueenQtlHaplo getQueenSegSiteGeno getQueenSegSiteHaplo getQueenSnpGeno getQueenSnpHaplo getQueenYearOfBirth getSegSiteGeno getSegSiteHaplo getSnpGeno getSnpHaplo getVirginQueens getVirginQueensCsdAlleles getVirginQueensCsdGeno getVirginQueensGv getVirginQueensIbdHaplo getVirginQueensPheno getVirginQueensQtlGeno getVirginQueensQtlHaplo getVirginQueensSegSiteGeno getVirginQueensSegSiteHaplo getVirginQueensSnpGeno getVirginQueensSnpHaplo getWorkers getWorkersCsdAlleles getWorkersCsdGeno getWorkersGv getWorkersIbdHaplo getWorkersPheno getWorkersQtlGeno getWorkersQtlHaplo getWorkersSegSiteGeno getWorkersSegSiteHaplo getWorkersSnpGeno getWorkersSnpHaplo hasCollapsed hasSplit hasSuperseded hasSwarmed isCaste isColony isCsdActive isCsdHeterozygous isDrone isDronesPresent isEmpty isFather isFathersPresent isMultiColony isNULLColonies isProductive isQueen isQueenPresent isSimParamBee isVirginQueen isVirginQueenPresent isVirginQueens isVirginQueensPresent isWorker isWorkersPresent mapCasteToColonyGv mapCasteToColonyPheno mapCasteToColonyValue nCaste nColonies nCsdAlleles nDrones nDronesColonyPhenotype nDronesPoisson nDronesTruncPoisson nEmptyColonies nFathers nFathersPoisson nFathersTruncPoisson nHomBrood nNULLColonies nQueens nVirginQueens nVirginQueensColonyPhenotype nVirginQueensPoisson nVirginQueensTruncPoisson nWorkers nWorkersColonyPhenotype nWorkersPoisson nWorkersTruncPoisson pHomBrood pullCastePop pullColonies pullDroneGroupsFromDCA pullDrones pullInd pullQueen pullVirginQueens pullWorkers rcircle reduceDroneGeno reduceDroneHaplo removeCastePop removeColonies removeDrones removeQueen removeVirginQueens removeWorkers replaceCastePop replaceDrones replaceVirginQueens replaceWorkers reQueen resetEvents selectColonies setLocation setMisc setQueensYearOfBirth SimParamBee simulateHoneyBeeGenomes split splitPColonyStrength splitPUnif supersede swarm swarmPUnif

Dependencies:AlphaSimR BH extraDistr R6 RANN rbibutils Rcpp RcppArmadillo Rdpack

Crossing

Introduction | Option 1: Cross a single virgin queen/colony | Option2: Cross with drone packages (pre-selecting drone populations) | Option 3: Cross according to a provided cross plan | Options 4 and 5: Cross according to an internally created cross plan | Special cases | Cross virgin queens at a mating station | Cross colonies with varying methods

Rendered fromD_Crossing.Rmdusingknitr::rmarkdown

Last update: 2024-09-19
Started: 2022-11-08

Colony events

Rendered fromC_Colony_events.Rmdusingknitr::rmarkdown

Last update: 2024-08-29
Started: 2022-11-08

Honeybee biology

Rendered fromA_Honeybee_biology.Rmdusingknitr::rmarkdown

Last update: 2024-08-29
Started: 2022-11-08

Frequently asked questions

Introduction | Why aren't drones removed from colonies when creating a DCA?

Rendered fromZ_FAQ.Rmdusingknitr::rmarkdown

Last update: 2023-12-22
Started: 2022-12-12

Genomics

Introduction | Obtaining genomic information | Pooling genotypic information | Computing Genomic Relationship Matrices | References

