Pop-class: Population

In AlphaSimR: Breeding Program Simulations

Population

Description

Extends RawPop-class to add sex, genetic values, phenotypes, and pedigrees.

Usage

## S4 method for signature 'Pop'
x[i]

## S4 method for signature 'Pop'
c(x, ...)

## S4 method for signature 'Pop'
show(object)

## S4 method for signature 'Pop'
length(x)

Arguments

x	a 'Pop' object
i	index of individuals
...	additional 'Pop' objects
object	a 'Pop' object

Methods (by generic)

• [: Extract Pop by index or id

• c(Pop): Combine multiple Pops

• show(Pop): Show population summary

• length(Pop): Number of individuals in Pop (the same as nInd())

Slots

id

an individual's identifier

iid

an individual's internal identifier

mother

the identifier of the individual's mother

father

the identifier of the individual's father

sex

sex of individuals: "M" for males, "F" for females, and "H" for hermaphrodites

nTraits

number of traits

gv

matrix of genetic values. When using GxE traits, gv reflects gv when p=0.5. Dimensions are nInd by nTraits.

pheno

matrix of phenotypic values. Dimensions are nInd by nTraits.

ebv

matrix of estimated breeding values. Dimensions are nInd rows and a variable number of columns.

gxe

list containing GxE slopes for GxE traits

fixEff

a fixed effect relating to the phenotype. Used by genomic selection models but otherwise ignored.

misc

a list whose elements correspond to additional miscellaneous nodes with the items for individuals in the population (see example in newPop) - we support vectors and matrices or objects that have a generic length and subset method. This list is normally empty and exists solely as an open slot available for uses to store extra information about individuals.

miscPop

a list of any length containing optional meta data for the population (see example in newPop). This list is empty unless information is supplied by the user. Note that the list is emptied every time the population is subsetted or combined because the meta data for old population might not be valid anymore.

See Also

newPop, newEmptyPop, resetPop

AlphaSimR documentation built on Nov. 1, 2024, 5:07 p.m.