Pop-class {AlphaSimR} | R Documentation |
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)
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
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 individuals in the population. 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. This list is empty unless information is supplied by the user. Note that the list is emptied every time the population is subsetted.