[R] Multcomp

[Gabor Grothendieck]

Here is a minor simplication:

my.hmtest <- structure(list(
   estimate = t(t(out.data.mat[,"estimate",drop=FALSE])),
   conf.int = out.data.mat[,2:3],
   ctype = "Dunnett"),
      class = "hmtest")
plot(my.hmtest)

On 7/26/06, Gabor Grothendieck <ggrothendieck at gmail.com> wrote:
> Look through
>   multcomp:::plot.hmtest
> to find out which components of an hmtest object are actually used.
> Now look at what an hmtest object looks like by doing this
>
> dput(Dcirec)
>
> or looking through the source of the function that produces hmtest
> objects.  With this information in hand we can construct one from
> out.data.mat:
>
> my.hmtest <- structure(list(
>  estimate = t(t(structure(out.data.mat[,"estimate"],
>     .Names = rownames(out.data.mat)))),
>  conf.int = out.data.mat[,2:3],
>  ctype = "Dunnett"),
>  class = "hmtest")
> plot(my.hmtest)
>
> Note that this is a bit fragile since changes to the internal
> representation of hmtest objects could cause your
> object to cease working although as long as those
> changes do not affect the three components we are
> using it should be ok.  By the way I hard coded
> "Dunnett" above since ctype is not available
> in out.data.mat .
>
> On 7/26/06, Nair, Murlidharan T <mnair at iusb.edu> wrote:
> > Let me clarify with a simpler example what I want to accomplish
> > library(multcomp)
> > data(recovery)
> > Dcirec<-simint(minutes~blanket,data=recovery, conf.level=0.9,
> > alternative="less") out.data.mat <- with(Dcirec,data.frame(estimate,
> > conf.int, p.value.raw = c(p.value.raw), p.value.bon, p.value.adj))
> >
> >
> > I want to generate the same type of plot using out.data.mat that I get
> > by plot(Dcirec)
> >
> > How do I specify the plot method how the data in out.data.mat is to be
> > plotted?
> >
> > I am interested in doing this because, I am running about 1500 different
> > comparisons, which creates 1500 different objects. I need to analyze
> > them and combine significant ones into one plot.
> >
> > -----Original Message-----
> > From: Greg Snow [mailto:Greg.Snow at intermountainmail.org]
> > Sent: Tuesday, July 25, 2006 12:12 PM
> > To: Nair, Murlidharan T
> > Subject: RE: [R] Multcomp
> >
> > Doing:
> >
> > > str( fungus.cirec )
> >
> > Suggests that fungus.cirec$conf.int contains the confidence intervals,
> > you can manually plot the subset that you are intereseted in (and label
> > them whatever you want)
> >
> >
> > --
> > Gregory (Greg) L. Snow Ph.D.
> > Statistical Data Center
> > Intermountain Healthcare
> > greg.snow at intermountainmail.org
> > (801) 408-8111
> >
> >
> > -----Original Message-----
> > From: r-help-bounces at stat.math.ethz.ch
> > [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Nair, Murlidharan
> > T
> > Sent: Saturday, July 22, 2006 11:00 AM
> > To: R-help at stat.math.ethz.ch
> > Subject: [R] Multcomp
> >
> > Here it is again, hope this is more clear
> >
> > I am using the following data (only a small subset is given):
> >
> > Habitat Fungus.yield
> > Birch 20.83829053
> > Birch 22.9718181
> > Birch 22.28216829
> > Birch 24.23136797
> > Birch 22.32147961
> > Birch 20.30783598
> > Oak 27.24047258
> > Oak 29.7730014
> > Oak 30.12608508
> > Oak 25.76088669
> > Oak 30.14750974
> > Hornbeam 17.05307949
> > Hornbeam 15.32805111
> > Hornbeam 18.26920177
> > Hornbeam 21.30987049
> > Hornbeam 21.7173223
> >
> > I am using the multcomp package to do multiple comparisons as follows
> >
> > library(multcomp) # loads the package
> >
> > fungus<-read.table("fungi.txt", Header=T)    # Reads the data from file
> > saved as fungi.txt
> >
> >
> > fungus.cirec<-simint(Fungus.yield~Habitat,
> > data=fungus,conf.level=0.95,type =c("Tukey"))  # Computes cimultaneous
> > intervals using Tukey's method
> >
> >
> > plot(fungus.cirec)   # plots the data
> >
> > The plot function plots all the comparisons, I want to plot only part of
> > the data since it clutters the graph.
> >
> > How do I plot only part of the data ?
> >
> > How do I tell it to mark the significant comparisons?
> >
> > How do I get rid of the field names in the plot? For eg. The plot labels
> > are HabitatBirch-HabitatOak, I want it to be labeled as Birch-Oak.
> >
> >
> >
> > Hope I have posted it according to the guidelines, let me know
> > otherwise.
> >
> > Cheers .../Murli
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>