Breeding Program Simulations

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Documentation for package ‘AlphaSimR’ version 1.5.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D E F G H I L M N P Q R S T U V W misc

-- A --

aa	Additive-by-additive epistatic deviations
addSegSite	Add segregating site to MapPop
attrition	Lose individuals at random

-- B --

bv	Breeding value

-- C --

c-method	Hybrid population
c-method	Raw population with genetic map
c-method	Multi-Population
c-method	Raw population with genetic map and id
c-method	Population
c-method	Raw Population
calcGCA	Calculate GCA
cChr	Combine MapPop chromosomes

-- D --

dd	Dominance deviations
doubleGenome	Double the ploidy of individuals

-- E --

ebv	Estimated breeding value
editGenome	Edit genome
editGenomeTopQtl	Edit genome - the top QTL

-- F --

fastRRBLUP

Fast RR-BLUP

-- G --

genicVarA	Additive genic variance
genicVarAA	Additive-by-additive genic variance
genicVarD	Dominance genic variance
genicVarG	Total genic variance
genParam	Sumarize genetic parameters
getGenMap	Get genetic map
getMisc	Get miscelaneous information in a population
getNumThreads	Number of available threads
getPed	Get pedigree
getQtlMap	Get QTL genetic map
getSnpMap	Get SNP genetic map
gv	Genetic value

-- H --

hybridCross	Hybrid crossing
HybridPop-class	Hybrid population

-- I --

importGenMap	Import genetic map
importHaplo	Import haplotypes
importInbredGeno	Import inbred, diploid genotypes
isFemale	Test if individuals of a population are female or male
isHybridPop	Hybrid population
isMale	Test if individuals of a population are female or male
isMapPop	Raw population with genetic map
isMultiPop	Multi-Population
isNamedMapPop	Raw population with genetic map and id
isPop	Test if object is of a Population class
isRawPop	Raw Population

-- L --

LociMap-class

Loci metadata

-- M --

makeCross	Make designed crosses
makeCross2	Make designed crosses
makeDH	Generates DH lines
MapPop-class	Raw population with genetic map
meanG	Mean genetic values
meanP	Mean phenotypic values
mergeGenome	Combine genomes of individuals
mergePops	Merge list of populations
MultiPop-class	Multi-Population
mutate	Add Random Mutations

-- N --

NamedMapPop-class	Raw population with genetic map and id
newEmptyPop	Creates an empty population
newMapPop	New MapPop
newMultiPop	Create new Multi Population
newPop	Create new population
nInd	Number of individuals

-- P --

pedigreeCross	Pedigree cross
pheno	Phenotype
Pop-class	Population
popVar	Population variance
pullIbdHaplo	Pull IBD haplotypes
pullMarkerGeno	Pull marker genotypes
pullMarkerHaplo	Pull marker haplotypes
pullQtlGeno	Pull QTL genotypes
pullQtlHaplo	Pull QTL haplotypes
pullSegSiteGeno	Pull segregating site genotypes
pullSegSiteHaplo	Pull seg site haplotypes
pullSnpGeno	Pull SNP genotypes
pullSnpHaplo	Pull SNP haplotypes

-- Q --

quickHaplo

Quick founder haplotype simulation

-- R --

randCross	Make random crosses
randCross2	Make random crosses
RawPop-class	Raw Population
reduceGenome	Create individuals with reduced ploidy
resetPop	Reset population
RRBLUP	RR-BLUP Model
RRBLUP2	RR-BLUP Model 2
RRBLUPMemUse	RRBLUP Memory Usage
RRBLUP_D	RR-BLUP Model with Dominance
RRBLUP_D2	RR-BLUP with Dominance Model 2
RRBLUP_GCA	RR-BLUP GCA Model
RRBLUP_GCA2	RR-BLUP GCA Model 2
RRBLUP_SCA	RR-BLUP SCA Model
RRBLUP_SCA2	RR-BLUP SCA Model 2
RRsol-class	RR-BLUP Solution
runMacs	Create founder haplotypes using MaCS
runMacs2	Alternative wrapper for MaCS

-- S --

sampleHaplo	Sample haplotypes from a MapPop
selectCross	Select and randomly cross
selectFam	Select families
selectInd	Select individuals
selectOP	Select open pollinating plants
selectWithinFam	Select individuals within families
self	Self individuals
selIndex	Selection index
selInt	Selection intensity
setEBV	Set EBV
setMarkerHaplo	Set marker haplotypes
setMisc	Set miscelaneous information in a population
setPheno	Set phenotypes
setPhenoGCA	Set GCA as phenotype
setPhenoProgTest	Set progeny test as phenotype
show-method	Population
show-method	Raw Population
SimParam	Simulation parameters
smithHazel	Calculate Smith-Hazel weights
solveMKM	Solve Multikernel Model
solveMVM	Solve Multivariate Model
solveRRBLUP	Solve RR-BLUP
solveRRBLUPMK	Solve Multikernel RR-BLUP
solveRRBLUPMV	Solve Multivariate RR-BLUP
solveRRBLUP_EM	Solve RR-BLUP with EM
solveRRBLUP_EM2	Solve RR-BLUP with EM and 2 random effects
solveRRBLUP_EM3	Solve RR-BLUP with EM and 3 random effects
solveUVM	Solve Univariate Model

-- T --

TraitA-class	Additive trait
TraitA2-class	Sex specific additive trait
TraitA2D-class	Sex specific additive and dominance trait
TraitAD-class	Additive and dominance trait
TraitADE-class	Additive, dominance, and epistatic trait
TraitADEG-class	Additive, dominance, epistasis, and GxE trait
TraitADG-class	Additive, dominance and GxE trait
TraitAE-class	Additive and epistatic trait
TraitAEG-class	Additive, epistasis and GxE trait
TraitAG-class	Additive and GxE trait
transMat	Linear transformation matrix

-- U --

usefulness

Usefulness criterion

-- V --

varA	Additive variance
varAA	Additive-by-additive epistatic variance
varD	Dominance variance
varG	Total genetic variance
varP	Phenotypic variance

-- W --

writePlink	Writes a Pop-class as PLINK files
writeRecords	Write data records

-- misc --

.newPop	Create new population (internal)
[-method	Hybrid population
[-method	Raw population with genetic map
[-method	Multi-Population
[-method	Raw population with genetic map and id
[-method	Population
[-method	Raw Population
[[-method	Multi-Population