fai_blup: Multi-trait selection index

Description Usage Arguments Value Author(s) References Examples

View source: R/fai_blup.R

Description

[Stable]

Multitrait index based on factor analysis and ideotype-design proposed by Rocha et al. (2018).

Usage

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fai_blup(
  .data,
  use_data = "blup",
  DI = NULL,
  UI = NULL,
  SI = 15,
  mineval = 1,
  verbose = TRUE
)

Arguments

.data

An object of class waasb or a two-way table with genotypes in the rows and traits in columns. In the last case the row names must contain the genotypes names.

use_data

Define which data to use If .data is an object of class gamem. Defaults to "blup" (the BLUPs for genotypes). Use "pheno" to use phenotypic means instead BLUPs for computing the index.

DI, UI

A vector of the same length of .data to construct the desirable (DI) and undesirable (UI) ideotypes. For each element of the vector, allowed values are 'max', 'min', 'mean', or a numeric value. Use a comma-separated vector of text. For example, DI = c("max, max, min, min"). By default, DI is set to "max" for all traits and UI is set to "min" for all traits.

SI

An integer (0-100). The selection intensity in percentage of the total number of genotypes. Defaults to 15.

mineval

The minimum value so that an eigenvector is retained in the factor analysis.

verbose

Logical value. If TRUE some results are shown in console.

Value

An object of class fai_blup with the following items:

Author(s)

Tiago Olivoto tiagoolivoto@gmail.com

References

Rocha, J.R.A.S.C.R, J.C. Machado, and P.C.S. Carneiro. 2018. Multitrait index based on factor analysis and ideotype-design: proposal and application on elephant grass breeding for bioenergy. GCB Bioenergy 10:52-60. doi: 10.1111/gcbb.12443

Examples

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library(metan)

mod <- waasb(data_ge,
             env = ENV,
             gen = GEN,
             rep = REP,
             resp = c(GY, HM))

FAI <- fai_blup(mod,
                SI = 15,
                DI = c('max, max'),
                UI = c('min, min'))

metan documentation built on Nov. 10, 2021, 9:11 a.m.