R help - Jul 2010 - Producing residual plots by time for lme object

Fellow R-users,

I have a longitudinal data set with missing values in it. I would like to
produce a residual plot for each time using panel.xyplot function but I get an
error message. Here's a simple example,

library(nlme)
set.seed(1544)
longdata <- data.frame(ID=gl(10,1,50), y=rnorm(50), time =
as.numeric(gl(5,10,50)), x = rnorm(50))
longdata$y[5] <- NA
longdata$x[35] <- NA

modlme<- lme(fixed=y ~ time + x,
                random= ~ 1 | ID,
                na.action=na.exclude, data=longdata)


plot( modlme, abs( resid(., type = 'p')) ~ fitted(.) | time,
          panel = function(x, y, ...) {
                panel.xyplot( x, y, ...)
                panel.loess( x, y,...)
          })

where the last call produces the error message
Error in `[[<-.data.frame`(`*tmp*`, j, value = c(1, 1, 1, 1, 1, 1, 1,  : 
  replacement has 48 rows, data has 50


How do I fix this?

Any help would be greatly appreciated.

Greg

ps my sessioninfo is 
> sessionInfo()
R version 2.9.1 (2009-06-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY=English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] nlme_3.1-96

loaded via a namespace (and not attached):
[1] grid_2.9.1      lattice_0.17-25
> 


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On Fri, Jul 2, 2010 at 11:40 AM, Gregory Gentlemen
<gregory_gentlemen at yahoo.ca> wrote:
> Fellow R-users,
>
> I have a longitudinal data set with missing values in it. I would like to
produce a residual plot for each time using panel.xyplot function but I get an
error message. Here's a simple example,
>
> library(nlme)
> set.seed(1544)
> longdata <- data.frame(ID=gl(10,1,50), y=rnorm(50), time =
as.numeric(gl(5,10,50)), x = rnorm(50))
> longdata$y[5] <- NA
> longdata$x[35] <- NA
>
> modlme<- lme(fixed=y ~ time + x,
> ??????????????? random= ~ 1 | ID,
> ??????????????? na.action=na.exclude, data=longdata)
>
>
> plot( modlme, abs( resid(., type = 'p')) ~ fitted(.) | time,
> ????????? panel = function(x, y, ...) {
> ??????????????? panel.xyplot( x, y, ...)
> ??????????????? panel.loess( x, y,...)
> ????????? })
>
> where the last call produces the error message
> Error in `[[<-.data.frame`(`*tmp*`, j, value = c(1, 1, 1, 1, 1, 1, 1,? :
> ? replacement has 48 rows, data has 50
>
>
> How do I fix this?
NA-handling is not working right, it seems. Would it make any real
difference to your analysis to do

modlme<- lme(fixed=y ~ time + x,
                random= ~ 1 | ID, data = na.omit(longdata))

(in which case the subsequent plot call works)?

-Deepayan