anova.gls from nlme on multiple arguments within a function fails

The error is in anova.gls(): traceback() would have told you that was 
involved.  It ends

do.call("anova.lme", as.list(match.call()[-1]))

and that call needs to be evaluated in the parent, not in the body of 
anova.lme.  Several similar errors (e.g. in the update methods) in 
package nlme have been corrected over the years.

Replacing anova() by anova.lme() in dummy() works.

If you want to do this sort of thing more generally (e.g. messing with 
the contents of '...'), the elegant way is

Call <- match.call()
Call[[1]] <- as.name("anova.lme")
eval.parent(Call)

and that works here.

Since at some later point substitute() is used to find the arguments, 
here you don't want to use do.call() with the evaluated arguments, which 
is the way it is intended to be used.  Similarly, anova.lme(object, ...) 
is not what you want.


On Sun, 27 Nov 2005, Spencer Graves wrote:

      You've posed an excellent question with simple and elegant,
reproducible example.  I've seen no replies, so I will attempt a partial
response.  RSiteSearch("lexical scoping") produced some potentially
useful comments (e.g.,
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/37769.html), but nothing
that allowed me to work around the problem.

      The following modification of your example makes it clear that
"anova.lme" (called by "anova.gls") choked on the second argument not
the first:

It actually chokes on both.

dummy2 <- function(obj)

+   {
+     obj2 <- obj[[2]]
+     anova(obj[[1]], obj2)
+   }

dummy2(list(fm1, fm2))

Error in anova.lme(object = obj[[1]], obj2) :
    object "obj2" not found

      The following helped isolate this further to "dots <- 
list(...)", the
second line in "anova.lme":

debug(anova.lme)
dummy2(list(fm1, fm2))

      I don't know why your example fails, especially "anova.lm" worked.
Also, there should be a way  to use something like "assign" to work
around this problem, but nothing I tried worked.

      I know this is not a complete reply, but I hope it helps.
      spencer graves

Markus Jantti wrote:

Dear All --

I am trying to use within a little table producing code an anova
comparison of two gls fitted objects, contained in a list of such
object, obtained using nlme function gls.
The anova procedure fails to locate the second of the objects.

The following code, borrowed from the help page of anova.gls,
exemplifies:
--------------- start example code ---------------
library(nlme)

## stolen from example(anova.gls)
# AR(1) errors within each Mare
fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
           correlation = corAR1(form = ~ 1 | Mare))
anova(fm1)
# variance changes with a power of the absolute fitted values?
fm2 <- update(fm1, weights = varPower())
anova(fm1, fm2)

## now define a little function
dummy <- function(obj)
  {
    anova(obj[[1]], obj[[2]])
  }
dummy(list(fm1, fm2))

## compare with what happens in anova.lm:

lm1 <- lm(follicles ~ sin(2*pi*Time), Ovary)
lm2 <- lm(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary)
dummy(list(lm1, lm2))
------------- end example code ------------------

It is not the end of the world: I can easily work around this.
But it would be nice to know why this does not work.

Digging around using options(error=recover) did not help my much, I'm
afraid.

Best,

Markus

-- 
Spencer Graves, PhD
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