mmc: MMC (mean--mean multiple comparisons) plots.

Description

Constructs a "mmc.multicomp" object from the formula and other arguments. The object must be explicitly plotted.

Usage

mmc(model, ...)  ## R

## S3 method for class 'glht':
mmc(model, ...)


## S3 method for class 'default':
mmc(model,       ## lm object
    linfct=NULL,
    focus=
    if (is.null(linfct))
    {
      if (length(model$contrasts)==1) names(model$contrasts)
      else stop("focus or linfct must be specified.")
    }
    else
    {
      if (is.null(names(linfct)))
        stop("focus must be specified.")
      else names(linfct)
    },
    focus.lmat,
    ylabel=deparse(terms(model)[[2]]),
    lmat=if (missing(focus.lmat)) {
      t(linfct)
    } else {
      lmatContrast(t(none.glht$linfct), focus.lmat)
      },
    lmat.rows=lmatRows(model, focus),
    lmat.scale.abs2=TRUE,
    estimate.sign=1,
    order.contrasts=TRUE,
    level=.95,
    calpha=NULL,
    alternative = c("two.sided", "less", "greater"),
    ...
    )
	   
multicomp.mmc(x,  ## S-Plus
              focus=dimnames(attr(x$terms,"factors"))[[2]][1],
              comparisons="mca",
              lmat,
              lmat.rows=lmatRows(x, focus),
              lmat.scale.abs2=TRUE,
              ry,
              plot=TRUE,
              crit.point,
              iso.name=TRUE,
              estimate.sign=1,
              x.offset=0,
              order.contrasts=TRUE,
              main,
              main2,
              focus.lmat,
              ...)

## S3 method for class 'mmc.multicomp':
[(x, ..., drop = TRUE)

Arguments

model

"aov" object in "lm" method.

ylabel

name of the response variable.

lmat

contrast matrix as in the S-Plus multicomp. The convention for lmat in R is to use the transpose of the linfct component produced by glht. Required for user-specified contrasts.

lmat.rows

rows in lmat for the focus factor.

focus

define the factor to compute contrasts of. See#ifndef S-Plus glht. #endif #ifdef S-Plus glht. #endif in R.

focus.lmat

R only. Contrast matrix used in the user-specified comparisons of the focus factor. This is the matrix the user constructs. This matrix is multiplied by the lmat from the none component to create the lmat for t

linfct

In R, see#ifndef S-Plus glht. #endif #ifdef S-Plus glht. #endif

...

other arguments. alternative and base are frequently used with glht.

comparisons

argument to multicomp

lmat.scale.abs2

logical, scale the contrasts in the columns of lmat to make the sum of the absolute values of each column equal 2.

estimate.sign

numeric. If 0, leave contrasts in the default lexicographic direction. If positive, force all contrasts to positive, reversing their names if needed (if contrast A-B is negative, reverse it to B-A). If negative, the force al

order.contrasts

sort the contrasts in the (mca, none, lmat) components by height on the MMC plot. This will place the contrasts in the multicomp plots in the same order as in the MMC plot.

alternative

Direction of alternative hypothesis. See#ifndef S-Plus glht #endif #ifdef S-Plus glht #endif in R. S-Plus multicomp uses the argument bounds

level

Confidence level. Defaults to 0.95.

crit.point, calpha

critical value for the tests. The value from the specified multicomp method is used for the user-specified contrasts when lmat is specified. This argument is called crit.point with multicomp

plot

logical, display the plot if TRUE.

ry, iso.name, x.offset, main, main2

arguments to plot.mmc.multicomp.

x, drop

See "[".

Value

An "mmc.multicomp" object contains either the first two or all three of the "multicomp" components mca, none, lmat described here. Each "multicomp" component in R also contains a "glht" object.
mcaObject containing the pairwise comparisons.
noneObject comparing each mean to 0.
lmatObject for the contrasts specified in the lmat argument.
"[.mmc.multicomp" is a subscript method.

