when vectorising does not work: silent function fail?

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

-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

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