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

[Spencer Graves]

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	  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   23.50000    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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> 
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