Your question is entirely too complex for me to try to answer in a
reasonable amount of time, especially since your example in not self
contained.
If you would still like help on this, I suggest you try to generate a
self contained example that is as simple as you can make it that
illustrates your problem, as suggested in the posting guide
www.R-project.org/posting-guide.html. With only a modest amount of
luck, the things you try to simplify your example will lead to
enlightenment. If that fails, please submit another question that is
self contained, simple and clear. Doing so should substantially
increase your chances of getting a quick, useful reply.
I know this doesn't answer your question, but I hope it helps.
Spencer Graves
Greg Distiller wrote:
Hi
I am following the model building strategy that is outlined in the Pinheiro
and Bates book wrt including covariates but am having a problem with the
plot. Basically I am using 4 covariates (1 of them is continuous) and 3 of
them are fine but the 4th one is being shown as a scatterplot despite the
fact that it is a factor. I have explicitly declared this to be a factor
(pcat-as.factor(pcat)) and have also checked by using the is.factor and
the levels command that it is a factor. Yet despite this the plot command
is not recognising it as a factor.
Here is more information about my problem:
I am reading in the data by:
Data-read.csv(Data1_93_2.csv,header=T)
attach(Data)
Data1_93-transform(Data,log2game=log2(gamedens+1))
pcat-as.factor(pcat)
Data1_93-groupedData(log2game ~ day | subjectno, data=Data1_93)
detach(Data)
Here is the code to check that the covariate called pcat is indeed a factor:
levels(pcat)
[1] 1 2 3
is.factor(pcat)
[1] TRUE
and then after the model is fitted I extract the random effects:
D1C2.ran - ranef(mod11.103nlme,augFrame=T)
and here is an extract from the object:
C R day gamedens pcat site
mutcat1 pdens0 log2game
NA02_259 -1.016987007 0.0162825099 15.75000 23.51 Namaacha
Mixed 15018 3.761099
NA02_073 -0.939355374 0.0132589702 10.5 23.750001 Namaacha
Resistant6170 3.675543
M00_12 -0.775048474 0.0047124742 10.5 25.01 Mpumulanga
Sensitive 17525 3.768326
M00_93 -0.555801118 0.0053872868 14.0 37.52 Mpumulanga
Sensitive 332000 4.254319
NA02_053 -0.327990343 -0.0037659864 6.0 39.250001 Namaacha
Resistant 65529 4.292481
Note that this output also seems to indicate that pcat is a factor as it is
summarised correctly.
I then generate plots for my random effects:
plot(D1C2.ran,form= C ~site+mutcat2+pcat+pdens0)
and the problem is that the panel for my random effects vs pcat is displayed
as a scatterplot rather than as a boxplot.
I am getting told to check warnings and these warnings look like:
Warning messages:
1: at 0.99
2: radius 0.0001
3: all data on boundary of neighborhood. make span bigger
4: pseudoinverse used at 0.99
5: neighborhood radius 0.01
6: reciprocal condition number -1.#IND
7: zero-width neighborhood. make span bigger
I do not get these warnings if I exclude the problematic variable pcat so
must be something to do with this. Any ideas?
Many thanks
Greg
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