Skip to contents

Modified AMMI stability value

Source: R/stab_masv.R
stab_masv.Rd

stab_masv() computes the modified AMMI stability value (MASV) of Zali et al. (2012), which extends the ASV (stab_asv) beyond the first interaction axis, and its yield stability index. The earlier versions of the package computed it on two axes (.m = 2); the package author (Muhammad Yaseen) extended the function to any number of axes .m, from 2 up to the number of non-zero interaction axes.

Usage

stab_masv(.data, .y, .rep, .gen, .env, .m = 2L)

# Default S3 method
stab_masv(.data, .y, .rep, .gen, .env, .m = 2L)

Arguments

.data

a data frame (or data.table) with one row per plot.

.y

response: a column of .data given by name (.y = Yield or .y = "Yield") or a numeric vector of length nrow(.data).

.rep

replicate: not used (kept for compatibility); may be omitted.

.gen

genotype: a column of .data or a vector, as for .y.

.env

environment: a column of .data or a vector, as for .y.

.m

number of interaction axes (default 2).

Value

An object of class c("stab_masv", "stab_result", "list") with the component of earlier versions:

MASD

data.table sorted by MYSI: Gen, Mean, MASD (the MASV), rMean, rMASD, MYSI.

Methods: print(), summary(), plot() (which = c("ranks", "mean")), stab_interpret().

Details

With the genotype scores \(PC_{in}\) and the sums of squares \(SS_n\) of the axes (\(SS_n \propto \lambda_n^2\)), $$MASV_i = \sqrt{\sum_{n=1}^{m-1}\frac{SS_n}{SS_{n+1}}PC_{in}^2 + PC_{im}^2}, \qquad MYSI_i = R(MASV_i) + R(\bar{y}_{i\cdot}),$$ with \(m\) = .m axes; ranks as in stab_asv. Each axis is weighted by the ratio of its sum of squares to that of the next, so the first axes dominate; choose .m as the number of significant axes in ammi().

Changes from the earlier version. The weights were the ratios of the singular values \(\lambda_n/\lambda_{n+1}\) instead of the ratios of the sums of squares; the stability values were paired with other genotypes' means unless the data were sorted by genotype.

References

Zali, H., Farshadfar, E., Sabaghpour, S. H. and Karimizadeh, R. (2012). Evaluation of genotype x environment interaction in chickpea using measures of stability from AMMI model. Annals of Biological Research, 3(7), 3126–3136.

See also

stab_asv, ammi, stab_interpret

Other stability analyses: add_anova(), ammi(), ammi_biplot(), er_anova(), ge_effects(), ge_means(), gge_biplot(), indiv_anova(), stab_asv(), stab_dist(), stab_eskridge(), stab_fox(), stab_huehn(), stab_kang(), stab_measures(), stab_par(), stab_reg(), stab_reliability(), stab_superiority()

Author

Muhammad Yaseen (myaseen208@gmail.com), Kent M. Eskridge (keskridge1@unl.edu)

Examples

data(ge_data)
fit <-
  stab_masv(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    , .m    = 2
    )
head(fit$MASD)
#>            Gen     Mean      MASD rMean rMASD  MYSI
#>         <char>    <num>     <num> <int> <int> <int>
#> 1:       PR115 4444.273 1.0539686     3     2     5
#> 2:      V14154 4364.727 2.6547487     5     5    10
#> 3:        MSH3 4247.045 1.8257523    12     3    15
#> 4:      V14168 4342.045 5.3105278     7    12    19
#> 5:       PR119 4156.727 0.6058308    24     1    25
#> 6: LOCAL CHECK 4280.136 7.6760527     9    19    28