Re: [Rd] trouble with accentuated characters in \title tag in Rd file

[LaurentRdevel]

Le 09/02/2013 19:54, Uwe Ligges a écrit :

See Writing R Extensions:

"Since R version 2.12.0 markup has been supported in the text, but use 
of characters other than English text and punctuation (e.g., ‘<’) may 
limit portability."


So the answer is: Don't do that.

Best,
Uwe Ligges



On 09.02.2013 19:27, LaurentRdevel wrote:

Dear R-devel-list,

   Since I had no answer on the R-help-list
(http://permalink.gmane.org/gmane.comp.lang.r.general/284539) I try to
present my trouble on the R-devel-list. I am sure in the past (one year
ago) to succeed in putting accentuated characters in the \title tag in a
.Rd file. Recently, creating a package, I have NA in the title function
instead of the text containing the accentuated character.

Could you please tell me what I missed in the understanding of package
documentation creation ? Except the title, all works fine.

Best regards
Laurent

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Thank you very much for your answer.

I didn't think that it was the cause of my trouble because it worked for 
the \description tag, so I will not do that in title tags.


Thank you again
Laurent

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Re: [Rd] Regression stars

[Frank Harrell]

Great discussion.   Tim's Sinclair quote is priceless and relates to the
non-reproducible research done in some quarters.   Norm's wish to remove
stars altogether is entirely consistent with good statistical practice and
would make a statement that R base adheres to good practice.  I don't think
it will work to add confidence intervals because models can have nonlinear
or interaction terms, and the reference cell for a factor variable may not
be what the analyst chooses for a comparison group.

I would like for us to find a way to, over time, implement Norm's wish to
de-emphasize P-values in general.  The harm done  by P-values is
immeasureable.

Frank

Norm Matloff wrote
> I appreciate Tim's comments.
> 
> I myself have a "social science" paper coming out soon in which I felt
> forced to use p-values, given their ubiquity.  However, I also told
> readers of the paper that confidence intervals are much more informative
> and I do provide them.  As I said earlier, there is no avoiding that,
> and R needs to report p-values for that reason.  
> 
> Instead, the question is what to do about the stars; I proposed
> eliminating them altogether.  Star-crazed users know how to determine
> them themselves from the p-values, but deleting them from R would send a
> message.
> 
> I did say my proposal was "bold," which really meant I was suggesting
> that R do SOMETHING to send that message, not necessarily star
> elimination.
> 
> One such "something" would be the proposal I made, which would be to add
> confidence intervals to the output.  This too could be just an option,
> but again offering that option would send a message.  Indeed, I would
> suggest that the help page explain that confidence intervals are more
> informative.  (The help page could make a similar statement regarding
> the stars.)
> 
> When I pitch R to people, I say that in addition to the large function
> and library base and the nice graphics capabilities, R is above all
> Statistically Correct--it's written by statisticians who know what they
> are doing, rather than some programmer simply implementing a formula
> from a textbook.  I know that a lot of people feel this is one of R's
> biggest strengths.  Given that, one might argue that R should do what it
> can to help users engage in good statistical practice.  I think this was
> Frank's point.
> 
> Norm
> 
> __

> R-devel@

>  mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel





-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context: 
http://r.789695.n4.nabble.com/Regression-stars-tp4657795p4658084.html
Sent from the R devel mailing list archive at Nabble.com.

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Re: [Rd] large sysdata.rda file --- strategies?

[Uwe Ligges]

On 07.02.2013 15:41, Dr. Peter Ruckdeschel wrote:

Hi,

to speed up computations in our RobASt family of packages, we use
interpolation on a grid of precomputed values which we save together
with the interpolating functions (results of splinefun essentially)
in sysdata.rda in the R folder of our pkg.

After adding grids for some more models, this file has grown
considerably, even after application of tools::resaveRdaFiles.
At the moment we are at about 2MB (compressed) and 8.8 MB
(uncompressed) and hence R CMD check --as-cran issues a NOTE.

We want to comply with cran policies,
   http://cran.r-project.org/web/packages/policies.html
in particular with

Where a large amount of data is required (even after compression),
consideration should be given to a separate data-only package which
can be updated only rarely (since older versions of packages are
archived in perpetuity).


Q1: Are packages only consisting of a sysdata.rda file thinkable for
submission on CRAN ? Are such pkgs the way to go for w.r.t. to the
cited policy?


Yes, given this package needs less updates than the main package, one 
should consider such a data only package that needs rare updates and 
does not flood the space with archived versions.




If this is the case, how  would one document such a package, in particular
if we do not export any objects in the NAMESPACE file?
In addition, with a sysdata.rda-only pkg,  R CMD check issues a warning
"Found directory 'R' with no source files"  Of course a workaround is
adding a comment-only file comment.R to the R folder.


If the checks will be changed not to warn in such a case, this can only 
happen for R >= 3.0.0, so your workaround to tell the checks you really 
intended such a package with R folder not containing any code sounds 
plausible for now.




Q2: Is there a lazy load / lazy data mechanism available for
sysdata.rda ? If so how would one enforce it?


It is lazy loaded. From WRE:
"if the ‘R’ subdirectory contains a file ‘sysdata.rda’ [...] this will 
be lazy-loaded into the namespace/package environment"



Best,
Uwe




Any suggestions appreciated,

Best, Peter



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Re: [Rd] Regression stars

[Duncan Murdoch]

On 13-02-09 3:49 PM, Tim Triche, Jr. wrote:

To clarify, I favor changing the defaults for stringsAsFactors and
show.signif.stars to FALSE in R-3.0.0, and view any attempt to remove
either functionality as a seemingly simple but fundamentally misguided idea.


