[R] Continuing on with a loop when there's a failure
David Winsemius
dwinsemius at comcast.net
Tue Jul 13 16:34:16 CEST 2010
On Jul 13, 2010, at 10:26 AM, David Winsemius wrote:
>
> 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:
rather: "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
>
> ______________________________________________
> 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
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