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.bonn...@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.honey...@gmail.com]
> Sent: 15 September 2011 16:17
> To: Bonnett, Laura
> Cc: r-help@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.bonn...@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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