How to set alpha in R?

Question

I have this example from the coin package of R:

  library(coin)
  library(multcomp)
  ### Length of YOY Gizzard Shad from Kokosing Lake, Ohio,
  ### sampled in Summer 1984, Hollander & Wolfe (1999), Table 6.3, page 200
  YOY <- data.frame(length = c(46, 28, 46, 37, 32, 41, 42, 45, 38, 44, 
                               42, 60, 32, 42, 45, 58, 27, 51, 42, 52, 
                               38, 33, 26, 25, 28, 28, 26, 27, 27, 27, 
                               31, 30, 27, 29, 30, 25, 25, 24, 27, 30),
                    site = factor(c(rep("I", 10), rep("II", 10),
                                    rep("III", 10), rep("IV", 10))))

  ### Nemenyi-Damico-Wolfe-Dunn test (joint ranking)
  ### Hollander & Wolfe (1999), page 244 
  ### (where Steel-Dwass results are given)
  NDWD <- oneway_test(length ~ site, data = YOY,
      ytrafo = function(data) trafo(data, numeric_trafo = rank),
      xtrafo = function(data) trafo(data, factor_trafo = function(x)
          model.matrix(~x - 1) %*% t(contrMat(table(x), "Tukey"))),
      teststat = "max", distribution = approximate(B = 90000))

  ### global p-value
  print(pvalue(NDWD))

  ### sites (I = II) != (III = IV) at alpha = 0.01 (page 244)
  print(pvalue(NDWD, method = "single-step"))

I want to assign alpha a different value, how can I do this??

This doesn't work!

  library(coin)
  library(multcomp)
  ### Length of YOY Gizzard Shad from Kokosing Lake, Ohio,
  ### sampled in Summer 1984, Hollander & Wolfe (1999), Table 6.3, page 200
  YOY <- data.frame(length = c(46, 28, 46, 37, 32, 41, 42, 45, 38, 44, 
                               42, 60, 32, 42, 45, 58, 27, 51, 42, 52, 
                               38, 33, 26, 25, 28, 28, 26, 27, 27, 27, 
                               31, 30, 27, 29, 30, 25, 25, 24, 27, 30),
                    site = factor(c(rep("I", 10), rep("II", 10),
                                    rep("III", 10), rep("IV", 10))))

  ### Nemenyi-Damico-Wolfe-Dunn test (joint ranking)
  ### Hollander & Wolfe (1999), page 244 
  ### (where Steel-Dwass results are given)
  NDWD <- oneway_test(length ~ site, data = YOY,
      ytrafo = function(data) trafo(data, numeric_trafo = rank),
      xtrafo = function(data) trafo(data, factor_trafo = function(x)
          model.matrix(~x - 1) %*% t(contrMat(table(x), "Tukey"))),
      teststat = "max", distribution = approximate(B = 90000),
      alpha = 0.05)

  ### global p-value
  print(pvalue(NDWD))

  ### sites (I = II) != (III = IV) at alpha = 0.05 (default was 0.01) (page 244)
  print(pvalue(NDWD, method = "single-step"))

Answer 1

It would appear that you cannot: oneway_test() has no argument conf.level whereas wilcox_test and normal_test do. This is all documented, see help(oneway_test).

Answer 2

The alpha levels are hardcoded and fixed at 0.99 If you want to change that, then you have to download the package source, change the levels and compile the package. The levels are coded in the Methods.R file. Search for binom.test or conf.level

You could ask the package author to change the package so you can set the level yourself. But bear in mind that the package author is not obliged to do that!