Both of these were discussed by R Core.  I think it's unlikely the 
default for stringsAsFactors will be changed (some R Core members like 
the current behaviour), but it's fairly likely the show.signif.stars 
default will change.  (That's if someone gets around to it:  I 
personally don't care about that one.  P-values are commonly used 
statistics, and the stars are just a simple graphical display of them. 
I find some p-values to be useful, and the display to be harmless.)


I think it's really unlikely the more extreme changes (i.e. dropping 
show.signif.stars completely, or dropping p-values) will happen.


Regarding stringsAsFactors:  I'm not going to defend keeping it as is, 
I'll let the people who like it defend it.  What I will likely do is 
make a few changes so that character vectors are automatically changed 
to factors in modelling functions, so that operating with 
stringsAsFactors=FALSE doesn't trigger silly warnings.


Duncan Murdoch



This is just my opinion, of course.  The change could easily be accompanied
by a startup notice or release notes indicating that the changes have been
made, and can be reverted to past behavior if the user so desires.  Perhaps
more users will investigate the various settings, as a happy side effect.

My thanks to everyone who spends time supporting and working on R-core.



On Sat, Feb 9, 2013 at 12:44 PM, Tim Triche, Jr. wrote:


Changing the default for show.signif.stars should be sufficient to ensure
that, if people are going to get themselves into trouble, they will have to
do it on purpose.  It's just a visual cue; removing it will not remove the
underlying issue, namely blind acceptance of unlikely null models and
distributions.

For any complex problem, there is a solution that is simple, elegant, and
wrong.  As grants and careers can depend on these magic numbers, Upton
Sinclair might save everyone some trouble... It is difficult to get a man
to understand something, when his salary depends upon his not
understanding.

stringsAsFactors, however, is responsible for an endless stream of mildly
irritating misunderstandings, and defaulting that to FALSE would be very
nice.

Just my $0.02.  Defaults are one of the most powerful forces in the
universe.

Also, I liked your book.



On Sat, Feb 9, 2013 at 10:48 AM, Norm Matloff wrote:


Thanks for bringing this up, Frank.

Since many of us are "educators," I'd like to suggest a bolder approach.
Discontinue even offering the stars as an option.  Sadly, we can't stop
reporting p-values, as the world expects them, but does R need to cater
to that attitude by offering star display?  For that matter, why not
have R report confidence intervals as a default?

Many years ago, I wrote a short textbook on stat, and included a
substantial section on the dangers of significance testing.  All three
internal reviewers liked it, but the funny part is that all three said,
"I agree with this, but no one else will." :-)

Norm

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--
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper







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Re: [Rd] large sysdata.rda file --- strategies?

[Dr. Peter Ruckdeschel]

Dear Uwe,
>
> On 07.02.2013 15:41, Dr. Peter Ruckdeschel wrote:
>> Hi,
>>
>> to speed up computations in our RobASt family of packages, we use
>> interpolation on a grid of precomputed values which we save together
>> with the interpolating functions (results of splinefun essentially)
>> in sysdata.rda in the R folder of our pkg.
>>
>> After adding grids for some more models, this file has grown
>> considerably, even after application of tools::resaveRdaFiles.
>> At the moment we are at about 2MB (compressed) and 8.8 MB
>> (uncompressed) and hence R CMD check --as-cran issues a NOTE.
>>
>> We want to comply with cran policies,
>>http://cran.r-project.org/web/packages/policies.html
>> in particular with
>>> Where a large amount of data is required (even after compression),
>>> consideration should be given to a separate data-only package which
>>> can be updated only rarely (since older versions of packages are
>>> archived in perpetuity).
>>
>> Q1: Are packages only consisting of a sysdata.rda file thinkable for
>> submission on CRAN ? Are such pkgs the way to go for w.r.t. to the
>> cited policy?
>
> Yes, given this package needs less updates than the main package, one
> should consider such a data only package that needs rare updates and
> does not flood the space with archived versions.
>
Fine. We are going to do this then (albeit possibly not yet with
the next release). 

BTW: Of course the code to generate the grids would be accessible in
the main package to be compliant with open source ideas.
>> If this is the case, how  would one document such a package, in
>> particular
>> if we do not export any objects in the NAMESPACE file?
>> In addition, with a sysdata.rda-only pkg,  R CMD check issues a warning
>> "Found directory 'R' with no source files"  Of course a workaround is
>> adding a comment-only file comment.R to the R folder.
>
> If the checks will be changed not to warn in such a case, this can
> only happen for R >= 3.0.0, so your workaround to tell the checks you
> really intended such a package with R folder not containing any code
> sounds plausible for now.
>
>
>> Q2: Is there a lazy load / lazy data mechanism available for
>> sysdata.rda ? If so how would one enforce it?
>
> It is lazy loaded. From WRE:
> "if the ‘R’ subdirectory contains a file ‘sysdata.rda’ [...] this will
> be lazy-loaded into the namespace/package environment"
>
Ah must have missed this.

Many thanks for your comments.

Best, Peter
>
> Best,
> Uwe
>
>
>
>> Any suggestions appreciated,
>>
>> Best, Peter
>>


-- 
Dr. habil. Peter Ruckdeschel, Abteilung Finanzmathematik, F3.17
Fraunhofer ITWM, Fraunhofer Platz 1, 67663 Kaiserslautern
Telefon:  +49 631/31600-4699   Fax:  +49 631/31600-5699
E-Mail :  peter.ruckdesc...@itwm.fraunhofer.de
http://www.itwm.fraunhofer.de/abteilungen/finanzmathematik/mitarbeiterinnen/mitarbeiter/dr-peter-ruckdeschel.html

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