R help - Mar 2000 - summary.negbin broken in R-1.0.0, VR_6.1-7

Dear R people,

I am not sure if this is the correct place to tell about problems in evolving 
programmes, but it seems that the `summary.negbin' function of the excellent
`MASS' library is now broken, and gives the following error message:
> summary(hm)
Error in summary.negbin(hm) : subscript out of bounds

`summary.negbin' calls `summary.glm' which seems to work and give the
desired
output like called there, but calls to `object["SE"]' fails (and
later, if it
would get there, `object["th.warn"]' would fail). The first entity
seems to be
now "SE.theta", and I did not find "th.warn" at all in my
objects.

Really a tiny thing, and if I understood the behaviour correctly, easily to 
cure by the user herself.

For the record: these errors came in R 1.0.0 from the CRAN site rpm package 
for RH Linux 6.2 and with R INSTALLed VR_6.1-7.tar.gz from the same site.

cheers, jari oksanen 
-- 
Jari Oksanen - Dept Ecol Env Sci, Univ Helsinki, 15140 Lahti
Ph. +358 3 89220312, Fax -- 89220289, Mobile +358 40 5136529
jari.oksanen at helsinki.fi    http://www.helsinki.fi/~jhoksane



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On Tue, 21 Mar 2000, Jari Oksanen wrote:
> Dear R people,
> 
> I am not sure if this is the correct place to tell about problems in
evolving
> programmes, but it seems that the `summary.negbin' function of the
excellent
> `MASS' library is now broken, and gives the following error message:
The correct thing to do with contributed code is to tell the porter/author
given in the DESCRIPTION file.  Not all of them read R-help.
> > summary(hm)
> Error in summary.negbin(hm) : subscript out of bounds
> 
> `summary.negbin' calls `summary.glm' which seems to work and give
the desired
> output like called there, but calls to `object["SE"]' fails
(and later, if it
> would get there, `object["th.warn"]' would fail). The first
entity seems to be
> now "SE.theta", and I did not find "th.warn" at all in
my objects.
Not really. S has partial matching, so object["SE"] should find 
"SE.theta".  Unfortunately, R's cloning is imperfect here, and it
fails.
There is no problem with "th.warn": it is usually missing and does
not cause a failure, as the code is (in print.summary.negbin)

    if (!is.null(x$th.warn)) 
        cat("Warning while fitting theta:", x$th.warn, "\n")
> Really a tiny thing, and if I understood the behaviour correctly, easily to
> cure by the user herself.
In this case, yes (just replace SE by SE.theta everywhere).  However, there
is a fundamental incompatibility we need to resolve.  It might be
deliberate, but I can't see it is documented.

The next release of VR will have this fixed (and a couple of other things).

-- 
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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