MMC (Mean--mean Multiple Comparisons) plots.

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

mmc(model, ...)  ## R

# S3 method for glht mmc(model, ...)

# S3 method for 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,, estimate.sign=1, x.offset=0, order.contrasts=TRUE, main, main2, focus.lmat, ...)

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


"aov" object in "lm" method.


name of the response variable.


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.


rows in lmat for the focus factor.


define the factor to compute contrasts of. In R this argument often can be used to simplify the call. The statement mmc(my.aov, focus="factorA") is interpreted as mmc(my.aov, factorA="Tukey", `interaction_average`=TRUE, `covariate_average`=TRUE) With TRUE, TRUE, multcomp::glht always gives the same result as the S-Plus multcomp function. Without the TRUE, TRUE, multcomp::glht gives a different answer when there are interactions or covariates in the model. See


R only. Contrast matrix used in the user-specified comparisons of the focus factor. This is the matrix the user constructs. Row names must include all levels of the factor. Column names are the names the user assigns to the contrasts. Each column must sum to zero. See catalystm.lmat in the Examples section for an example. The focus.lmat matrix is multiplied by the lmat from the none component to create the lmat for the user-specified contrasts. Display the hibrido.lmat and maiz2.lmat in the maiz example below to see what is happening.


In R, see

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


argument to multicomp


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


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 all contrasts to positive.


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.


Direction of alternative hypothesis. See


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 in S-Plus and calpha when used with glht and confint in R. In R, with a large number of levels for the focus factor, calpha should be specified. See notes below for discussion of the timing issues and the examples for an illustration how to use calpha.


logical, display the plot if TRUE.

ry,, x.offset, main, main2

arguments to plot.mmc.multicomp.

x, drop

See "[".


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.


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.


Object containing the pairwise comparisons.


Object comparing each mean to 0.


Object for the contrasts specified in the lmat argument.

"[.mmc.multicomp" is a subscript method.


The multiple comparisons calculations in R and S-Plus use completely different functions. MMC plots in R are constructed by mmc based on


Heiberger, Richard M. and Holland, Burt (2015). Statistical Analysis and Data Display: An Intermediate Course with Examples in R. Second Edition. Springer-Verlag, New York.

Heiberger, Richard M. and Holland, Burt (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.

  • mmc
  • MMC
  • multicomp
  • multicomp.mmc
  • mmc
  • mmc.glht
  • mmc.default
  • [.mmc.multicomp
Documentation reproduced from package HH, version 3.1-43, License: GPL (>= 2)

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