John Nolan wrote:
There is a contradiction between what the help page says and what constrOptim
actually
does with the constraints. The issue is what happens on the boundary.
I don't know if this was a recent change, but the current help says:
"The starting value must be in the interior o
I agree with Hadley, and add that trying
to have an example be both an example and
a test may not be good for the example
aspect either.
Examples should make people who are ignorant
of the function twig as to how the function
works. Creating good examples is hard.
Problems that really test the
On Thu, Jun 17, 2010 at 5:22 AM, Patrick Burns wrote:
> I agree with Hadley, and add that trying
> to have an example be both an example and
> a test may not be good for the example
> aspect either.
>
> Examples should make people who are ignorant
> of the function twig as to how the function
> wo
There are a few errors in the R manual about Solaris.
1) Firstly you may know that Sun is now owned by Oracle.
2) "(Recent Sun machines are Opterons (‘amd64’) rather than ‘x86’, but 32-bit
‘x86’ executables are the default.) "
It's not true to say that recent machines are Opterons rather than
> The creation of a research compendium can be viewed as
> a form of unit testing, and the fact that R has powerful tools
> that support this process (Sweave) could be viewed as one of
> its outstanding features (relating these comments back to
> the topic of this thread).
If anything, a research
Nolan,
You are correct that there is inconsistency. The feasible region should be ui
%*% theta - ci > 0, so that log(ui %*% theta - ci) is defined.
There is a more serious problem in termination criterion for iterations:
if (is.finite(r) && is.finite(r.old) && abs(r - r.old)/(outer.eps
In `constrOptim', there is also a mistake in the reporting of function and
gradient counts. These counts, as reported, correspond to that of the vary
last "inner" iteration. However, they should be cumulatively summed up over
each outer iteration.
I have fixed this and the convergence criteri
On Thu, Jun 17, 2010 at 9:23 AM, Hadley Wickham wrote:
> > The creation of a research compendium can be viewed as
> > a form of unit testing, and the fact that R has powerful tools
> > that support this process (Sweave) could be viewed as one of
> > its outstanding features (relating these commen
One more bug in `constrOptim' that I have reported before and have also
suggested a fix, but this has also not been corrected:
if (obj > obj.old) break
This is obviously wrong when the user is trying to maximize by specifying
control$fnscale = -1.
The correct statement is the following:
if (o
On Thu, Jun 17, 2010 at 7:45 AM, Dominick Samperi wrote:
>
> On Thu, Jun 17, 2010 at 5:22 AM, Patrick Burns
> wrote:
>
> > I agree with Hadley, and add that trying
> > to have an example be both an example and
> > a test may not be good for the example
> > aspect either.
> >
> > Examples should m
On Thu, Jun 17, 2010 at 5:01 PM, Vincenzo Carey wrote:
>
> "Rare" is vague. Almost every software package in the Bioconductor
> repository has a vignette; the informal advice to contributors is that
> the vignette should take the reader through all the steps of a
> substantively interesting anal
Indeed, the R version is 2.9.2. But the package was built on the very
same system. Besides, another package built with the same version of R
but on another machine does not show this nasty behavior. Upgrading,
however, could pose more problems as it solves, since even if I could
upgrade locally, it
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