## continue with the example in mmc
catalystm <- read.table(hh("datasets/catalystm.dat"), header=FALSE,
col.names=c("catalyst","concent"))
if.R(r=
oldcon <- options(contrasts = c("contr.treatment", "contr.treatment"))
,s={})
catalystm$catalyst <- factor(catalystm$catalyst, labels=c("A","B","C","D"))
catalystm1.aov <- aov(concent ~ catalyst, data=catalystm)
if.R(r=
options(oldcon)
,s={})
catalystm.mca <-
if.R(r=glht(catalystm1.aov, linfct = mcp(catalyst = "Tukey")),
s=multicomp(catalystm1.aov, plot=FALSE))
catalystm.lmat <- cbind("AB-D" =c(0, 1, 1, 0,-2),
"A-B" =c(0, 1,-1, 0, 0),
"ABD-C"=c(0, 1, 1,-3, 1))
if.R(r=catalystm.lmat.glht <- catalystm.lmat[-2,],
s={})
if.R(s=dimnames(catalystm.lmat)[[1]] <-dimnames(catalystm.mca$lmat)[[1]],
r=dimnames(catalystm.lmat.glht)[[1]] <-dimnames(catalystm.mca$linfct)[[2]])
catalystm.mmc <-
if.R(r=glht.mmc(catalystm1.aov, linfct = mcp(catalyst = "Tukey"),
lmat=catalystm.lmat.glht, focus.lmat=catalystm.lmat[-1,])
,s=multicomp.mmc(catalystm1.aov, lmat=catalystm.lmat,
plot=FALSE)
)
old.mar <- if.R(s=par(mar=c(5,12,4,6)+.1),
r=par(mar=c(5,6,4,4)+.1))
## pairwise contrasts, default settings
plot(catalystm.mmc, print.lmat=FALSE)
## centering, scaling, emphasize significant contrasts
plot(catalystm.mmc, x.offset=1.6, ry.mmc=c(50,58), print.lmat=FALSE,
col.mca.signif='red')
## user-specified contrasts
plot(catalystm.mmc, x.offset=1.6, ry.mmc=c(50,58),
col.lmat.signif='blue')
## reduce intensity of isomeans grid, number isomeans grid lines
plot(catalystm.mmc, x.offset=1.6, ry.mmc=c(50,58),
lty.iso=2, col.iso='darkgray', iso.name=FALSE,
col.lmat.signif='blue')
## both pairwise contrasts and user-specified contrasts
plot(catalystm.mmc, x.offset=1.6, ry.mmc=c(50,58), lty.iso=2,
col.iso='darkgray', print.mca=TRUE,
col.lmat.signif='blue', col.mca.signif='red')
par(old.mar)
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