[R] Multcomp

Nair, Murlidharan T mnair at iusb.edu
Wed Jul 26 18:23:15 CEST 2006

Let me clarify with a simpler example what I want to accomplish
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

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


> 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
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

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

Cheers .../Murli

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