Re: [Rd] step() in sink() and Sweave()
On Wed, 13 Jun 2007 16:43:32 +0300, Jari Oksanen (JO) wrote: On Wed, 2007-06-13 at 13:33 +0100, Gavin Simpson wrote: Dear Developers, This change also just bit me whilst updating Sweave documents for some computer classes. Is there a work-around that can be employed so that we get both the message() bits and the print() bits in the same place for our Sweave files? If not, is there any point in filing this as a bug in R? I see there have been no (public) responses to Jari's email, yet the change is rather annoying, and I do not see the rationale for printing different parts of the output from step() in two different ways. I think this is a bug. You should not use message() with optional trace. The template for the usage in step() is first if (trace) message() and later if (trace) print() If you specifically request printing setting trace = TRUE, then you should not get message(). Interestingly, message() seems to be a warning() that cannot be suppressed by setting options. This is so annoying that I haven't updated some of my Sweave documents. It is better to have outdated documents than crippled documents. You can handle this in sink(), but I don't know any trick for Sweave (and it's a nuisance in sink() as well). The topic is on the agenda, but no released code yet. Hadley Wickham has code collecting all output, messages, warning etc that arise when an expression is evaluated which can be used in various places like sink or Sweave to solve this problem. We have already scheduled discussions for a workshop which we both attend in 3 weeks. Sorry for not replying to the original email. Best, Fritz -- --- Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München http://www.stat.uni-muenchen.de/~leisch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] step() in sink() and Sweave()
Jari Oksanen [EMAIL PROTECTED] writes:
On Wed, 2007-06-13 at 13:33 +0100, Gavin Simpson wrote:
Dear Developers,
This change also just bit me whilst updating Sweave documents for some
computer classes.
Is there a work-around that can be employed so that we get both the
message() bits and the print() bits in the same place for our Sweave
files?
If not, is there any point in filing this as a bug in R? I see there
have been no (public) responses to Jari's email, yet the change is
rather annoying, and I do not see the rationale for printing different
parts of the output from step() in two different ways.
I think this is a bug. You should not use message() with optional trace.
The template for the usage in step() is first
if (trace) message()
and later
if (trace) print()
If you specifically request printing setting trace = TRUE, then you
should not get message().
Interestingly, message() seems to be a warning() that cannot be
suppressed by setting options.
message is a condition and so is a warning. This means you have some
control over them. For example, you can create a wrapper for step
that uses withCallingHandlers to cat out all messages (or print them,
or email them to your friends :-)
mystep - function(object, scope, scale = 0,
direction = c(both, backward, forward),
trace = 1, keep = NULL, steps = 1000, k = 2,
...)
{
withCallingHandlers(step(object=object, scope=scope, scale=scale,
direction=direction, trace=trace,
keep=keep, steps=steps, k=k, ...),
message=function(m) {
cat(conditionMessage(m))
})
}
This is so annoying that I haven't updated some of my Sweave documents.
It is better to have outdated documents than crippled documents.
I'm not trying to argue that the function shouldn't change, but if it
is so annoying, you can also resolve this problem by defining your own
step function and calling it (forgetting about withCallingHandlers).
Clearly not ideal, but at the same time in the spirit of open source,
no?
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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Re: [Rd] step() in sink() and Sweave()
On Wed, 2007-06-13 at 08:04 -0700, Seth Falcon wrote:
Jari Oksanen [EMAIL PROTECTED] writes:
On Wed, 2007-06-13 at 13:33 +0100, Gavin Simpson wrote:
Dear Developers,
This change also just bit me whilst updating Sweave documents for some
computer classes.
Is there a work-around that can be employed so that we get both the
message() bits and the print() bits in the same place for our Sweave
files?
If not, is there any point in filing this as a bug in R? I see there
have been no (public) responses to Jari's email, yet the change is
rather annoying, and I do not see the rationale for printing different
parts of the output from step() in two different ways.
I think this is a bug. You should not use message() with optional trace.
The template for the usage in step() is first
if (trace) message()
and later
if (trace) print()
If you specifically request printing setting trace = TRUE, then you
should not get message().
Interestingly, message() seems to be a warning() that cannot be
suppressed by setting options.
message is a condition and so is a warning. This means you have some
control over them. For example, you can create a wrapper for step
that uses withCallingHandlers to cat out all messages (or print them,
or email them to your friends :-)
mystep - function(object, scope, scale = 0,
direction = c(both, backward, forward),
trace = 1, keep = NULL, steps = 1000, k = 2,
...)
{
withCallingHandlers(step(object=object, scope=scope, scale=scale,
direction=direction, trace=trace,
keep=keep, steps=steps, k=k, ...),
message=function(m) {
cat(conditionMessage(m))
})
}
This is so annoying that I haven't updated some of my Sweave documents.
It is better to have outdated documents than crippled documents.
I'm not trying to argue that the function shouldn't change, but if it
is so annoying, you can also resolve this problem by defining your own
step function and calling it (forgetting about withCallingHandlers).
Clearly not ideal, but at the same time in the spirit of open source,
no?
Thanks for the info on bypassing this issue Seth.
I disagree about your final comment though. If one is trying to teach
the use of step() to people in a computer practical class and you want
to show example output along with the commands used to produce it, you
can't do what you did and produce your own function - it wouldn't be a
good way to teach step() if I was using mystep() in the example code!
If this had been a report I was writing, I'd have just hacked my own
version of step that used print() all the time; one of the reasons I use
R in the first place is that I can go and do this. But this isn't an
option when teaching.
I am still a little mystified as to why the message() and print() bits
are used anyway. I mean, someone obviously felt this was a good idea or
they wouldn't have spent their time making the changes, and I accept
that I am probably not seeing the bigger picture here, but I don't see
the difference between the two bits of information and why you'd want to
treat them differently - why isn't the bit that is print()ed considered
a message for example?
Cheers,
G
+ seth
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Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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[Rd] step() in sink() and Sweave()
Dear developers, I just noticed that step() function currently prints the current model using message(), but the resulting model using print(). The relevant commands within the step() body are: if (trace) message(Start: AIC=, format(round(bAIC, 2)), \n, cut.string(deparse(as.vector(formula(fit, \n) (with example() output:) Start: AIC=190.69 Fertility ~ Agriculture + Examination + Education + Catholic + Infant.Mortality And later: if (trace) print(aod[o, ]) (with example() output:) Df Sum of SqRSSAIC - Examination 1 53.0 2158.1 189.9 none 2105.0 190.7 - Agriculture 1 307.7 2412.8 195.1 - Infant.Mortality 1 408.8 2513.8 197.0 - Catholic 1 447.7 2552.8 197.8 - Education 11162.6 3267.6 209.4 This is a nuisance if you want to divert output to a file with sink() or use step() in Sweave: the header and the table go to different places, and without message() part the print() part is crippled. It may be that there is some way to avoid this, but obviously that needs some degree of acrobatic R skills. An example of the behaviour: sink(tempfile()) example(step) sink() I assueme that the behaviour is intentional but searching NEWS did not give any information or reasoning. Would it be sensible to go back to the old behaviour? I found some Swoven files from R 2.4.0 that still put both parts of the output to the same place. For the sake of Sweave and sink, I'd prefer the one place to be stdout instead of stderr. Best wishes, Jari Oksanen -- Jari Oksanen [EMAIL PROTECTED] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