Rendered fromE_Genomics.Rmdusingknitr::rmarkdown

Last update: 2023-12-22
Started: 2022-11-08

Multiple colonies

Rendered fromB_Multiple_colonies.Rmdusingknitr::rmarkdown

Last update: 2023-12-22
Started: 2022-11-08

Quantitative genetics

Rendered fromF_Quantitative_Genetics.Rmdusingknitr::rmarkdown

Last update: 2023-12-22
Started: 2022-11-08

Sampling functions

Introduction | Functions to sample numbers | Functions that sample proportions

Rendered fromG_Sampling_functions.Rmdusingknitr::rmarkdown

Last update: 2023-12-22
Started: 2022-11-08

Help page	Topics
Add caste individuals to the colony	addCastePop addDrones addVirginQueens addWorkers
Build up Colony or MultiColony object by adding (raising) workers and drones	buildUp
Combine a NULL and AlphaSimR population	c,NULLOrPop-method
Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By Descent genomic data	calcBeeGRMIbd
Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By State genomic data	calcBeeAlleleFreq calcBeeGRMIbs
Calculate colony value(s)	calcColonyAa calcColonyBv calcColonyDd calcColonyGv calcColonyPheno calcColonyValue
Calculate the inheritance criterion	calcInheritanceCriterion
Calculate the performance criterion	calcPerformanceCriterion
The expected proportion and a realised number of csd homozygous brood	calcQueensPHomBrood nHomBrood pHomBrood
Calculate the selection criterion	calcSelectionCriterion
Collapse	collapse
Honeybee colony	c,ColonyOrNULL-method Colony-class isColony show,Colony-method
Combine two colony objects	combine
Create diploid gametes from a mated queen	combineBeeGametes
Create diploid gametes from a mated queen	combineBeeGametesHaploDiploid
Creates caste population individuals from the colony	createCastePop createDrones createVirginQueens createWorkers
Create a new Colony	createColony
Create a plan for crossing virgin queens	createCrossPlan
Create a drone congregation area (DCA)	createDCA
Create a DCA of drones at a mating stations	createMatingStationDCA
Create MultiColony object	createMultiColony
Cross (mate) virgin queen(s) as a population, of a colony, or of all given colonies	cross
Reduce number of workers and remove all drones and virgin queens from a Colony or MultiColony object	downsize
Sample the downsize proportion - proportion of removed workers in downsizing	downsizePUnif
Edit the csd locus	editCsdLocus
Access epistasis values of individuals in a caste	getAa getDronesAa getFathersAa getQueenAa getVirginQueensAa getWorkersAa
Access breeding values of individuals in a caste	getBv getDronesBv getFathersBv getQueenBv getVirginQueensBv getWorkersBv
Report caste of an individual	getCaste
Get IDs of individuals of a caste, or ID of all members of colony	getCasteId
Access individuals of a caste	getCastePop getDrones getFathers getQueen getVirginQueens getWorkers
Get sex of individuals of a caste, or sex of all members of colony	getCasteSex
Get csd alleles	getCsdAlleles getDronesCsdAlleles getFathersCsdAlleles getQueenCsdAlleles getVirginQueensCsdAlleles getWorkersCsdAlleles
Get genotypes from the csd locus	getCsdGeno getDronesCsdGeno getFathersCsdGeno getQueenCsdGeno getVirginQueensCsdGeno getWorkersCsdGeno
Access dominance values of individuals in a caste	getDd getDronesDd getFathersDd getQueenDd getVirginQueensDd getWorkersDd
Report which colony events have occurred	getEvents
Access genetic values of individuals in a caste	getDronesGv getFathersGv getGv getQueenGv getVirginQueensGv getWorkersGv
Access IBD haplotypes of individuals in a caste	getDronesIbdHaplo getFathersIbdHaplo getIbdHaplo getQueenIbdHaplo getVirginQueensIbdHaplo getWorkersIbdHaplo
Get the colony ID	getId
Get the colony location	getLocation
Get miscellaneous information in a population	getMisc
Access phenotype values of individuals in a caste	getDronesPheno getFathersPheno getPheno getQueenPheno getVirginQueensPheno getWorkersPheno
Get a pooled genotype from true genotypes	getPooledGeno
Access QTL genotypes of individuals in a caste	getDronesQtlGeno getFathersQtlGeno getQtlGeno getQueenQtlGeno getVirginQueensQtlGeno getWorkersQtlGeno
Access QTL haplotypes of individuals in a caste	getDronesQtlHaplo getFathersQtlHaplo getQtlHaplo getQueenQtlHaplo getVirginQueensQtlHaplo getWorkersQtlHaplo
Get (calculate) the queen's age	getQueenAge
Access the queen's year of birth	getQueenYearOfBirth
Access genotypes for all segregating sites of individuals in a caste	getDronesSegSiteGeno getFathersSegSiteGeno getQueenSegSiteGeno getSegSiteGeno getVirginQueensSegSiteGeno getWorkersSegSiteGeno
