[R] Multcomp

[Gabor Grothendieck]

On 7/22/06, Nair, Murlidharan T <mnair at iusb.edu> wrote:
> -----Original Message-----
> From: Gabor Grothendieck [mailto:ggrothendieck at gmail.com]
> Sent: Saturday, July 22, 2006 1:37 PM
> To: Nair, Murlidharan T
> Cc: R-help at stat.math.ethz.ch
> Subject: Re: [R] Multcomp
>
> On 7/22/06, Nair, Murlidharan T <mnair at iusb.edu> wrote:
> > 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 ?
>
> Don't understand what "part of the data" means.  Use data =
> fungus[1:10,]
> in the simint call to just process the first 10 data rows.  To
> eliminate a portion of
> the plot note in ?plot.hmtest that there is a ... argument and its
> description
> is that its passed to plot which in turn passes them to plot.default so
> you
> could use ylim = 1:2, say, to show only part of the plot vertically.
>
>
> >>I have to use all the data for my computation. Since the number of
> >>comparisons are many I want to plot it in different graphs so that the
> >>graph does not look cluttered. So "part of the data" means a subset of
> the >>comparisons in one graph and another subset in another and so
> on....
> >> Can you give me an example of the  "ylim" parameter. I tried
> >>plot(fungus.cirec, ylim=1:2) and it was not happy with it. I am not
> >>completely comfortable with the ... argument. I am trying to read up
> on >>it.
>
>
> >
> > How do I tell it to mark the significant comparisons?
>
> # after your plot statement:
> pp <- locator()
> # now click on a spot on the plot
> # and then right click and choose stop
> text(pp$x, pp$y, "some text")
>
> >> This is very useful
>
> >
> > 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.
>
> # change rownames of the estimates which has the effect
> # of changing the y axis labels
> rownames(fungus.cirec$estimate) <- LETTERS[1:3]
> plot(fungus.cirec)
>
> >>This only labels it a A,B or C. What I wanted was to remove the field
> name >>"Habitat" in this case and out put the label as Birch-Oak.
>

See ?gsub