Dear all,
I was trying to understand how "multcomp" package works by running the
examples given in the documentation.
However I still don't understand when it comes to multiple comparison set by
user (please refer to "Ksub" in the code).   Therefore I run 2 other cases
along with the original example (case 1), with the expectation I'll get the
point from the output. The three cases only differ in the index I gave for
"Ksub".

### Script start####
library(mvtnorm)
library(multcomp)

data("cholesterol")
summary(cholesterol)

### adjusted p-values for all-pairwise comparisons in a one-way layout
### set up ANOVA model
amod <- aov(response ~ trt, data = cholesterol)

### set up multiple comparisons object for all-pair comparisons
cht <- glht(amod, linfct = mcp(trt = "Tukey"))

summary(cht, test = adjusted("Westfall"))

### use only a subset of all pairwise hypotheses
K <- contrMat(table(cholesterol$trt), type="Tukey")

Ksub <- rbind(K[c(1,2,5),],"D - test" = c(-1, -1, -1, 3, 0),"E - test" =
c(-1, -1, -1, 0, 3))

### reproduce results in Westfall et al. (1999, page 172)
amod <- aov(response ~ trt - 1, data = cholesterol)

# case 1
summary(glht(amod, linfct = mcp(trt = Ksub[,5:1])),test =
adjusted("Westfall"))

# case 2
summary(glht(amod, linfct = mcp(trt = Ksub[,1:5])),test =
adjusted("Westfall"))

# case 3
summary(glht(amod, linfct = mcp(trt = Ksub[,])),test = adjusted("Westfall"))

## end of script


All help are much appreciated.

-- 
Agus Susanto

	[[alternative HTML version deleted]]

