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 <dwinsem...@comcast.net>
To: David Winsemius <dwinsem...@comcast.net>
Cc: Josh B <josh...@yahoo.com>; R Help <r-help@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 <dwinsem...@comcast.net>
>> To: Josh B <josh...@yahoo.com>
>> Cc: R Help <r-help@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@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
