Oops, forgot to add the line:
library(Design)
#the lrm function is in the Design library
...but even when I load the Design library, the loop still doesn't work. It
stops after failing on the second run of the loop:
> results
y1 y2 y3
[1,] 0.6976063 NA NA
(The third run through the loop should have succeeded and left numeric output
in
the matrix called "results", but it did not).
________________________________
To: Peter Konings <peter.l.e.koni...@gmail.com>
Cc: R Help <r-help@r-project.org>
Sent: Sun, July 18, 2010 12:25:42 PM
Subject: Re: [R] Continuing on with a loop when there's a failure
Hello Peter,
I tried your suggestion, but I was still not able to get it to work. Would you
mind looking at my code again? Here's what I'm trying:
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)
results <- matrix(nrow = 1, ncol = 3)
colnames(results) <- c("y1", "y2", "y3")
for (i in 1:2) {
mod.poly3 <- try(lrm(x[,i] ~ pol(x1, 3) + pol(x2, 3), data=x))
if(class(mod.poly3) == 'try-error')
{results[1,i] <- NA}
else {mod.poly3 <- lrm(x[,i] ~ pol(x1, 3) + pol(x2, 3), data=x)
results[1,i] <- anova(mod.poly3)[1,3]
}
}
...and here's the output:
> results
y1 y2 y3
[1,] NA NA NA
[[elided Yahoo spam]]
________________________________
From: Peter Konings <peter.l.e.koni...@gmail.com>
Sent: Tue, July 13, 2010 5:45:17 PM
Subject: Re: [R] Continuing on with a loop when there's a failure
Hi Josh,
Test the class of the resulting object. If it is 'try-error' fill your result
with NA or do some other error handling.
result <- try(somemodel)
if(class(result) == 'try-error')
{
# some error handling
} else {
# whatever happens if the result is ok
}
HTH
Peter.
In my opinion the try and tryCatch commands are written and documented rather
>poorly. Thus I am not sure what to program exactly.
>
>For instance, I could query mod.poly3 and use an if/then statement to proceed,
>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>
>
>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.
>>>
>[[elided Yahoo spam]]
>
>
>(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>
>
>
>>> 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
>>>
>>>f
>>>
>>> (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
>[[elided Yahoo spam]]
>
>>>
>>> --
>>> 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
>
>
>
>
[[alternative HTML version deleted]]
>
>
>______________________________________________
>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.
>
[[alternative HTML version deleted]]
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