Details

By default, if lmat is not specified, we plot the isomeans grid and the pairwise comparisons for the focus factor. By default, we plot the specified contrasts if the lmat is specified. Each contrast is plotted at a height which is the weighted average of the means being compared. The weights are scaled to the sum of their absolute values equals 2. We get the right contrasts automatically if the aov is oneway. If we specify an lmat for oneway it must have a leading row of 0. For any more complex design, we must study the lmat from the mca component of the result to see how to construct the lmat (with the extra rows as needed) and how to specify the lmat.rows corresponding to the rows for the focus factor. mmc in R works from either an "glht" object or an "aov" object. multicomp.mmc in S-Plus works from an "aov" object.

References

Heiberger, Richard M. and Holland, Burt (2004b). Statistical Analysis and Data Display: An Intermediate Course with Examples in S-Plus, R, and SAS. Springer Texts in Statistics. Springer. ISBN 0-387-40270-5. Heiberger, R.~M. and Holland, B. (2006). "Mean--mean multiple comparison displays for families of linear contrasts." Journal of Computational and Graphical Statistics, 15:937--955. Hsu, J. and Peruggia, M. (1994). "Graphical representations of Tukey's multiple comparison method." Journal of Computational and Graphical Statistics, 3:143--161.

Examples

Run this code

## Use mmc with R.
## Use multicomp.mmc with S-Plus.

## data and ANOVA
## catalystm example
data(catalystm)

if.R(r=
  bwplot(concent ~ catalyst, data=catalystm,
         scales=list(cex=1.5),
         ylab=list("concentration", cex=1.5),
         xlab=list("catalyst",cex=1.5))
,s=
t(bwplot(catalyst ~ concent, data=catalystm,
         scales=list(cex=1.5),
         xlab=list("concentration", cex=1.5),
         ylab=list("catalyst",cex=1.5)))
)


catalystm1.aov <- aov(concent ~ catalyst, data=catalystm)
summary(catalystm1.aov)

catalystm.mca <-
if.R(r=glht(catalystm1.aov, linfct = mcp(catalyst = "Tukey")),
     s=multicomp(catalystm1.aov, plot=FALSE))
## plot(catalystm.mca)
if.R(s=catalystm.mca,
     r=confint(catalystm.mca))

## pairwise comparisons
old.omd <- par(omd=c(0,.95,0,1))
catalystm.mmc <-
if.R(r=mmc(catalystm1.aov, linfct = mcp(catalyst = "Tukey")),
     s=multicomp.mmc(catalystm1.aov, plot=FALSE))
catalystm.mmc
if.R(s=plot(catalystm.mmc, x.offset=1),
     r=plot(catalystm.mmc, ry=c(50,58), x.offset=1.8))
## tiebreaker
plotMatchMMC(catalystm.mmc$mca, xlabel.print=FALSE)

## user-specified contrasts
catalystm.lmat <- cbind("AB-D" =c( 1, 1, 0,-2),
                        "A-B"  =c( 1,-1, 0, 0),
                        "ABD-C"=c( 1, 1,-3, 1))
dimnames(catalystm.lmat)[[1]] <- levels(catalystm$catalyst)

catalystm.mmc <-
if.R(r=mmc(catalystm1.aov,
       linfct = mcp(catalyst = "Tukey"),
       focus.lmat=catalystm.lmat),
     s=multicomp.mmc(catalystm1.aov,
       focus.lmat=catalystm.lmat, plot=FALSE))
catalystm.mmc

if.R(s=plot(catalystm.mmc, x.offset=1),
     r=plot(catalystm.mmc, ry=c(50,58), x.offset=1.8))
## tiebreaker
plotMatchMMC(catalystm.mmc$lmat, xlabel.print=FALSE, col.signif='blue')
par(old.omd)


