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.
--
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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.nieuwenhuis@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.html<http://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]]
> -----Original Message----- > From: r-help-bounces at r-project.org > [mailto:r-help-bounces at r-project.org] On Behalf Of Rense > Sent: Monday, January 11, 2010 3:07 PM > To: r-help at 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:> withWarningsfunction (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 at 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. >