From: Gabor Grothendieck <ggrothendieck_at_gmail.com>

Date: Thu 27 Jul 2006 - 02:49:13 EST

R-help@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. Received on Thu Jul 27 08:27:57 2006

Date: Thu 27 Jul 2006 - 02:49:13 EST

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@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@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@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@intermountainmail.org
**> > (801) 408-8111
**> >
**> >
**> > -----Original Message-----
**> > From: r-help-bounces@stat.math.ethz.ch
**> > [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Nair, Murlidharan
**> > T
**> > Sent: Saturday, July 22, 2006 11:00 AM
**> > To: R-help@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@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@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.
**> >
**>
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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. Received on Thu Jul 27 08:27:57 2006

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