## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = FALSE, comment = "", fig.width = 7, fig.height = 4.2,
                      dev = if (knitr::is_latex_output()) "cairo_pdf" else
                        if (requireNamespace("svglite", quietly = TRUE)) "svglite" else "png")
if (requireNamespace("DiallelAnalysisR", quietly = TRUE)) library(DiallelAnalysisR) else
  pkgload::load_all(export_all = FALSE, helpers = FALSE, quiet = TRUE)


## ----env----------------------------------------------------------------------
d <-
  DiallelSim(
      Parents = 6
    , Method  = 2
    , Rep     = 3
    , Env     = 3
    , Mean    = 50
    , gca     = 4
    , sca     = 2
    , rec     = 0
    , gcaEnv  = 1.5
    , scaEnv  = 1
    , EnvSD   = 2
    , Block   = 1
    , Error   = 3
    , seed    = 1
    )
fe <-
  GriffingEnv(
      y      = y
    , Rep    = Rep
    , Cross1 = Cross1
    , Cross2 = Cross2
    , Env    = Env
    , data   = d
    , Method = 2
    , Model  = 2
    )
fe$ANOVA
fe$Genetic.Components


## ----env-plot-----------------------------------------------------------------
plot(x = fe, which = c("gca", "gcaenv", "sca", "residuals", "qq")[2])


## ----biplot, fig.height = 6---------------------------------------------------
g4 <-
  Griffing(
      y          = Yield
    , Rep        = Rep
    , Cross1     = Cross1
    , Cross2     = Cross2
    , data       = GriffingData4
    , Method     = 4
    , Model      = 1
    , Reciprocal = c("combined", "split")[1]
    )
plot(x = g4, which = c("gca", "sca", "biplot", "residuals", "qq")[3])