[R] Multcomp

Nair, Murlidharan T mnair at iusb.edu
Sat Jul 22 23:28:02 CEST 2006

-----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 =
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
is that its passed to plot which in turn passes them to plot.default so
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
>> 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

# change rownames of the estimates which has the effect
# of changing the y axis labels
rownames(fungus.cirec$estimate) <- LETTERS[1:3]

>>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. 

Thanks ../Murli

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