metan (version 1.10.0)

mtsi: Multi-trait stability index

Description

Computes the multi-trait stability index proposed by Olivoto et al. (2019)

Usage

mtsi(.data, index = "waasby", SI = 15, mineval = 1, verbose = TRUE)

Arguments

.data

An object of class waasb or waas.

index

If index = 'waasby' (default) both stability and mean performance are considered. If index = 'waasb' the multi-trait index will be computed considering the stability of genotypes only. More details can be seen in waasb and waas functions.

SI

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

mineval

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

verbose

If verbose = TRUE (Default) then some results are shown in the console.

Value

An object of class mtsi with the following items:

• data The data used to compute the factor analysis.

• cormat The correlation matrix among the environments.

• PCA The eigenvalues and explained variance.

• FA The factor analysis.

• KMO The result for the Kaiser-Meyer-Olkin test.

• MSA The measure of sampling adequacy for individual variable.

• communalities The communalities.

• communalities_mean The communalities' mean.

• initial_loadings The initial loadings.

• finish_loadings The final loadings after varimax rotation.

• canonical_loadings The canonical loadings.

• scores_gen The scores for genotypes in all retained factors.

• scores_ide The scores for the ideotype in all retained factors.

• MTSI The multi-trait stability index.

• contri_fac The relative contribution of each factor on the MTSI value. The lower the contribution of a factor, the close of the ideotype the variables in such factor are.

• contri_fac_rank, contri_fac_rank_sel The rank for the contribution of each factor for all genotypes and selected genotypes, respectively.

• sel_dif_trait, sel_dif_waasb, sel_dif_waasby The selection differential (gains) for the traits, and for the WAASB and WAASBY indexes.

• stat_dif_var, stat_dif_waasb, stat_dif_waasby A descriptive statistic for the selection gains of the traits and WAASB and WAASBY indexes. The minimum, mean, confidence interval, standard deviation, maximum, and sum of selection gain values are computed. If traits have negative and positive desired gains, the statistics are computed for by strata.

• sel_gen The selected genotypes.

References

Olivoto, T., A.D.C. L\'ucio, J.A.G. da silva, B.G. Sari, and M.I. Diel. 2019. Mean performance and stability in multi-environment trials II: Selection based on multiple traits. Agron. J. 111:2961-2969. 10.2134/agronj2019.03.0220

Examples

# NOT RUN {
library(metan)
# Based on stability only, for both GY and HM, higher is better
mtsi_model <- waasb(data_ge,
                    env = ENV,
                    gen = GEN,
                    rep = REP,
                    resp = c(GY, HM))
mtsi_index <- mtsi(mtsi_model, index = 'waasb')


# Based on mean performance and stability (using pipe operator %>%)
# GY: higher is better
# HM: lower is better

mtsi_index2 <- data_ge %>%
 waasb(ENV, GEN, REP,
       resp = c(GY, HM),
       mresp = c("h, l")) %>%
 mtsi()
# }