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## This example is from Hsu and Peruggia
##
## Hsu, J. and Peruggia, M. (1994).
## "Graphical representations of {Tukey's} multiple comparison method."
## Journal of Computational and Graphical Statistics, 3:143--161.
data(pulmonary)
pulmonary
pulmonary.aov <- aovSufficient(FVC ~ smoker,
data=pulmonary,
weights=pulmonary$n,
sd=pulmonary$s)
summary(pulmonary.aov)
## glht or multicomp object
pulmonary.mca <-
if.R(r=
glht(pulmonary.aov,
linfct=mcp(smoker="Tukey"),
df=pulmonary.aov$df.residual,
vcov.=vcovSufficient)
,s=
multicomp.mean(pulmonary$smoker,
pulmonary$n,
pulmonary$FVC,
pulmonary$s,
ylabel="pulmonary",
focus="smoker")
)
pulmonary.mca
## lexicographic ordering of contrasts, some positive and some negative
plot(pulmonary.mca)
pulm.lmat <- cbind("npnl-mh"=c( 1, 1, 1, 1,-2,-2), ## not.much vs lots
"n-pnl" =c( 3,-1,-1,-1, 0, 0), ## none vs light
"p-nl" =c( 0, 2,-1,-1, 0, 0), ## {} arbitrary 2 df
"n-l" =c( 0, 0, 1,-1, 0, 0), ## {} for 3 types of light
"m-h" =c( 0, 0, 0, 0, 1,-1)) ## moderate vs heavy
dimnames(pulm.lmat)[[1]] <- row.names(pulmonary)
if.R(r={pulm.lmat.glht <- rbind(Int=0, pulm.lmat[-1,])
print(pulm.lmat.glht)},
s={})
pulm.lmat
## mmc.multicomp object
pulmonary.mmc <-
if.R(r=
mmc(pulmonary.aov,
linfct=mcp(smoker="Tukey"),
df=pulmonary.aov$df.residual,
vcov.=vcovSufficient,
lmat=pulm.lmat.glht, focus.lmat=pulm.lmat,
calpha=attr(confint(pulmonary.mca)$confint,"calpha"))
,s=
multicomp.mmc.mean(pulmonary$smoker,
pulmonary$n,
pulmonary$FVC,
pulmonary$s,
ylabel="pulmonary",
focus="smoker",
lmat=pulm.lmat,
plot=FALSE)
)
old.par <- if.R(s=par(mar=c(5,4,4,4)+.1),
r=par(mar=c(15,4,4,4)+.1))
## pairwise comparisons
## MMC Figure 7a
plot(pulmonary.mmc, print.mca=TRUE, print.lmat=FALSE)
## tiebreaker plot, with contrasts ordered to match MMC plot,
## with all contrasts forced positive and with names also reversed,
## and with matched x-scale.
plotMatchMMC(pulmonary.mmc$mca)
## orthogonal contrasts
## MMC Figure 7b
plot(pulmonary.mmc, print.lmat=TRUE, col.lmat.signif='blue', col.iso='gray')
## pairwise and orthogonal contrasts on the same plot
plot(pulmonary.mmc, print.mca=TRUE, print.lmat=TRUE,
col.mca.signif='red', col.lmat.signif='blue', col.iso='gray',
lty.lmat.not.signif=2)
par(old.par)
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