Re: [R] Multcomp

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Thu 27 Jul 2006 - 02:32:00 EST

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
>
> ______________________________________________
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>
> ______________________________________________
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> 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. Received on Thu Jul 27 02:37:48 2006

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