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

David Winsemius dwinsemius at comcast.net
Tue Jul 13 16:26:10 CEST 2010 

On Jul 13, 2010, at 9:24 AM, Josh B wrote:

> In my opinion the try and tryCatch commands are written and  
> documented rather poorly. Thus I am not sure what to program exactly.

Didn't  you see the "silent" parameter? Its seems to be documented  
fairly clearly to me.

The testing of try at the console is not going to be very  
illuminating, since it really only has value within a function that  
you want to continue despite an error. try() WILL provide that  
facility but _you_ need to decide what you do with the information it  
returns, which in the case of its use with the default silent=FALSE is  
just the error message itself.


>
> For instance, I could query mod.poly3 and use an if/then statement  
> to proceed,

  So why didn't you? A good result would be signaled by: "lrm" %in&  
class(mod.poly3)

-- 
David.

> but querying mod.poly3 is weird. For instance, here's the output  
> when it fails:
>
> > mod.poly3 <- try(lrm(x[,2] ~ pol(x1, 3) + pol(x2, 3), data=x))
> Error in fitter(X, Y, penalty.matrix = penalty.matrix, tol = tol,  
> weights = weights,  :
>   NA/NaN/Inf in foreign function call (arg 1)
> > mod.poly3
> [1] "Error in fitter(X, Y, penalty.matrix = penalty.matrix, tol =  
> tol, weights = weights,  : \n  NA/NaN/Inf in foreign function call  
> (arg 1)\n"
> attr(,"class")
> [1] "try-error"
>
> ...and here's the output when it succeeds:
> > mod.poly3 <- try(lrm(x[,1] ~ pol(x1, 3) + pol(x2, 3), data=x))
> > mod.poly3
>
> Logistic Regression Model
>
> lrm(formula = x[, 1] ~ pol(x1, 3) + pol(x2, 3), data = x)
>
>
> Frequencies of Responses
> bagels donuts
>     10      5
>
>        Obs  Max Deriv Model L.R.       d.f.          P          C
>         15      4e-04       3.37          6     0.7616       0.76
>        Dxy      Gamma      Tau-a         R2      Brier          g
>       0.52       0.52      0.248      0.279      0.183      1.411
>         gr         gp
>        4.1      0.261
>
>           Coef     S.E.    Wald Z P
> Intercept -5.68583 5.23295 -1.09  0.2772
> x1         1.87020 2.14635  0.87  0.3836
> x1^2      -0.42494 0.48286 -0.88  0.3788
> x1^3       0.02845 0.03120  0.91  0.3618
> x2         3.49560 3.54796  0.99  0.3245
> x2^2      -0.94888 0.82067 -1.16  0.2476
> x2^3       0.06362 0.05098  1.25  0.2121
>
> ...so what exactly would I query to design my if/then statement?
>
> From: David Winsemius <dwinsemius at comcast.net>
> To: David Winsemius <dwinsemius at comcast.net>
> Cc: Josh B <joshb41 at yahoo.com>; R Help <r-help at r-project.org>
> Sent: Tue, July 13, 2010 9:09:04 AM
> Subject: Re: [R] Continuing on with a loop when there's a failure
>
>
> On Jul 13, 2010, at 9:04 AM, David Winsemius wrote:
>
> >
> > On Jul 13, 2010, at 8:47 AM, Josh B wrote:
> >
> >> Thanks again, David.
> >>
> >> ...but, alas, I still can't get it work!
>
> (BTW, it did 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.
>
> (Or I suppose you could wrap both the lrm and the anova calls in try.)
>
> > 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
> >
> > ______________________________________________
> > 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.
>
> David Winsemius, MD
> West Hartford, CT
>
>
>

David Winsemius, MD
West Hartford, CT

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