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 23.50000 1 Namaacha
Mixed 15018 3.761099
NA02_073 -0.939355374 0.0132589702 10.50000 23.75000 1 Namaacha
Resistant 6170 3.675543
M00_12 -0.775048474 0.0047124742 10.50000 25.00000 1 Mpumulanga
Sensitive 17525 3.768326
M00_93 -0.555801118 0.0053872868 14.00000 37.50000 2 Mpumulanga
Sensitive 332000 4.254319
NA02_053 -0.327990343 -0.0037659864 6.00000 39.25000 1 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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