| as.multicomp {HH} | R Documentation |
MMC plots: In R, functions used to interface the glht in R to the MMC
functions designed with S-Plus multicomp notation. These are
all internal functions that the user doesn't see.
## S3 method for class 'mmc.multicomp':
print(x, ...)
## S3 method for class 'multicomp':
print(x, ...)
## print.multicomp.hh(x, digits = 4, ..., height=T) ## S-Plus only
## S3 method for class 'multicomp.hh':
print(x, ...) ## R only
print.glht.mmc.multicomp(x, ...) ## R. yes, spell it out.
as.multicomp(x, ...)
## S3 method for class 'glht':
as.multicomp(x, ## glht object
focus, ## currently required
ylabel=as.character(terms(x$model)[[2]]),
means=model.tables(x$model, type="means",
cterm=focus)$tables[[focus]],
lmat=t(x$linfct),
lmat.rows=-1,
lmat.scale.abs2=TRUE,
estimate.sign=1,
order.contrasts=TRUE,
contrasts.none=FALSE,
level=0.95,
calpha=NULL,
method=x$type,
...
)
as.glht(x, ...)
## S3 method for class 'multicomp':
as.glht(x, ...)
x |
"glht" object for as.multicomp.
A "mmc.multicomp" object for print.mmc.multicomp and
print.glht.mmc.multicomp.
A "multicomp" object for as.glht and print.multicomp. |
... |
other arguments. |
focus |
name of focus factor. |
ylabel |
response variable name on the graph. |
means |
means of the response variable on the focus factor. |
lmat, lmat.rows |
mmc |
lmat.scale.abs2 |
logical, almost always TRUE. If it is
not TRUE, then the contrasts will not be properly placed
on the MMC plot. |
estimate.sign |
numeric. 1: force all contrasts to be positive by
reversing negative contrasts. $-1$: force all contrasts to be negative by
reversing positive contrasts. Leave contrasts as they are constructed
by glht. |
order.contrasts |
logical. If TRUE, order contrasts by
height (see MMC). |
contrasts.none |
logical. This is an internal detail. The
``contrasts'' for the group means are not real contrasts in the
sense they don't compare anything. glht.mmc.glht sets this
argument to TRUE for the none component.
|
level |
Confidence level. Defaults to 0.95. |
calpha |
User-specified critical point.
See confint.glht.hh and
confint.glht. |
method |
See type in confint.glht. |
The mmc.multicomp print
method displays the confidence intervals and heights on the
MMC plot for each component of the mmc.multicomp object.
print.multicomp displays the confidence intervals and heights for
a single component.
print.glht.mmc.multicomp(x, ...) uses print.glht on each
component of a mmc.multicomp object and therefore prints only
the estimates of the comparisons.
as.multicomp is a generic function to change its argument to a
"multicomp" object.
as.multicomp.glht changes an "glht" object to a
"multicomp" object. If the model component of the argument "x"
is an "aov" object then the standard error is taken from the
anova(x$model) table, otherwise from the summary(x).
With a large number of levels for the focus factor, the
summary(x)
function is exceedingly slow (80 minutes for 30 levels on 1.5GHz Windows
XP).
For the same example, the anova(x$model) takes a fraction of
a second.
The multiple comparisons calculations in R and S-Plus use
completely different libraries.
MMC plots in R are based on glht.
MMC plots in S-Plus are based on multicomp.
The MMC plot is the same in both systems. The details of gettting the
plot differ.
Richard M. Heiberger <rmh@temple.edu>
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.
mmc,
glht in R,
multicomp in S-Plus.