[R] Where to put tryCatch or similar in a very big for loop

[Jan van der Laan]

Laura,

Perhaps the following example helps:

nbstr <- 100
result <- numeric(nbstr)
for (i in seq_len(nbstr)) {
   # set the default value for when the current bootstrap fails
   result[i] <- NA
   try({
     # estimate your cox model here
     if (runif(1) < 0.1) stop("ERROR")
     result[i] <- i
   }, silent=TRUE)
}

Regards,
Jan




Quoting "Bonnett, Laura" <L.J.Bonnett at liverpool.ac.uk>:

> Hi,
>
> The simulation occasionally generates either a rare event meaning   
> that the Cox model is not appropriate or it generates a covariate   
> with most responses being the same which means that the Cox model   
> cannot be fit.
>
> At bootstrap sample number 10, the variable c11 is considered   
> singular by model cox1.
>
> Thanks,
> Laura
>
> -----Original Message-----
> From: Ken [mailto:vicvoncastle at gmail.com]
> Sent: 15 September 2011 21:43
> To: Bonnett, Laura
> Cc: Steve Lianoglou; r-help at r-project.org
> Subject: Re: [R] Where to put tryCatch or similar in a very big for loop
>
> What type of singularity exactly, if you're working with counts is   
> it a special case? If using a Monte Carlo generation scheme, there   
> are various workarounds such as while(sum(vec)!=0) {sample} for   
> example. More info on the error circumstances would help.
>
>    Good luck!
>     Ken Hutchison
>
> On Sep 15, 2554 BE, at 11:41 AM, "Bonnett, Laura"   
> <L.J.Bonnett at liverpool.ac.uk> wrote:
>
>> Hi Steve,
>>
>> Thanks for your response.  The slight issue is that I need to use a  
>>  different starting seed for each simulation.  If I use 'lapply'   
>> then I end up using the same seed each time.  (By contrast, I need   
>> to be able to specify which starting seed I am using).
>
>>
>> Thanks,
>> Laura
>>
>> -----Original Message-----
>> From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com]
>> Sent: 15 September 2011 16:17
>> To: Bonnett, Laura
>> Cc: r-help at r-project.org
>> Subject: Re: [R] Where to put tryCatch or similar in a very big for loop
>>
>> Hi Laura,
>>
>> On Thu, Sep 15, 2011 at 10:53 AM, Bonnett, Laura
>> <L.J.Bonnett at liverpool.ac.uk> wrote:
>>> Dear all,
>>>
>>> I am running a simulation study to test variable imputation   
>>> methods for Cox models using R 2.9.0 and Windows XP.  The code I   
>>> have written (which is rather long) works (if I set nsim = 9) with  
>>>  the following starting values.
>>>
>>>> bootrs(nsim=9,lendevdat=1500,lenvaldat=855,ac1=-0.19122,bc1=-0.18355,cc1=-0.51982,cc2=-0.49628,eprop1=0.98,eprop2=0.28,lda=0.003)
>>>
>>> I need to run the code 1400 times in total (bootstrap resampling)   
>>> however, occasionally the random numbers generated lead to a   
>>> singularity and hence the code crashes as one of the Cox model   
>>> cannot be fitted (the 10th iteration is the first time this   
>>> happens).
>>>
>>> I've been trawling the internet for ideas and it seems that there   
>>> are several options in the form of try() or tryCatch() or next.    
>>> I'm not sure however, how to include them in my code (attached).    
>>> Ideally I'd like it to run everything simulation from 1 to 1400   
>>> and if there is an error at some point get an error message   
>>> returned (I need to count how many there are) but move onto the   
>>> next number in the loop.
>>>
>>> I've tried putting try(....,silent=TRUE) around each cox model   
>>> (cph statement) but that hasn't work and I've also tried putting   
>>> try around the whole for loop without any success.
>>
>> Let's imagine you are using an `lapply` instead of `for`, only because
>> I guess you want to store the results of `bootrs` somewhere, you can
>> adapt this to your `for` solution. I typically return NULL when an
>> error is caught, then filter those out from my results, or whatever
>> you like:
>>
>> results <- lapply(1:1400, function(i) {
>>  tryCatch(bootrs(...whatever...), error=function(e) NULL)
>> })
>> went.south <- sapply(results, is.null)
>>
>> The `went.south` vector will be TRUE where an error occurred in your
>> bootrs call.
>>
>> HTH,
>> -steve
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>  | Memorial Sloan-Kettering Cancer Center
>>  | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
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>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>