## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = FALSE, comment = "", fig.width = 7, fig.height = 4.6,
                      dev = if (knitr::is_latex_output()) "cairo_pdf" else
                        if (requireNamespace("svglite", quietly = TRUE)) "svglite" else "png")
if (requireNamespace("stability", quietly = TRUE)) library(stability) else
  pkgload::load_all(export_all = FALSE, helpers = FALSE, quiet = TRUE)


## ----ammi---------------------------------------------------------------------
am <-
  ammi(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
am$pc_anova
am$ammi_model
plot(x = am, which = "scree")


## ----ammi-int-----------------------------------------------------------------
stab_interpret(
    x             = am
  , higher_better = TRUE
  , top           = 5
  )


## ----biplot, fig.height = 6---------------------------------------------------
ab <-
  ammi_biplot(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
plot(x = ab, which = "ammi1")
plot(x = ab, which = "ammi2")


## ----asv----------------------------------------------------------------------
asv <-
  stab_asv(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
head(x = asv$ASD, n = 6)
masv <-
  stab_masv(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    , .m    = 4
    )
head(x = masv$MASD, n = 6)
dst <-
  stab_dist(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    , .m    = 4
    )
head(x = dst$stabDist, n = 6)
plot(x = asv, which = "ranks")


## ----asv-int------------------------------------------------------------------
stab_interpret(
    x             = masv
  , higher_better = TRUE
  , top           = 5
  )