boxplot(cost ~ type)

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  A         B

bymedian <- with(InsectSprays, reorder(spray, -count, median))
  boxplot(count ~ bymedian, data = InsectSprays,
          xlab = "Type of spray", ylab = "Insect count",
          main = "InsectSprays data", varwidth = TRUE,
          col = "lightgray")

> set.seed(42)                     # fix seed
> DF <- data.frame(type=sample(LETTERS[1:5], 100, replace=TRUE),
+                  cost=rnorm(100))
>
> boxplot(cost ~ type, data=DF)    # not ordered by median
>
> # compute index of ordered 'cost factor' and reassign
> oind <- order(as.numeric(by(DF$cost, DF$type, median)))
> DF$type <- ordered(DF$type, levels=levels(DF$type)[oind])
>
> boxplot(cost ~ type, data=DF)    # now it is ordered by median

bymedian <- with(InsectSprays, reorder(spray, -count, median, **na.rm = TRUE**)
  boxplot(count ~ bymedian, data = InsectSprays,
          xlab = "Type of spray", ylab = "Insect count",
          main = "InsectSprays data", varwidth = TRUE,
          col = "lightgray")