[R] Continuing on with a loop when there's a failure

[David Winsemius]

On Jul 13, 2010, at 8:47 AM, Josh B wrote:

> Thanks again, David.
>
> ...but, alas, I still can't get it work! Here's what I'm trying now:
>
> for (i in 1:2) {
>     mod.poly3 <- try(lrm(x[,i] ~ pol(x1, 3) + pol(x2, 3), data=x))
>     results[1,i] <- anova(mod.poly3)[1,3]
> }

You need to do some programming. You did not get an error from the lrm  
but rather from the anova call because you tried to give the results  
of the try function to anova without first checking to see if an error  
had occurred.

-- 
David.
>
> Here's what happens (from the console):
>
> Error in fitter(X, Y, penalty.matrix = penalty.matrix, tol = tol,  
> weights = weights,  :
>   NA/NaN/Inf in foreign function call (arg 1)
> Error in UseMethod("anova") :
>   no applicable method for 'anova' applied to an object of class  
> "try-error"
>
> ...so I still can't make my results matrix. Could I ask you for some  
> specific code to make this work? I'm not that familiar with the  
> syntax for try or tryCatch, and the help files for them are pretty  
> bad, in my humble opinion.
>
> I should clarify that I actually don't care about the failed runs  
> per se. I just want R to keep going in spite of them and give me my  
> results matrix.
>
> From: David Winsemius <dwinsemius at comcast.net>
> To: Josh B <joshb41 at yahoo.com>
> Cc: R Help <r-help at r-project.org>
> Sent: Mon, July 12, 2010 8:09:03 PM
> Subject: Re: [R] Continuing on with a loop when there's a failure
>
>
> On Jul 12, 2010, at 6:18 PM, Josh B wrote:
>
> > Hi R sages,
> >
> > Here is my latest problem. Consider the following toy example:
> >
> > x <- read.table(textConnection("y1 y2 y3 x1 x2
> > indv.1 bagels donuts bagels 4 6
> > indv.2 donuts donuts donuts 5 1
> > indv.3 donuts donuts donuts 1 10
> > indv.4 donuts donuts donuts 10 9
> > indv.5 bagels donuts bagels 0 2
> > indv.6 bagels donuts bagels 2 9
> > indv.7 bagels donuts bagels 8 5
> > indv.8 bagels donuts bagels 4 1
> > indv.9 donuts donuts donuts 3 3
> > indv.10 bagels donuts bagels 5 9
> > indv.11 bagels donuts bagels 9 10
> > indv.12 bagels donuts bagels 3 1
> > indv.13 donuts donuts donuts 7 10
> > indv.14 bagels donuts bagels 2 10
> > indv.15 bagels donuts bagels 9 6"), header = TRUE)
> >
> > I want to fit a logistic regression of y1 on x1 and x2. Then I  
> want to run a
> > logistic regression of y2 on x1 and x2. Then I want to run a  
> logistic regression
> > of y3 on x1 and x2. In reality I have many more Y columns than  
> simply "y1,"
> > "y2," and "y3," so I must design a loop. Notice that y2 is  
> invariant and thus it
> > will fail. In reality, some y columns will fail for much more  
> subtle reasons.
> > Simply screening my data to eliminate invariant columns will not  
> eliminate the
> > problem.
> >
> > What I want to do is output a piece of the results from each run  
> of the loop to
> > a matrix. I want the to try each of my y columns, and not give up  
> and stop
> > running simply because a particular y column is bad. I want it to  
> give me "NA"
> > or something similar in my results matrix for the bad y columns,  
> but I want it
> > to keep going give me good data for the good y columns.
> >
> > For instance:
> > results <- matrix(nrow = 1, ncol = 3)
> > colnames(results) <- c("y1", "y2", "y3")
> >
> > for (i in 1:2) {
> > mod.poly3 <- lrm(x[,i] ~ pol(x1, 3) + pol(x2, 3), data=x)
> > results[1,i] <- anova(mod.poly3)[1,3]
> > }
> >
> > If I run this code, it gives up when fitting y2 because the y2 is  
> bad. It
> > doesn't even try to fit y3. Here's what my console shows:
> >
> >> results
> >            y1 y2 y3
> > [1,] 0.6976063 NA NA
> >
> > As you can see, it gave up before fitting y3, which would have  
> worked.
> >
> > How do I force my code to keep going through the loop, despite the  
> rotten apples
> > it encounters along the way?
>
> ?try
>
> http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-capture-or-ignore-errors-in-a-long-simulation_003f
>
> (Doesn't only apply to simulations.)
>
> > Exact code that gets the job done is what I am
> > interested in. I am a post-doc -- I am not taking any classes. I  
> promise this is
> > not a homework assignment!
>
> --
> David Winsemius, MD
> West Hartford, CT
>
>
>

David Winsemius, MD
West Hartford, CT