[R] NLME: Problem with plotting ranef vs a factor

From: Greg Distiller <gregd_at_stats.uct.ac.za>
Date: Thu 03 Aug 2006 - 19:58:58 EST


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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