Usage
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 classgamem
. 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:
data The data (BLUPS) used to compute the index.
eigen The eigenvalues and explained variance for each axis.
FA The results of the factor analysis.
canonical_loadings The canonical loadings for each factor retained.
FAI A list with the FAI-BLUP index for each ideotype design.
sel_dif_trait A list with the selection differential for each ideotype design.
sel_gen The selected genotypes.
ideotype_construction A list with the construction of the ideotypes.
total_gain A list with the total gain for variables to be increased or decreased.
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
Author
Tiago Olivoto tiagoolivoto@gmail.com
Examples
# \donttest{
library(metan)
mod <- waasb(data_ge,
env = ENV,
gen = GEN,
rep = REP,
resp = c(GY, HM))
#> Evaluating trait GY |====================== | 50% 00:00:02
Evaluating trait HM |============================================| 100% 00:00:05
#> Method: REML/BLUP
#> Random effects: GEN, GEN:ENV
#> Fixed effects: ENV, REP(ENV)
#> Denominador DF: Satterthwaite's method
#> ---------------------------------------------------------------------------
#> P-values for Likelihood Ratio Test of the analyzed traits
#> ---------------------------------------------------------------------------
#> model GY HM
#> COMPLETE NA NA
#> GEN 1.11e-05 5.07e-03
#> GEN:ENV 2.15e-11 2.27e-15
#> ---------------------------------------------------------------------------
#> All variables with significant (p < 0.05) genotype-vs-environment interaction
FAI <- fai_blup(mod,
SI = 15,
DI = c('max, max'),
UI = c('min, min'))
#>
#> -----------------------------------------------------------------------------------
#> Principal Component Analysis
#> -----------------------------------------------------------------------------------
#> eigen.values cumulative.var
#> PC1 1.1 55.23
#> PC2 0.9 100.00
#>
#> -----------------------------------------------------------------------------------
#> Factor Analysis
#> -----------------------------------------------------------------------------------
#> FA1 comunalits
#> GY -0.74 0.55
#> HM 0.74 0.55
#>
#> -----------------------------------------------------------------------------------
#> Comunalit Mean: 0.5523038
#> Selection differential
#> -----------------------------------------------------------------------------------
#> VAR Factor Xo Xs SD SDperc sense goal
#> 1 GY 1 2.674242 2.594199 -0.08004274 -2.9931005 increase 0
#> 2 HM 1 48.088286 48.005568 -0.08271774 -0.1720122 increase 0
#>
#> -----------------------------------------------------------------------------------
#> Selected genotypes
#> G4 G9
#> -----------------------------------------------------------------------------------
# }