Cetin Sert - 1 day ago 4
R Question

# How to set alpha in R?

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"))
``````