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 ?
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 otherwise.
Cheers .../Murli
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.> > 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$estimate) <- LETTERS[1:3] plot(fungus.cirec)
Let me clarify with a simpler example what I want to accomplish library(multcomp) data(recovery) Dcirec<-simint(minutes~blanket,data=recovery, conf.level=0.9, alternative="less") out.data.mat <- with(Dcirec,data.frame(estimate, conf.int, p.value.raw c(p.value.raw), p.value.bon, p.value.adj)) I want to generate the same type of plot using out.data.mat that I get by plot(Dcirec) How do I specify the plot method how the data in out.data.mat is to be plotted? I am interested in doing this because, I am running about 1500 different comparisons, which creates 1500 different objects. I need to analyze them and combine significant ones into one plot. -----Original Message----- From: Greg Snow [mailto:Greg.Snow at intermountainmail.org] Sent: Tuesday, July 25, 2006 12:12 PM To: Nair, Murlidharan T Subject: RE: [R] Multcomp Doing:> str( fungus.cirec )Suggests that fungus.cirec$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 T 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 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 ? 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 otherwise. Cheers .../Murli ______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Let me clarify with a simpler example what I want to accomplish library(multcomp) data(recovery) 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 plotted? 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 Doing:> 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 T 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 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 ? 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 otherwise. Cheers .../Murli ______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.