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Fox's top-third ranking

Source: R/stab_fox.R
stab_fox.Rd

stab_fox() counts, for every genotype, the environments in which its mean ranks in the top third of all genotypes (Fox et al. 1990). A genotype often in the top third is widely adapted; the count needs no assumption about the distribution of yield.

Usage

stab_fox(.data, .y, .rep, .gen, .env)

# Default S3 method
stab_fox(.data, .y, .rep, .gen, .env)

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.

Value

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

Fox

data.table sorted by TOP and mean: Gen, Mean, TOP, and the new column TOP.pct (percent of the environments).

Methods: print(), summary(), plot() (counts as bars), stab_interpret().

Details

In environment \(j\) the genotypes are ranked by their means \(\bar{y}_{ij}\) (1 = highest); with \(T = \lceil G/3 \rceil\), $$TOP_i = \#\{j : R_j(\bar{y}_{ij}) \le T\},$$ which lies between 0 and \(E\).

Change from the earlier version. The earlier version ranked the single plots and counted plots, so that TOP could exceed the number of environments (it reached 12 with 11 environments in ge_data); the ranking is now of the genotype means in each environment, as Fox et al. define it.

References

Fox, P. N., Skovmand, B., Thompson, B. K., Braun, H. J. and Cormier, R. (1990). Yield and adaptation of hexaploid spring triticale. Euphytica, 47(1), 57–64.

See also

ge_means, 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_huehn(), stab_kang(), stab_masv(), 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_fox(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
head(fit$Fox)
#>         Gen     Mean   TOP  TOP.pct
#>      <char>    <num> <int>    <num>
#> 1:    DN126 4480.864     9 81.81818
#> 2:   V14170 4463.818     8 72.72727
#> 3:   V14154 4364.727     8 72.72727
#> 4:    PR115 4444.273     7 63.63636
#> 5:    NR491 4319.500     7 63.63636
#> 6: 013BT034 4247.500     7 63.63636
plot(x = fit)