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

[Federico Calboli]

On 10 Nov 2009, at 17:16, tlumley at u.washington.edu wrote:

> 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)

Both suggestions work beautifully, thanks to both!
>
> Also, you probably get less data copying by using a for() or while()  
> loop than by using apply() in this context.

I'm happy to take this in, I am not sure I can see how it would work  
(the less data copying) though.
>
> 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.

The markers are ~ 1.5M, but I don't do this kind of analysis often  
enough to justify any more work than a measly script.

Cheers,

Fede


>
>      -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

--
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 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com