sommer: add.diallel.vars – R documentation

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add.diallel.vars

Description

'add.diallel.vars' adds 4 columns to the provided diallel dataset. Specifically, the user provides a dataset with indicator variables for who is the male and female parent and the function returns the same dataset with 4 new dummy variables to allow the model fit of diallel models.

Usage

add.diallel.vars(df, par1="Par1", par2="Par2",sep.cross="-")

Arguments

`df`	a dataset with the two indicator variables for who is the male and female parent.
`par1`	the name of the column indicating who is the first parent (e.g. male).
`par2`	the name of the column indicating who is the second parent (e.g. female).
`sep.cross`	the character that should be used when creating the column for cross.id. A simple paste of the columns par1 and par2.

Value

A new data set with the following 4 new dummy variables to allow the fit of complex diallel models:

is.cross: returns a 0 if is a self and a 1 for a cross.
is.self: returns a 0 if is a cross and a 1 is is a self.
cross.type: returns a -1 for a direct cross, a 0 for a self and a 1 for a reciprocal cross.
cross.id: returns a column psting the par1 and par2 columns.

Author(s)

Giovanny Covarrubias-Pazaran

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

Examples

####=========================================####
#### For CRAN time limitations most lines in the
#### examples are silenced with one '#' mark,
#### remove them and run the examples
####=========================================####
data(DT_mohring)
DT <- DT_mohring
head(DT)
DT2 <- add.diallel.vars(DT,par1="Par1", par2="Par2")
head(DT2)
## see ?DT_mohring for an example on how to use the data to fit diallel models.

sommer

Solving Mixed Model Equations in R

v4.1.3

GPL (>= 2)

Authors