R devel - Jul 2013 - Problem with anova and the new abbreviation restrictions

An unwanted side effect of the new restrictions on abrreviated names.

The anova.coxph command, in a slavish copy of anova.lm etc, returns a data frame
with
column labels of
     loglik  Chisq  Df  Pr(>|Chi|)

If one tries to extract the final column of the table errors result since it is
not a
standard R variable name.

 > afit <- anova(lm(conc ~ uptake, CO2))
 > afit$P
[1] 2.905607e-06           NA
Warning message:
In `$.data.frame`(afit, P) : Name partially matched in data frame
 > afit$Pr(>F)
Error: unexpected '>' in "afit$Pr(>"

The second is a result of allowing TAB completion of the name.

Yes, experienced folks can sneak around it, but should this be upgraded to match
and "ease
of use" criteria?  Add an [.anova subscript method that allows for
shortened names?

I'm still in favor of an option() that controls this new behavior with
values of "allow",
"warn", and "error" so that I can at least turn it off for
me.  (I work on many data sets
created by SAS programmers that are in love with excessively long names, and use
batch
scripts so name completion isn't avail during script creation).  But this is
more local to
me, and does not address the primary question above in a general way.

Terry T

On Mon, Jul 1, 2013 at 3:51 PM, Terry Therneau <therneau at mayo.edu>
wrote:
> An unwanted side effect of the new restrictions on abrreviated names.
>
> The anova.coxph command, in a slavish copy of anova.lm etc, returns a data
> frame with column labels of
>     loglik  Chisq  Df  Pr(>|Chi|)
>
> If one tries to extract the final column of the table errors result since
it
> is not a standard R variable name.
>
>> afit <- anova(lm(conc ~ uptake, CO2))
>> afit$P
> [1] 2.905607e-06           NA
> Warning message:
> In `$.data.frame`(afit, P) : Name partially matched in data frame
I think it's reasonable to emit a warning in that case, although it
would be more useful to say:

Warning message:
P partially matched to `Pr(>|Chi|)` in data frame

Hadley

--
Chief Scientist, RStudio
http://had.co.nz/

On Mon, Jul 1, 2013 at 1:51 PM, Terry Therneau <therneau@mayo.edu> wrote:
> > afit <- anova(lm(conc ~ uptake, CO2))
> > afit$P
> [1] 2.905607e-06           NA
> Warning message:
> In `$.data.frame`(afit, P) : Name partially matched in data frame
> > afit$Pr(>F)
> Error: unexpected '>' in "afit$Pr(>"
>
> The second is a result of allowing TAB completion of the name.
>
I also noticed that  tab--completion of afit$`P gives nothing useful.

Tab-completion should definitely insert backticks when necessary and
interpret backticks when they are present.

Peter

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