## Dunnett's test
## weightloss example
data(weightloss)
if.R(r=
bwplot(loss ~ group, data=weightloss,
       scales=list(cex=1.5),
       ylab=list("Weight Loss", cex=1.5),
       xlab=list("group",cex=1.5))
,s=
t(bwplot(group ~ loss, data=weightloss,
       scales=list(cex=1.5),
       xlab=list("Weight Loss", cex=1.5),
       ylab=list("group",cex=1.5)))
)

weightloss.aov <- aov(loss ~ group, data=weightloss)
summary(weightloss.aov)

if.R(r={
group.count <- table(weightloss$group)
},s={})

tmp.dunnett <- 
if.R(r=
glht(weightloss.aov,
     linfct=mcp(group=contrMat(group.count, base=4)),
     alternative="greater")
,s=
multicomp(weightloss.aov,
          method="dunnett", comparisons="mcc",
          bounds="lower", control=4,
          valid.check=FALSE)
)
plot(tmp.dunnett)

tmp.dunnett.mmc <-
if.R(r=
   mmc(weightloss.aov,
       linfct=mcp(group=contrMat(group.count, base=4)),
       alternative="greater")
,s=
   multicomp.mmc(weightloss.aov,
                 method="dunnett", comparisons="mcc",
                 bounds="lower", control=4,
                 valid.check=FALSE, plot=FALSE)
)

tmp.dunnett.mmc
plot(tmp.dunnett.mmc)



## two-way ANOVA
## display example

data(display)

if.R(r=
interaction2wt(time ~ emergenc * panel.ordered, data=display)
     ,s=
interaction2wt(time ~ emergenc * panel.ordered, data=display,
               xlim=c(.5,4.5), key.in=list(x=-1.8))
)

displayf.aov <- aov(time ~ emergenc * panel, data=display)
anova(displayf.aov)

## multiple comparisons
## MMC plot
displayf.mmc <-
if.R(r={
        ## mmc(displayf.aov, linfct=mcp(panel="Tukey"), ## averaging not right
        ##     `interaction_average`=TRUE)
	displayf.mca <- glhtWithMCP.993(displayf.aov, linfct=mcp(panel="Tukey"))
	mmc(displayf.aov, linfct=displayf.mca$linfct, focus="panel")
},
     s=multicomp.mmc(displayf.aov, "panel", plot=FALSE))

if.R(s=
       plot(displayf.mmc)
    ,r=
       plot(displayf.mmc, x.offset=1, ry=c(17,26))
)


panel.lmat <- cbind("3-12"=c(-1,-1,2),
                     "1-2"=c( 1,-1,0))
dimnames(panel.lmat)[[1]] <- levels(display$panel)

displayf.mmc <-
if.R(r={
        mmc(displayf.aov, linfct=mcp(panel="Tukey"),
            `interaction_average`=TRUE, focus.lmat=panel.lmat)
},
     s=multicomp.mmc(displayf.aov, "panel",
       focus.lmat=panel.lmat, plot=FALSE))

if.R(s=
       plot(displayf.mmc)
    ,r=
       plot(displayf.mmc, x.offset=1, ry=c(17,26))
)



## split plot design with tiebreaker plot
##
## This example is based on the query by Tomas Goicoa to R-news
## http://article.gmane.org/gmane.comp.lang.r.general/76275/match=goicoa
## It is a split plot similar to the one in HH Section 14.2 based on
## Yates 1937 example.  I am using the Goicoa example here because its
## MMC plot requires a tiebreaker plot.


data(maiz)

if.R(s={old.omd <- par(omd=c(.1,1,.05,1))},
     r={})
interaction2wt(yield ~ hibrido+nitrogeno+bloque, data=maiz,
               key.in=list(x=-5), ## ignored by R
               par.strip.text=list(cex=.7))
interaction2wt(yield ~ hibrido+nitrogeno, data=maiz)
 if.R(s={par(old.omd)},
      r={})

maiz.aov <- aov(yield ~ nitrogeno*hibrido + Error(bloque/nitrogeno), data=maiz) 

summary(maiz.aov)
summary(maiz.aov,
        split=list(hibrido=list(P3732=1, Mol17=2, A632=3, LH74=4)))

