AlphaSimR1.6.0 package

Solve Multikernel RR-BLUP

Edit genome

Number of available threads

Get pedigree

Get QTL genetic map

Get SNP genetic map

Genetic value

Hybrid crossing

Hybrid population

Import genetic map

Import haplotypes

Import inbred, diploid genotypes

Solve Multivariate RR-BLUP

Solve Univariate Model

Additive trait

Sex specific additive trait

Sex specific additive and dominance trait

Additive and dominance trait

Additive, dominance, and epistatic trait

Additive, dominance, epistasis, and GxE trait

Additive, dominance and GxE trait

Additive and epistatic trait

Additive, epistasis and GxE trait

Additive and GxE trait

Test if individuals of a population are female or male

Test if object is of a Population class

Loci metadata

Make designed crosses

Make designed crosses

Dominance deviations

Create new population (internal)

Pull QTL genotypes

Double the ploidy of individuals

Estimated breeding value

Sample haplotypes from a MapPop

Additive-by-additive epistatic deviations

Add segregating site to MapPop

AlphaSimR: Breeding Program Simulations

Lose individuals at random

Breeding value

Calculate GCA

Combine MapPop chromosomes

Edit genome - the top QTL

Fast RR-BLUP

Additive genic variance

Additive-by-additive genic variance

Dominance genic variance

Total genic variance

Sumarize genetic parameters

Get genetic map

Generates DH lines

Raw population with genetic map

Mean estimated breeding values

Mean genetic values

Mean phenotypic values

Combine genomes of individuals

Merge list of populations

Multi-Population

Add Random Mutations

Raw population with genetic map and id

Creates an empty population

New MapPop

Create new Multi Population

Create new population

Number of individuals

Pedigree cross

Phenotype

Population

Population variance

Pull IBD haplotypes

Pull marker genotypes

Pull marker haplotypes

Pull QTL haplotypes

Pull segregating site genotypes

Pull seg site haplotypes

Pull SNP genotypes

Pull SNP haplotypes

Quick founder haplotype simulation

Make random crosses

Make random crosses

Raw Population

Create individuals with reduced ploidy

Reset population

RR-BLUP Model with Dominance

Solve RR-BLUP with EM and 2 random effects

RR-BLUP with Dominance Model 2

RR-BLUP GCA Model

RR-BLUP GCA Model 2

RR-BLUP SCA Model

RR-BLUP SCA Model 2

RR-BLUP Model

RR-BLUP Model 2

RRBLUP Memory Usage

RR-BLUP Solution

Create founder haplotypes using MaCS

Alternative wrapper for MaCS

Select and randomly cross

Select families

Select individuals

Select open pollinating plants

Solve RR-BLUP with EM and 3 random effects

Select individuals within families

Self individuals

Selection index

Selection intensity

Set estimated breeding values (EBV)

Set marker haplotypes

Solve RR-BLUP

Set phenotypes

Set GCA as phenotype

Set progeny test as phenotype

Simulation parameters

Calculate Smith-Hazel weights

Solve Multikernel Model

Solve Multivariate Model

Solve RR-BLUP with EM

Linear transformation matrix

Usefulness criterion

Additive variance

Additive-by-additive epistatic variance

Dominance variance

Variance of estimated breeding values

Total genetic variance

Phenotypic variance

Writes a Pop-class as PLINK files

Write data records