R help - Sep 2011 - Where to put tryCatch or similar in a very big for loop

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.

Many thanks for any suggestions you can offer.
Laura

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