From: Greg Distiller <gregd_at_stats.uct.ac.za>

Date: Thu 03 Aug 2006 - 19:58:58 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Thu Aug 03 20:07:15 2006

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:

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 3.768326M00_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

[[alternative HTML version deleted]]

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Thu Aug 03 20:07:15 2006

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.1.8, at Wed 09 Aug 2006 - 16:18:37 EST.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*