Dear R list.,
I am running a script to get a compact letter display.
library(lme4)
library(multcomp)
library(gplots)
####### Mixed Effects Model #########
data <- read.table("AJmix.txt",header=TRUE, sep="\t")
attach(data)
y<-cbind(positive,negative)
treatment<-factor(treatment)
mouse<-factor(mouse)
data$obs<-1:nrow(data)
names(data)
detach(data)
attach(data)
Mixmodel<-lmer(y~treatment+(1|mouse:treatment)+(1|obs) ,family=binomial)
summary(Mixmodel)
model.mc<-glht(Mixmodel,linfct=mcp(treatment="Tukey"))
summary(model.mc, test=adjusted(type="Westfall"))
model.ci <- confint(model.mc, level= 0.95)
model.ci
par(mar=c(5,10,3,2)+.1)
plot(model.ci,main="AJ Pairwise Differences of Logit(Proportion) OggI",
xlab="Difference in logit(Proportion) Between Treatments")
model.cld<-cld(model.mc)
par(mar=c(3,4,6,2)+.1)
plot(model.cld)
The last command resulted in a blank screen.
Here is my session and the class of similar objects.:
version 2.13.0 (2011-04-13)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid splines stats graphics grDevices utils
datasets methods base
other attached packages:
[1] gplots_2.8.0 caTools_1.12 bitops_1.0-4.1
gdata_2.8.1 gtools_2.6.2 multcomp_1.2-6
[7] survival_2.36-9 mvtnorm_0.9-9991 lme4_0.999375-39
Matrix_0.999375-50 lattice_0.19-26
loaded via a namespace (and not attached):
[1] nlme_3.1-101 stats4_2.13.0
> class(model.cld)
[1] "cld"
> class(model.mc)
[1] "glht"
When I ran a very similar script with a normally distributed mixed
model it worked just fine.
I am sending this to r-help rather than the mixed effects list because
the problem is with plot(cld)
which is part of mutcomp rather than lme4. However, I can repost to
the mixed effects list if anyone thinks
that might be more appropriate.
Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
fried...@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/
I am a Bayesian. When I see a multiple-choice question on a test and I
don't
know the answer I say "eeney-meaney-miney-moe".
Rose Friedman, Age 14
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