## ----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)


## ----het----------------------------------------------------------------------
het <-
  Heterosis(
      y      = Yield
    , Rep    = Rep
    , Cross1 = Cross1
    , Cross2 = Cross2
    , data   = GriffingData2
    , Check  = 3
    , Better = c("higher", "lower")[1]
    )
het$StdErr
head(x = het$Heterosis[order(-het$Heterosis$MP)], n = 6)


## ----het-plot, fig.height = 6-------------------------------------------------
plot(x = het, which = c("MP", "BP", "SH", "residuals", "qq")[1])


## ----recip--------------------------------------------------------------------
rs <-
  Griffing(
      y          = Yield
    , Rep        = Rep
    , Cross1     = Cross1
    , Cross2     = Cross2
    , data       = GriffingData1
    , Method     = 1
    , Model      = 1
    , Reciprocal = c("combined", "split")[2]
    )
rs$ANOVA
round(x = rs$Maternal, digits = 3)
round(x = rs$StdErr[c("mi", "mi_mj", "nij")], digits = 3)


## ----ge2----------------------------------------------------------------------
ge2 <-
  GardnerEberhart(
      y        = Yield
    , Rep      = Rep
    , Cross1   = Cross1
    , Cross2   = Cross2
    , data     = GriffingData2
    , Analysis = 2
    , Model    = 1
    )
ge2$ANOVA
ge2$Average


## ----ge2-plot-----------------------------------------------------------------
plot(x = ge2, which = c("effects", "specific", "residuals", "qq")[1])


## ----ge3----------------------------------------------------------------------
ge3 <-
  GardnerEberhart(
      y        = Yield
    , Rep      = Rep
    , Cross1   = Cross1
    , Cross2   = Cross2
    , data     = GriffingData2
    , Analysis = 3
    , Model    = 1
    )
ge3$ANOVA