Access haplotypes for all segregating sites of individuals in a caste	getDronesSegSiteHaplo getFathersSegSiteHaplo getQueenSegSiteHaplo getSegSiteHaplo getVirginQueensSegSiteHaplo getWorkersSegSiteHaplo
Access SNP array genotypes of individuals in a caste	getDronesSnpGeno getFathersSnpGeno getQueenSnpGeno getSnpGeno getVirginQueensSnpGeno getWorkersSnpGeno
Access SNP array haplotypes of individuals in a caste	getDronesSnpHaplo getFathersSnpHaplo getQueenSnpHaplo getSnpHaplo getVirginQueensSnpHaplo getWorkersSnpHaplo
Test if colony has collapsed	hasCollapsed
Test if colony has split	hasSplit
Test if colony has superseded	hasSuperseded
Test if colony has swarmed	hasSwarmed
Is individual a member of a specific caste	isCaste isDrone isFather isQueen isVirginQueen isVirginQueens isWorker
Is csd locus activated	isCsdActive
Test if individuals are heterozygous at the csd locus	isCsdHeterozygous
Are drones present	isDronesPresent
Check whether a population, colony or a multicolony object has no individuals within	isEmpty
Are fathers present (=queen mated)	areFathersPresent isFathersPresent
Test if a multilocus genotype is heterozygous	isGenoHeterozygous
Check which of the colonies in a multicolony are NULL	isNULLColonies
Test if colony is currently productive	isProductive
Is the queen present	isQueenPresent
Test if x is a SimParamBee class object	isSimParamBee
Are virgin queen(s) present	areVirginQueensPresent isVirginQueenPresent isVirginQueensPresent
Are workers present	areDronesPresent areWorkersPresent isWorkersPresent
Map caste member (individual) values to a colony value	mapCasteToColonyAa mapCasteToColonyBv mapCasteToColonyDd mapCasteToColonyGv mapCasteToColonyPheno mapCasteToColonyValue
Finds loci on a genetic map and return a list of positions	mapLoci
Honeybee multicolony object	c,MultiColony-method c,MultiColonyOrNULL-method isMultiColony MultiColony-class show,MultiColony-method [,MultiColony,character-method [,MultiColony,integerOrNumericOrLogical-method [<-,MultiColony,integerOrNumericOrLogicalOrCharacter,ANY,MultiColony-method [[,MultiColony,character-method [[,MultiColony,integerOrNumericOrLogical-method [[<-,MultiColony,integerOrNumericOrLogicalOrCharacter,ANY,Colony-method
Level 0 function that returns the number of individuals of a caste in a colony	nCaste nDrones nFathers nQueens nVirginQueens nWorkers
Number of colonies in a MultiColony object	nColonies nEmptyColonies nNULLColonies
Report the number of distinct csd alleles	nCsdAlleles
Sample a number of drones	nDronesColonyPhenotype nDronesPoisson nDronesTruncPoisson
Sample a number of fathers	nFathersPoisson nFathersTruncPoisson
Sample a number of virgin queens	nVirginQueensColonyPhenotype nVirginQueensPoisson nVirginQueensTruncPoisson
Sample a number of workers	nWorkersColonyPhenotype nWorkersPoisson nWorkersTruncPoisson
Pull individuals from a caste in a colony	pullCastePop pullDrones pullQueen pullVirginQueens pullWorkers
Pull out some colonies from the MultiColony object	pullColonies
Pulls drone groups from a Drone Congregation Area (DCA)	pullDroneGroupsFromDCA
Pull individuals from a population	pullInd
Sample random points within a circle	rcircle
Reduce drones' genotype to a single haplotype	reduceDroneGeno
Reduce drone's double haplotypes to a single haplotype	reduceDroneHaplo
Remove a proportion of caste individuals from a colony	removeCastePop removeDrones removeQueen removeVirginQueens removeWorkers
Remove some colonies from the MultiColony object	removeColonies
Replace a proportion of caste individuals with new ones	replaceCastePop replaceDrones replaceVirginQueens replaceWorkers
Re-queen	reQueen
Reset colony events	resetEvents
Select colonies from MultiColony object	selectColonies
Set colony location	setLocation
Set miscellaneous information in a population	setMisc
Set the queen's year of birth	setQueensYearOfBirth
Honeybee simulation parameters	SimParamBee
Simulate the Honey bee genome	simulateHoneyBeeGenomes
Split colony in two MultiColony	split
Sample the split proportion - proportion of removed workers in a managed split	splitPColonyStrength splitPUnif
Supersede	supersede
Swarm	swarm
Sample the swarm proportion - the proportion of workers that swarm	swarmPUnif

Package: SIMplyBee 0.4.1

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

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