[R] warning inside loop

[Rense]

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-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:
> 
>> 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 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.
>> 
> 
> ______________________________________________
> 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.
> 
> 

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