Pop-class | R Documentation |
Extends RawPop-class
to add sex, genetic values,
phenotypes, and pedigrees.
## 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)
x |
a 'Pop' object |
i |
index of individuals |
... |
additional 'Pop' objects |
object |
a 'Pop' object |
[
: 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())
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.
newPop
, newEmptyPop
, resetPop
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