## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = NA,
  fig.width = 7,
  fig.height = 4
)


## ----setup--------------------------------------------------------------------
library(biometryassist)


## -----------------------------------------------------------------------------
model <- aov(Petal.Width ~ Species, data = iris)


## -----------------------------------------------------------------------------
multiple_comparisons(model, classify = "Species")


## ----fig.height = 3-----------------------------------------------------------
autoplot(multiple_comparisons(model, classify = "Species"), label_height = 0.95)


## -----------------------------------------------------------------------------
pairwise_comparisons(model, classify = "Species")


## -----------------------------------------------------------------------------
pairwise_comparisons(
  model,
  classify = "Species",
  pairs = c("setosa-versicolor", "versicolor-virginica")
)


## ----fig.height = 3-----------------------------------------------------------
autoplot(pairwise_comparisons(model, classify = "Species"))


## -----------------------------------------------------------------------------
pairwise_comparisons(
  model,
  classify = "Species",
  contrasts = list(
    "setosa vs rest" = c(setosa = 1, versicolor = -0.5, virginica = -0.5)
  )
)


## -----------------------------------------------------------------------------
model_cw <- aov(weight ~ feed, data = chickwts)
reference_comparisons(model_cw, classify = "feed", reference = "casein")


## ----fig.height = 3.5---------------------------------------------------------
autoplot(reference_comparisons(model_cw, classify = "feed", reference = "casein"))


## -----------------------------------------------------------------------------
mc <- multiple_comparisons(model, classify = "Species", adjust = "bonferroni")
mc$comparison_method


## -----------------------------------------------------------------------------
wb <- aov(breaks ~ wool * tension, data = warpbreaks)


## -----------------------------------------------------------------------------
pairwise_comparisons(wb, classify = "wool:tension", by = "wool")


## ----fig.height = 3.5---------------------------------------------------------
autoplot(multiple_comparisons(wb, classify = "wool:tension", by = "wool"))