R help - Jun 2005 - anova.lme error

Hi,

I am working with R version 2.1.0, and I seem to have run into what looks 
like a bug. I get the same error message when I run R on Windows as well as 
when I run it on Linux.

When I call anova to do a LR test from inside a function, I get an error. 
The same call works outside of a function. It appears to not find the right 
environment when called from inside a function. I have provided the code 
below.

Thanks,
Nisha Mulakken

############################

myFunction <- function(myDataFrame) {

  # Less restricted
  fit1 <- gls(y ~ dose,
              weights=varIdent(form=~1|dose),
              data=myDataFrame)

  # more restricted
  fit2 <- gls(y ~ dose,
              data=myDataFrame)

  anova.results <- anova(fit1, fit2)
  anova.results
}

df <- data.frame( y=c(12,3,45,1,53,6),
                   dose=c(0,10,200,0,10,200),
                   time=c("4.00 hrs", "4.00 hrs", "6.00
hrs", "6.00 hrs",
"8.00 hrs", "8.00 hrs"),
                   time.hours=c(4, 4, 6, 6, 8, 8),
                   rep=rep("a", 6)
                 )

## This leads to the following error:
##     Error in anova.lme(object = fit1, fit2) : Object "fit2" not
found
results <- myFunction(myDataFrame=df)

#####################################################
## The same thing outside of a function

# Less restricted
fit3 <- gls(y ~ dose,
              weights=varIdent(form=~1|dose),
              data=df)

# more restricted
fit4 <- gls(y ~ dose,
             data=df)

## This works:
anova(fit3, fit4)

## The results:
## > anova(fit3, fit4)
##     Model df      AIC      BIC    logLik   Test L.Ratio p-value
## fit3     1  5 57.98998 54.92145 -23.99499
## fit4     2  3 55.75284 53.91172 -24.87642 1 vs 2 1.76286  0.4142

You have already (incorrectly) filed this a bug report on *anova* and been 
asked to read the R FAQ and discuss this with the package maintainer.

Please do as we ask: only package maintainers can change contributed 
packages (here nlme).

On Tue, 14 Jun 2005, Nisha Mulakken wrote:
> Hi,
>
> I am working with R version 2.1.0, and I seem to have run into what looks
> like a bug. I get the same error message when I run R on Windows as well as
> when I run it on Linux.
>
> When I call anova to do a LR test from inside a function, I get an error.
> The same call works outside of a function. It appears to not find the right
> environment when called from inside a function. I have provided the code
> below.
>
> Thanks,
> Nisha Mulakken
>
> ############################
>
> myFunction <- function(myDataFrame) {
>
>  # Less restricted
>  fit1 <- gls(y ~ dose,
>              weights=varIdent(form=~1|dose),
>              data=myDataFrame)
>
>  # more restricted
>  fit2 <- gls(y ~ dose,
>              data=myDataFrame)
>
>  anova.results <- anova(fit1, fit2)
>  anova.results
> }
>
> df <- data.frame( y=c(12,3,45,1,53,6),
>                   dose=c(0,10,200,0,10,200),
>                   time=c("4.00 hrs", "4.00 hrs",
"6.00 hrs", "6.00 hrs",
> "8.00 hrs", "8.00 hrs"),
>                   time.hours=c(4, 4, 6, 6, 8, 8),
>                   rep=rep("a", 6)
>                 )
>
> ## This leads to the following error:
> ##     Error in anova.lme(object = fit1, fit2) : Object "fit2"
not found
> results <- myFunction(myDataFrame=df)
>
> #####################################################
> ## The same thing outside of a function
>
> # Less restricted
> fit3 <- gls(y ~ dose,
>              weights=varIdent(form=~1|dose),
>              data=df)
>
> # more restricted
> fit4 <- gls(y ~ dose,
>             data=df)
>
> ## This works:
> anova(fit3, fit4)
>
> ## The results:
> ## > anova(fit3, fit4)
> ##     Model df      AIC      BIC    logLik   Test L.Ratio p-value
> ## fit3     1  5 57.98998 54.92145 -23.99499
> ## fit4     2  3 55.75284 53.91172 -24.87642 1 vs 2 1.76286  0.4142
>
> ______________________________________________
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> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595