pesekbaker: Pesek-Baker Index

In reyzaguirre/st4gi: Statistical tools for genetic improvement

Pesek-Baker Index

Description

Function to compute the Pesek-Baker index (Pesek, J. and R.J. Baker., 1969).

Usage

pesekbaker(
  dfr,
  geno,
  G.cov,
  P.cov,
  vars = NULL,
  dgg = NULL,
  units = c("sdu", "actual"),
  sf = 0.1
)

Arguments

dfr	The name of the data frame with the values for each genotype with each variable.
geno	The name of the column in dfr that identifies the genotypes.
G.cov	Genotypic covariance matrix.
P.cov	Phenotypic covariance matrix.
vars	The names of the columns for the variables. The default are all the column names in dfr different from geno.
dgg	Desired genetic gains. The default is one standard deviation for each variable.
units	Units for dgg, "sdu" or "actual". See details for more information.
sf	Selected fraction. The default is 0.1.

Details

The Pesek-Baker is an index where relative economic weights have been replaced by desired gains. If dgg is not specified, the desired genetic gains are set to one standard deviation for each variable. dgg can be specified in actual units (units = "actual") or in standard deviations (units = "sdu"), defaults to "sdu". For example, if you have a variable which is expressed in kilograms with a standard deviation of 5 kilograms, typing dgg = 2 means a desired genetic gain of 2 standard deviations that corresponds to 10 kilograms. If you type dgg = 2 and units = "actual" then this means a desired genetic gain of 2 kilograms. If dgg = NULL then the desired genetic gains will be one standard deviation, no matter if units is set as "actual" or "sdu".

Value

It returns:

• $Desired.Genetic.Gains, the desired genetic gains in actual units,

• $Standard.Deviations, the estimated genotypic standard deviations,

• $Index.Coefficients, the index coefficients,

• $Response.to.Selection, the response to selection,

• $Std.Response.to.Selection, the standardized response to selection, and

• $Pesek.Baker.Index, a data frame with the genotypic means for each variable, the Pesek-Baker index, and the rank for each genotype according to the index.

Author(s)

Raul Eyzaguirre.

References

Pesek, J. and R.J. Baker.(1969). Desired improvement in relation to selection indices. Can. J. Plant. Sci. 9:803-804.

Examples

vars <- c("rytha", "bc", "dm", "star", "nocr")
output <- ecm(spg, vars, "geno", "loc", "rep")
colnames(output$blups) <- gsub('blup.', '', colnames(output$blups))
pesekbaker(output$blups, 'geno', output$G.cov, output$P.cov)
# More weight on bc and dm, less on star and nocr
dgg <- c(1, 1.5, 1.5, 0.8, 0.8)
pesekbaker(output$blups, 'geno', output$G.cov, output$P.cov, vars, dgg)

reyzaguirre/st4gi documentation built on July 5, 2025, 6:38 a.m.