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 ______________________________________________ R-help@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.
