Multcomp
-----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. Thanks ../Murli