R help - Nov 2005 - anova.gls from nlme on multiple arguments within a function fails

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 
-- 
Markus Jantti
Abo Akademi University
markus.jantti at iki.fi
http://www.iki.fi/~mjantti

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:

 > 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
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
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spencer.graves at pdf.com
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