Re: [R] Multcomp

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Sun 23 Jul 2006 - 03:37:01 EST

On 7/22/06, Nair, Murlidharan T <mnair@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.

>
> 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")

>
> 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)



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