plot.multicomp {HH} | R Documentation |
Multiple comparisons plot that gives independent user control
over the appearance of the significant and not significant
comparisons.
In R, both plot.multicomp
plot.multicomp.hh
coerce their argument
to an "glht"
object and plots
that with the appropriate plot
method.
In S-Plus,
plot.multicomp.hh
augments the standard plot.multicomp
to
give additional user arguments to control the appearance of the plot.
plot.matchMMC
uses the plot.multicomp.hh
code.
plot.matchMMC
must immediately follow a plot of an
mmc.multicomp
object and is applied to either the $mca
or $lmat
component of the mmc.multicomp
object.
plot.matchMMC
is used as a tiebreaker plot for the MMC
plot. plot.matchMMC
matches the horizontal scaling of the
MMC
plot and displays the individual contrasts in the same
order as the MMC
plot. See mmc
for examples.
## S3 method for class 'multicomp': plot(x, ...) ## R only ## S3 method for class 'multicomp.hh': plot(x, ylabel = x$ylabel, href = 0, uniform = TRUE, plt.in = c(0.2, 0.9, 0.1, 0.9), x.label.adj=1, xrange.include=href, xlim, comparisons.per.page=21, col.signif=1, col.not.signif=1, lty.signif=4, lty.not.signif=4, lwd.signif=1, lwd.not.signif=1, ..., xlabel.print=TRUE, y.axis.side=2, ylabel.inside=FALSE) plot.matchMMC(x, ..., xlabel.print=FALSE, cex.axis=par()$cex.axis, col.signif='red', main="", ylabel.inside=FALSE, y.axis.side=4)
x |
A "multicomp" object. |
ylabel |
Y label on graph. |
y.axis.side |
Y labels are on the left by default when plotting a
"multicomp" object. We move them to the
right when matching the x-axis of an MMC plot. |
... |
other arguments to plot.multicomp . |
ylabel.inside |
Logical value, if FALSE (the default), the
plot.matchMMC right-axis labels are in the margin. If
TRUE , the right-axis labels are in the figure area.
Setting the argument to
TRUE makes sense when plotting the lmat component of an
mmc.multicomp object. |
href |
reference line for the intervals. The default is 0. S-Plus only. |
xrange.include |
xlim
will be extended to include these values. S-Plus only. |
uniform |
S-Plus only. Logical value, if TRUE and the plots fill
more than one page, the scale will be uniform across pages. |
plt.in |
S-Plus only. Value for par("plt") to make better
use of the space on the plotting page. |
x.label.adj |
S-Plus only. This is the par("adj") applied
to the x-location of the y.labels on the multicomp plot. |
xlim |
x-range of the plot. |
comparisons.per.page |
The default S-Plus plot.multicomp
hardwires this to 21, which allows
for all pairwise comparisons of 7 levels taken 2 at a time.
The HH plot.multicomp makes it a variable.
Use it together with plt.in to make better use of the space
on the plot. S-Plus only. |
lty.signif, lwd.signif |
Line type, and line width for significant comparisons. S-Plus only. |
col.signif |
Color for significant comparisons. S-Plus only for
plot.multicomp . Both R and S-Plus for plot.matchMMC . |
col.not.signif, lty.not.signif, lwd.not.signif |
Color, line type, and line width for non-significant comparisons. S-Plus only. |
xlabel.print |
logical. When TRUE , the caption under the
plot is printed. When FALSE , the caption under the plot is not
printed. It is helpful to set this to FALSE when
the multicomp
plot is used as a tiebreaker plot for the MMC plot. S-Plus only. |
cex.axis |
cex for axis ticklabels. |
main |
Main title for plot. |
plot.multicomp
plots a "multicomp"
object. In S-Plus, this
masks the standard plot.multicomp
in order to provide additional
arguments for controlling the appearance. It defaults to the standard
appearance. In R, it coerces its argument to an "glht"
object and plots
that with the appropriate plot
method.
The multiple comparisons calculations in R and S-Plus use
completely different libraries.
Multiple comparisons in R are based on glht
.
Multiple comparisons in S-Plus are based on multicomp
.
The MMC plot in the HH library is the same in both systems.
The details of getting 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
in both languages,
glht
in R,
multicomp
in S-Plus.
## data and ANOVA 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) summary(catalystm1.aov) catalystm.mca <- if.R(r=glht(catalystm1.aov, linfct = mcp(catalyst = "Tukey")), s=multicomp(catalystm1.aov, plot=FALSE)) if.R(s=plot(catalystm.mca), r=plot(confint(catalystm.mca, calpha=qtukey(.95, 4, 12)/sqrt(2)))) ## calpha is strongly recommended in R with a large number of levels ## See ?MMC for details.