## continue with the example in simint.mmc in R, or mmc in S-Plus
catalystm <- read.table(hh("datasets/catalystm.dat"), header=FALSE,
col.names=c("catalyst","concent"))
catalystm$catalyst <- factor(catalystm$catalyst, labels=c("A","B","C","D"))
catalystm1.aov <- aov(concent ~ catalyst, data=catalystm)
class(catalystm1.aov) <- rev(class(catalystm1.aov))
catalystm.mca <-
if.R(r=simint(concent ~ catalyst, data=catalystm, type="Tukey"),
s=multicomp(catalystm1.aov))
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))
dimnames(catalystm.lmat)[[1]] <-
if.R(s=dimnames(catalystm.mca$lmat)[[1]],
r=c("(Intercept)", dimnames(catalystm.mca$cmatrix)[[2]][-1]))
if.R(r={
catalystm.mmc <- simint.mmc(concent ~ catalyst, data=catalystm,
lmat=catalystm.lmat, lmat.rows=2:5,
type="Tukey", whichf="catalyst")
catalystm.mmc <- multicomp.label.change(catalystm.mmc, "catalyst", "")
},
s={
catalystm.mmc <- multicomp.mmc(catalystm1.aov, lmat=catalystm.lmat)
})
gray <- if.R(r="gray", s=16)
red <- if.R(r="red", s=8)
blue <- if.R(r="blue", s=6)
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, 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=gray, 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=gray, print.mca=TRUE,
col.lmat.signif=blue, col.mca.signif=red)
par(old.mar)
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