## multicomp(maiz.aov, focus="hibrido")         ## can't use 'aovlist' objects
## glht(maiz.aov, linfct=mcp(hibrido="Tukey"))  ## can't use 'aovlist' objects

sapply(maiz[-1], contrasts)
if.R(r={
  ## R mmc requires treatment contrasts
  contrasts(maiz$nitrogeno) <- "contr.treatment"
  contrasts(maiz$bloque) <- "contr.treatment"
  sapply(maiz[-1], contrasts)
},
     s={})

## Both R glht() and S-Plus multicomp() require aov, not aovlist
maiz2.aov <- aov(terms(yield ~ bloque*nitrogeno + hibrido/nitrogeno,
                       keep.order=TRUE), data=maiz)
summary(maiz2.aov)

## There are many ties in the group means.
## These are easily seen in the MMC plot, where the two clusters
## c("P3747", "P3732", "LH74") and c("Mol17", "A632")
## are evident from the top three contrasts including zero and the
## bottom contrast including zero.  The significant contrasts are the
## ones comparing hybrids in the top group of three to ones in the
## bottom group of two.

## We have two graphical responses to the ties.
## 1. We constructed the tiebreaker plot.
## 2. We construct a set of orthogonal contrasts to illustrate
##    the clusters.

## pairwise contrasts with tiebreakers.
if.R(s={
  maiz2.mmc <- multicomp.mmc(maiz2.aov, focus="hibrido", plot=FALSE)
  old.omd <- par(omd=c(.05,.85,0,1))
  plot(maiz2.mmc, ry=c(145,170), x.offset=4)
  par(omd=c(.05,.85,0,1))
  plotMatchMMC(maiz2.mmc$mca)
  par(old.omd)
},r={
  ##   maiz2.mmc <- mmc(maiz2.aov, linfct=mcp(hibrido="Tukey"), ## averaging not right
  ##                    `interaction_average`=TRUE)
  maiz2.mca <- glhtWithMCP.993(maiz2.aov, linfct=mcp(hibrido="Tukey"))
  maiz2.mmc <- mmc(maiz2.aov, linfct=maiz2.mca$linfct,
                   focus="hibrido")
  old.omd <- par(omd=c(.05,.85,.35,1)) ## x1 x2 y1 y2
  plot(maiz2.mmc)
  par(omd=c(.05,.85,0,.5), new=TRUE)
  plotMatchMMC(maiz2.mmc$mca, cex.axis=.7)
  par(old.omd)
})


## orthogonal contrasts
## user-specified contrasts
hibrido.lmat <- cbind("PPL-MA" =c(2, 2,-3,-3, 2),
                      "PP-L"   =c(1, 1, 0, 0,-2),
                      "P47-P32"=c(1,-1, 0, 0, 0),
                      "M-A"    =c(0, 0, 1,-1, 0))
dimnames(hibrido.lmat)[[1]] <- levels(maiz$hibrido)
hibrido.lmat
maiz2.mmc <-
  if.R(s=multicomp.mmc(maiz2.aov, focus="hibrido",
         focus.lmat=hibrido.lmat,
         plot=FALSE),
       r=mmc(maiz2.aov, linfct=mcp(hibrido="Tukey"),
             `interaction_average`=TRUE, focus.lmat=hibrido.lmat)
       )

if.R(s={
  old.omd <- par(omd=c(.05,.85,0,1))
  plot(maiz2.mmc, ry=c(145,170), x.offset=4)
  par(omd=c(.05,.85,0,1))
  plotMatchMMC(maiz2.mmc$lmat, col.signif='blue')
  par(old.omd)
},r={
  old.omd <- par(omd=c(.05,.85,.35,1)) ## x1 x2 y1 y2
  plot(maiz2.mmc)
  par(omd=c(.05,.85,0,.45), new=TRUE)
  plotMatchMMC(maiz2.mmc$lmat, cex.axis=.7, col.signif='blue')
  par(old.omd)
})

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