[R] when vectorising does not work: silent function fail?

[tlumley at u.washington.edu]

On Tue, 10 Nov 2009, jim holtman wrote:

> Have you tried something like this:
>
> my.results = apply(chr, 2, function(x){
>    result <- try(anova(lrm( cpstc.f ~ x + time.cpstc + age + sex + mri))[1,3])
>    if (inherits(result, "try-error")) return(NULL)
>    result
> })
>
> This should catch the error and have NULL in that list element.

It's probably more useful to return a numeric vector of the right size, with tryCatch()

    tryCatch(anova(lrm( cpstc.f ~ x + time.cpstc + age + sex + mri))[1,3],
             error=function(e) NA)

Also, you probably get less data copying by using a for() or while() loop than by using apply() in this context.

Finally, the overhead of formula parsing and model matrix construction repeated thousands of times probably dominates this computation; if it isn't just a one-off it would probably be worth a lower-level implementation.

      -thomas


> On Tue, Nov 10, 2009 at 10:04 AM, Federico Calboli
> <f.calboli at imperial.ac.uk> wrote:
>> Dear All,
>>
>> I'm using apply to do some genetic association analysis along a chromosome,
>> with many thousands markers. For each marker the analysis is the same, so I
>> was planning to use apply(chrom, 2, somefunction)
>>
>> In the specific case I do:
>>
>> my.results = apply(chr, 2, function(x){anova(lrm( cpstc.f ~ x + time.cpstc +
>> age + sex + mri))[1,3]})
>>
>> This is all good and well in theory, but in practice the lrm() model will
>> fail for some markers and wreck the whole process. Failure for some markers
>> is no problem for me, but *predicting* which markers will fail can be hugely
>> problematic.
>>
>> I then though of creating some fucntion to catch the error messages that
>> would otherwise scr*w things over:
>>
>> my.lrm = function(x){
>> pol = NULL
>> pol = lrm( cpstc.f ~ x + time.cpstc + age + sex + mri)
>> if(length(pol) > 0)
>> rez = anova(pol)[1,3]
>> if(length(pol)  == 0)
>> rez = 1
>> rez}
>>
>> my.results = apply(chr, 2, my.lrm)
>>
>> Still no joy, even adding try() in the evaluation and
>> options(show.error.messages = F)
>>
>> I am at loss on how to get the darn function to bail out *silently* if needs
>> be so I can just smack a replacement value in --which would also have the
>> benefit of keeping the order of the markers.
>>
>> Any idea will be gratefully acknowledged.
>>
>> Best,
>>
>> Federico
>>
>>
>> --
>> Federico C. F. Calboli
>> Department of Epidemiology and Public Health
>> Imperial College, St Mary's Campus
>> Norfolk Place, London W2 1PG
>>
>> Tel  +44 (0)20 7594 1602     Fax (+44) 020 7594 3193
>>
>> f.calboli [.a.t] imperial.ac.uk
>> f.calboli [.a.t] gmail.com
>>
>> ______________________________________________
>> R-help at 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.
>>
>
>
>
> -- 
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem that you are trying to solve?
>
> ______________________________________________
> R-help at 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.
>

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle