On Jul 18, 2010, at 4:25 AM, Josh B wrote:
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)
closeAllConnections()
results <- matrix(nrow = 1, ncol = 3)
colnames(results) <- c("y1", "y2", "y3")
require(rms) # or Design
for (i in 1:2) {
mod.poly3 <- try(lrm(x[,i] ~ pol(x1, 3) + pol(x2, 3), data=x),
silent=TRUE)
if(class(mod.poly3)[1] != 'try-error')
{results[1,i] <- anova(mod.poly3)[1,3]}
}
> results
y1 y2 y3
[1,] 0.6976063 NA NA
...and here's the output:
results
y1 y2 y3
[1,] NA NA NA
The results matrix is empty!
________________________________
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]]
______________________________________________
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
______________________________________________
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.
