# multicomp.order

##### Update a multicomp object by ordering its contrasts.

Update a multicomp object by ordering its contrasts.
The default `sort.by = "height"`

matches the order in the MMC plot.
An alternate `sort.by = "estimate"`

matches the order of the
half-normal plot. Or the argument `sort.order`

can be used
to specify any other order.

- Keywords
- dplot

##### Usage

`multicomp.order(mca, sort.by = "height", sort.order = NULL)`multicomp.label.change(x, old="adj", new="new", how.many=2)

# S3 method for multicomp
multicomp.label.change(x, old="adj", new="new", how.many=2)

# S3 method for mmc.multicomp
multicomp.label.change(x, old="adj", new="new", how.many=2)

##### Arguments

- mca
`"multicomp"`

object. This is the result of`multicomp`

in S-Plus or the result from applying`as.multicomp`

to a`"glht"`

object in R.- sort.by
Either

`"height"`

or`"estimate"`

.- sort.order
Vector of indices by which the contrasts are to be sorted. When

`sort.order`

in non-`NULL`

, it is used.- x
`"multicomp"`

object.- old
character string to be removed from contrast names.

- new
replacement character string to be inserted in contrast names.

- how.many
number of times to make the replacement.

##### Value

The result is a `"multicomp"`

object containing the same
contrasts as the argument.
`multicomp.order`

sorts the contrasts
(and renames them consistently) according to the specifications.
`multicomp.label.change`

changes the contrast names according to the specifications.

When `sort.by=="height"`

, sort the contrasts by the reverse order
of the heights. This provides a `"multicomp"`

object that will be
plotted by `plot.multicomp`

in the same order used by
`mmcplot`

or the older `plot.mmc.multicomp`

. If there is not `"height"`

component,
the original `"multicomp"`

object is returned.

When `sort.by=="estimate"`

, sort the contrasts by the reverse order
of the contrast estimates. This provides the same order as the
half-normal plot.

When `sort.order`

in non-`NULL`

, sort the contrasts in
that order.

##### Note

S-Plus use the `multicomp`

functions
and R uses the `multcomp`

package.

##### References

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.
https://www.springer.com/us/book/9781493921218

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.

##### See Also

`MMC`

, `as.glht in R`

,
`multicomp.reverse`

##### Examples

```
# NOT RUN {
## continue with the example in mmc in R, or multicomp.mmc in S-Plus
data(catalystm)
catalystm1.aov <- aov(concent ~ catalyst, data=catalystm)
if.R(r={
catalystm.mca <-
glht(catalystm1.aov, linfct = mcp(catalyst = "Tukey"))
print(confint(catalystm.mca))
catalystm.mmc <-
mmc(catalystm1.aov, linfct = mcp(catalyst = "Tukey"))
## the contrasts have been ordered by height (see ?MMC),
## which in this example corresponds to sort.order=c(1,2,4,3,5,6),
## and reversed, to make the contrast Estimates positive.
print(as.glht(catalystm.mmc$mca))
## ## For consistency with the S-Plus example,
## ## we change all factor level "A" to "control".
## as.glht(multicomp.label.change(catalystm.mmc$mca, "A", "control"))
},s={
catalystm.mca <-
multicomp(catalystm1.aov, method="Tukey")
print(catalystm.mca)
catalystm.mmc <-
multicomp.mmc(catalystm1.aov, method="Tukey", plot=FALSE)
## the contrasts have been ordered by height (see ?MMC),
## which in this example corresponds to sort.order=c(1,2,4,3,5,6),
## and reversed, to make the contrast Estimates positive.
print(catalystm.mmc$mca)
## S-Plus multicomp already uses simple names. This function is
## therefore used in more complex two-way ANOVA examples. We illustrate
## here by changing all factor level "A" to "control".
print(multicomp.label.change(catalystm.mmc$mca, "A", "control"))
})
# }
```

*Documentation reproduced from package HH, version 3.1-42, License: GPL (>= 2)*