[R] How do I force confint() for glm() to be quiet?
I need confint() for glm() to supress the messages Waiting for profiling to be done... because they mess up the caching mechanism of pgfSweave (see https://github.com/cameronbracken/pgfSweave/issues/40). I have read the help page of confint(), but I do not know how to get the help page for the glm() version, if any such help page exists. Is there a general way of turning of output from functions in R, that would help here? Below is an example of an intended usage scenario: x - 1 set.seed(42) a - rnorm(x) b - factor(LETTERS[sample(1:7, x, replace = TRUE)]) c - factor(LETTERS[sample(1:4, x, replace = TRUE)]) my.fit - glm(c ~ b + a, family = binomial) my.results - confint(my.fit) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I force confint() for glm() to be quiet?
In stats:::confint.glm (actually it is MASS:::confint.glm) you see that the message() function is used to produce waiting for To avoid this message you can just use suppressMessages(confint(my.fit)) At least in R it works, hope it works with Sweave as well. Regards, Sina -- View this message in context: http://r.789695.n4.nabble.com/How-do-I-force-confint-for-glm-to-be-quiet-tp4459152p4459227.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I force confint() for glm() to be quiet?
On Mar 9, 2012, at 6:14 AM, Hans Ekbrand wrote:
I need confint() for glm() to supress the messages
I'm wondering if suppressMessages would be helpful? Which in turn
suggests that you do not know how to use ??, so firt you should get
in the habit of doing a helpSearch before posting.
??suppress messages
Waiting for profiling to be done...
because they mess up the caching mechanism of pgfSweave (see
https://github.com/cameronbracken/pgfSweave/issues/40).
I have read the help page of confint(), but I do not know how to get
the help page for the glm() version, if any such help page exists.
When I type ?confint.glm at my console I get this help page:
confint-MASS {MASS}
Is there a general way of turning of output from functions in R, that
would help here?
If suppressMessages is not effective then look at:
?sink
Below is an example of an intended usage scenario:
x - 1
set.seed(42)
a - rnorm(x)
b - factor(LETTERS[sample(1:7, x, replace = TRUE)])
c - factor(LETTERS[sample(1:4, x, replace = TRUE)])
my.fit - glm(c ~ b + a, family = binomial)
my.results - confint(my.fit)
G. A _minimal_ example would have had fewer iterations, but this
does seem to be effective:
suppressMessages(my.results - confint(my.fit))
--
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I force confint() for glm() to be quiet?
On 2012-03-09 15:30, David Winsemius wrote: On Mar 9, 2012, at 6:14 AM, Hans Ekbrand wrote: I need confint() for glm() to supress the messages I'm wondering if suppressMessages would be helpful? Which in turn suggests that you do not know how to use ??, so firt you should get in the habit of doing a helpSearch before posting. ??suppress messages OK, noted. Waiting for profiling to be done... because they mess up the caching mechanism of pgfSweave (see https://github.com/cameronbracken/pgfSweave/issues/40). I have read the help page of confint(), but I do not know how to get the help page for the glm() version, if any such help page exists. When I type ?confint.glm at my console I get this help page: Ah, I tried ?confint.lm without success and didn't go further. If suppressMessages is not effective then look at: ?sink OK, but since suppressMessages works, I'll stick to that. G. A _minimal_ example would have had fewer iterations, Sorry. but this does seem to be effective: suppressMessages(my.results - confint(my.fit)) Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
