[R] panel ordering in nlme and augPred plots

[Spencer Graves]

	  I'm not sufficiently familiar with 'trellis' / 'lattice' to provide 
an easy, complete answer to your question, but I can explain the current 
behavior and provide a hack to get you what you want.  With luck, 
someone else will suggest an improvement.

	  First, let's decompose your lovely, self-contained example in a more 
informative way:

fm <- lme(Orthodont)
ap <- augPred(fm, level = 0:1)
plot(ap, skip = rep(c(F,T), c(16, 2)))

	  Next, let's examine the structure of 'ap':

str(ap)
Classes augPred  and `data.frame':	2862 obs. of  4 variables:
  $ age     : num  8 10 12 14 8 10 12 14 8 10 ...
  $ .groups : Ord.factor w/ 27 levels "M16"<"M05"<"M02"<..: 15 15 15 15 
3 3 3 3 7 7 ...
   ..- attr(*, "label")= chr "Subject"
<snip ...>

	  The key here is that 'ap$.groups' is of class Ord.factor with levels 
as follows:

 > levels(ap$.groups)
  [1] "M16" "M05" "M02" "M11" "M07" "M08" "M03" "M12" "M13" "M14" "M09" 
"M15"
[13] "M06" "M04" "M01" "M10" "F10" "F09" "F06" "F01" "F05" "F07" "F02" "F08"
[25] "F03" "F04" "F11"
	
	  These names appear in the same order here that they appear in the 
trellis display, reading the display from left to right and bottom to 
top -- NOT top to bottom.

	  This also tells you one way to get around this:  Change the order of 
the levels.  We can do this as follows:

ap2 <- ap
ap2$.groups <- with(ap,
       ordered(as.character(.groups),
               sort(levels(.groups))))
plot(ap2, skip = rep(c(F,T), c(11, 1)))

	  Hope this helps.
	  Spencer Graves	

Nathaniel Derby wrote:
> Hi,
> 
> I'm new at this, I'm very confused, and I think I'm missing something
> important here.  In our pet example we have this:
> 
>> fm <- lme(Orthodont)
>> plot(Orthodont)
>> plot(augPred(fm, level = 0:1))
> 
> which gives us a trellis plot with the females above the males,
> starting with "F03", "F04", "F11", "F06", etc.  I thought the point of
> this was to create an ordering where the females are ordered ("F01",
> "F02", "F03", etc -- followed by the males being ordered).  However,
> the solution given ...
> 
>> fm <- lme(Orthodont)
>> plot(Orthodont)
>> plot(augPred(fm1, level = 0:1), skip = rep(c(F,T), c(16, 2)))
> 
> ... doesn't solve it -- although it does do all the females before
> starting on the males.  That is, it starts with "F02", "F08", "F03",
> ... which isn't in order either.
> 
> Running Petr's code also gave output which wasn't ordered by the subjects.
> 
> Could someone please explain to me how to order the panels of the
> trellis plot by the subjects?
> 
> 
> thanks,
> 
> Nandor
> 
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