[R] Logical Indicator for Warning and Error Messages?
David Winsemius
dwinsemius at comcast.net
Mon Jan 3 06:50:25 CET 2011
On Jan 2, 2011, at 11:41 PM, David Crow wrote:
> Dear R Community-
>
>
>
> Is there a logical variable indicating the presence of a warning or
> error
> message after executing a command? I’m bootstrapping a logit model
> (1,000
> iterations, relevant code posted below), but the model fails to
> converge on
> many iterations. (I’m guessing that a small sample size and the
> combination
> of sampling with replacement, high item missingness, and list-wise
> deletion
> leads to a sparse data problem for some iterations.)
>
>
>
> Even for the iterations that fail to converge, though, the program
> produces
> parameter estimates. I would like to remove these parameter
> estimates from
> N x k matrix containing the boostrapped parameter estimates. What I
> was
> thinking of is adding a line of code to check if there is a warning
> or error
> message present, recording the iteration numbers where there are
> error/warning messages, and replacing the parameters for those
> iterations
> with NA’s. I’ve checked the help pages for the “warning”,
> “getOption”, and
> other commands, but it’s not immediately apparent to me how to check
> for the
> presence of warning or error messages.
?options
#says that if "warn" is >= 2 that warnings are turned into errors
?try
# for handling of errors
--
David.
>
>
>
> Here’s the relevant portion of the code (I’ve omitted the parts that
> recover
> parameter and fit estimates for each iteration):
>
>
>
> *************************************
>
> [Code Starts Here]
>
>
>
> #Create Objects
>
> N = 1000 #1000 iterations
>
> set.seed(7843)
>
> seed = sample(10000000, 1000)
>
>
>
> #1000 Iterations
>
> for (i in 1:N){
>
>
>
> #Bootstap (Sampling with Replacement)
>
> set.seed(seed[i])
>
> pre <- subset(cainit, time==1)
>
> sampt1 <- sort(sample(nrow(pre), nrow(pre), replace=T))
>
> sampt1 <- pre[sampt1,]
>
>
>
>
>
> #T1 Model of Vote Intention
>
> try(T1A <- glm(prop1a ~ educ + age + inc + dem + appgov + appleg +
> budget +
> co1a +
>
> prop1b + prop1d,family=binomial(link="logit"),
>
> data=sampt1, na.action=na.exclude))
>
>
>
> ##[NOTE: the “lrm” command is part of the “Design” package]
>
> try(T1a <- lrm(prop1a ~ educ + age + inc + dem + appgov + appleg +
> budget +
> co1a +
>
> prop1b + prop1d, data=sampt1))
>
> }
>
>
>
> [Code Ends Here]
>
> ******************************************
>
>
>
>
>
>
>
> The following set of warning/error messages is repeated about a
> dozen times
> at the end of the loop:
>
>
>
> Error in lrm(prop1a ~ educ + age + inc + dem + appgov + appleg +
> budget + :
>
>
> Unable to fit model using “lrm.fit”
>
> In addition: Warning messages:
>
> 1: glm.fit: fitted probabilities numerically 0 or 1 occurred
>
> 2: glm.fit: fitted probabilities numerically 0 or 1 occurred
>
> 3: glm.fit: algorithm did not converge
>
> 4: glm.fit: fitted probabilities numerically 0 or 1 occurred
>
>
>
>
>
>
>
> Any help would be greatly appreciated.
>
>
>
> Happy New Year!
>
> David
>
>
>
> ==============================
>
> David Crow
>
> Profesor-Investigador / Assistant Professor
>
> División de Estudios Internacionales
>
> Centro de Investigación y Docencia Económicas
>
>
> Carretera México-Toluca 3655
> Col. Lomas de Santa Fe
> 01210 México, D.F.
> Tel.: (+011 52 55) 5727-9800, ext. 2152
>
>
>
> ==============================
>
>
>
>
> [[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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