Re: [R] warning inside loop
Dear William,
thank you kindly for this solution: it provides exactly what I need,
especially due to the fact that the encapsulating function returns a list,
from which I can extract all the information I need.
kind regards,
Rense Nieuwenhuis
William Dunlap wrote:
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Rense
Sent: Monday, January 11, 2010 3:07 PM
To: r-help@r-project.org
Subject: [R] warning inside loop
Hi,
I'm running some data simulations using (mixed effects)*
regression models
that show difficulty to converge. Therefore, I seek a way of capturing
warnings (of false convergence) inside a loop.
Inside that loop, I modify data and estimate a model. I do so
many times
with slightly different modifications of the data. Next, I
extract some of
the model parameters and store these in a matrix. However, as
some of the
models do not converge well, some of the stored parameters
are extracted
from the ill-converged models. Therefore, I seek a way of
automatically
detecting whether the estimation procedure has resulted in a
warning, so I
can distinguish between the well- and ill-converged models.
I have been trying to use functions as warnings(), as well as
using the
object last.warning, but unfortunately to no avail.
Try withCallingHandlers(), as in the following function
with returns the value of the expression along with
any warning messages as a list:
withWarnings
function (expr)
{
warnings - character()
retval - withCallingHandlers(expr, warning = function(ex) {
warnings - c(warnings, conditionMessage(ex))
invokeRestart(muffleWarning)
})
list(Value = retval, Warnings = warnings)
}
environment: R_GlobalEnv
Typical usage would be:
lapply(-1:1, function(i)withWarnings(log(i)))
[[1]]
[[1]]$Value
[1] NaN
[[1]]$Warnings
[1] NaNs produced
[[2]]
[[2]]$Value
[1] -Inf
[[2]]$Warnings
character(0)
[[3]]
[[3]]$Value
[1] 0
[[3]]$Warnings
character(0)
Perhaps there is some encapsulation of this already in some
package, as try() encapsulates error catching.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
Although I cannot provide a reproducible example, I
schematically represent
the procedure I seek to use below:
for (i in 1:10)
{
modify data
estimate model
evaluate whether estimation produced warning
extract model parameters, and store whether warning occured
}
I hope any one can give some guidelines on how to deal with
warnings inside
a loop.
With Kind regards,
Rense
*Although I use the lme4 package for that actual analysis, I sent my
question to this mailinglist (instead of the R mixed list)
because I believe
this is a general issue, rather than one associated
exclusively with mixed
models.
--
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and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
--
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Re: [R] warning inside loop
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Rense
Sent: Monday, January 11, 2010 3:07 PM
To: r-help@r-project.org
Subject: [R] warning inside loop
Hi,
I'm running some data simulations using (mixed effects)*
regression models
that show difficulty to converge. Therefore, I seek a way of capturing
warnings (of false convergence) inside a loop.
Inside that loop, I modify data and estimate a model. I do so
many times
with slightly different modifications of the data. Next, I
extract some of
the model parameters and store these in a matrix. However, as
some of the
models do not converge well, some of the stored parameters
are extracted
from the ill-converged models. Therefore, I seek a way of
automatically
detecting whether the estimation procedure has resulted in a
warning, so I
can distinguish between the well- and ill-converged models.
I have been trying to use functions as warnings(), as well as
using the
object last.warning, but unfortunately to no avail.
Try withCallingHandlers(), as in the following function
with returns the value of the expression along with
any warning messages as a list:
withWarnings
function (expr)
{
warnings - character()
retval - withCallingHandlers(expr, warning = function(ex) {
warnings - c(warnings, conditionMessage(ex))
invokeRestart(muffleWarning)
})
list(Value = retval, Warnings = warnings)
}
environment: R_GlobalEnv
Typical usage would be:
lapply(-1:1, function(i)withWarnings(log(i)))
[[1]]
[[1]]$Value
[1] NaN
[[1]]$Warnings
[1] NaNs produced
[[2]]
[[2]]$Value
[1] -Inf
[[2]]$Warnings
character(0)
[[3]]
[[3]]$Value
[1] 0
[[3]]$Warnings
character(0)
Perhaps there is some encapsulation of this already in some
package, as try() encapsulates error catching.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
Although I cannot provide a reproducible example, I
schematically represent
the procedure I seek to use below:
for (i in 1:10)
{
modify data
estimate model
evaluate whether estimation produced warning
extract model parameters, and store whether warning occured
}
I hope any one can give some guidelines on how to deal with
warnings inside
a loop.
With Kind regards,
Rense
*Although I use the lme4 package for that actual analysis, I sent my
question to this mailinglist (instead of the R mixed list)
because I believe
this is a general issue, rather than one associated
exclusively with mixed
models.
--
View this message in context:
http://n4.nabble.com/warning-inside-loop-tp1011667p1011667.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.
__
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] warning inside loop
What type of error do you get if it has a false converge? Does it raise an
error (if so, ?try). Is there some value you can test for? You need to
provide more details as to what happens.
On Mon, Jan 11, 2010 at 6:06 PM, Rense rense.nieuwenh...@gmail.com wrote:
Hi,
I'm running some data simulations using (mixed effects)* regression models
that show difficulty to converge. Therefore, I seek a way of capturing
warnings (of false convergence) inside a loop.
Inside that loop, I modify data and estimate a model. I do so many times
with slightly different modifications of the data. Next, I extract some of
the model parameters and store these in a matrix. However, as some of the
models do not converge well, some of the stored parameters are extracted
from the ill-converged models. Therefore, I seek a way of automatically
detecting whether the estimation procedure has resulted in a warning, so I
can distinguish between the well- and ill-converged models.
I have been trying to use functions as warnings(), as well as using the
object last.warning, but unfortunately to no avail.
Although I cannot provide a reproducible example, I schematically represent
the procedure I seek to use below:
for (i in 1:10)
{
modify data
estimate model
evaluate whether estimation produced warning
extract model parameters, and store whether warning occured
}
I hope any one can give some guidelines on how to deal with warnings inside
a loop.
With Kind regards,
Rense
*Although I use the lme4 package for that actual analysis, I sent my
question to this mailinglist (instead of the R mixed list) because I
believe
this is a general issue, rather than one associated exclusively with mixed
models.
--
View this message in context:
http://n4.nabble.com/warning-inside-loop-tp1011667p1011667.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.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
