Re: [R] How to say "if error"
Thanks again Joris - you've been very helpful J
From: Joris FA Meys [via R]
[mailto:ml-node+2267176-1824205151-120...@n4.nabble.com]
Sent: 24 June 2010 16:40
To: Paul Chatfield
Subject: Re: How to say "if error"
You could do that using the options, eg :
set.seed(1)
x <- rnorm(1:10)
y <- letters[1:10]
z <- rnorm(1:10)
warn <-getOption("warn")
options(warn=2)
for (i in list(x,y,z)){
cc <- try(mean(i), silent=T)
if(is(cc,"try-error")) {next}
print(cc)
}
options(warn=warn)
see ?options under "warn"
Cheers
Joris
On Thu, Jun 24, 2010 at 5:12 PM, Paul Chatfield
<[hidden email]> wrote:
>
> On a similar issue, how can you detect a warning in a loop - e.g. the
> following gives a warning, so I'd like to set up code to recognise
that and
> then carry on in a loop
>
> x<-rnorm(2);y<-c(1,0)
> ff<-glm(y/23~x, family=binomial)
>
> so this would be incorporated into a loop that might be
>
> x<-rnorm(10);y<-rep(c(1,0),5)
> for (i in 1:10)
> {ee<-glm(y~x, family=binomial)
> ff<-glm(y/23~x, family=binomial)}
>
> from which I would recognise the warning in ff and not those in ee,
saving
> results from ee and not from ff. The last bit would be easy adding a
line
> if(there_is_a_warning_message) {newvector<-NA} else {use results} but
how do
> you detect the warning message?
>
> Thanks all for your feedback so far,
>
> Paul
> --
> View this message in context:
http://r.789695.n4.nabble.com/How-to-say-if-error-tp2266619p2267140.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
[hidden email]
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Re: [R] How to say "if error"
On 24/06/2010 11:12 AM, Paul Chatfield wrote:
On a similar issue, how can you detect a warning in a loop - e.g. the
following gives a warning, so I'd like to set up code to recognise that and
then carry on in a loop
x<-rnorm(2);y<-c(1,0)
ff<-glm(y/23~x, family=binomial)
so this would be incorporated into a loop that might be
x<-rnorm(10);y<-rep(c(1,0),5)
for (i in 1:10)
{ee<-glm(y~x, family=binomial)
ff<-glm(y/23~x, family=binomial)}
from which I would recognise the warning in ff and not those in ee, saving
results from ee and not from ff. The last bit would be easy adding a line
if(there_is_a_warning_message) {newvector<-NA} else {use results} but how do
you detect the warning message?
Thanks all for your feedback so far,
tryCatch(..., warning=function(w) NA)
will work. For example,
x <- rnorm(10)
y <- rep(c(1,0),5)
ee <- list()
ff <- list()
for (i in 1:10) {
ee[[i]] <- glm(y~x, family=binomial)
ff[[i]] <- tryCatch(glm(y/i ~ x, family=binomial),
warning=function(w) NA)
}
will give 10 fits in ee, but only one in ff (along with 9 NAs).
Duncan Murdoch
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Re: [R] How to say "if error"
You could do that using the options, eg :
set.seed(1)
x <- rnorm(1:10)
y <- letters[1:10]
z <- rnorm(1:10)
warn <-getOption("warn")
options(warn=2)
for (i in list(x,y,z)){
cc <- try(mean(i), silent=T)
if(is(cc,"try-error")) {next}
print(cc)
}
options(warn=warn)
see ?options under "warn"
Cheers
Joris
On Thu, Jun 24, 2010 at 5:12 PM, Paul Chatfield
wrote:
>
> On a similar issue, how can you detect a warning in a loop - e.g. the
> following gives a warning, so I'd like to set up code to recognise that and
> then carry on in a loop
>
> x<-rnorm(2);y<-c(1,0)
> ff<-glm(y/23~x, family=binomial)
>
> so this would be incorporated into a loop that might be
>
> x<-rnorm(10);y<-rep(c(1,0),5)
> for (i in 1:10)
> {ee<-glm(y~x, family=binomial)
> ff<-glm(y/23~x, family=binomial)}
>
> from which I would recognise the warning in ff and not those in ee, saving
> results from ee and not from ff. The last bit would be easy adding a line
> if(there_is_a_warning_message) {newvector<-NA} else {use results} but how do
> you detect the warning message?
>
> Thanks all for your feedback so far,
>
> Paul
> --
> View this message in context:
> http://r.789695.n4.nabble.com/How-to-say-if-error-tp2266619p2267140.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> 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.
>
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
---
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to say "if error"
On a similar issue, how can you detect a warning in a loop - e.g. the
following gives a warning, so I'd like to set up code to recognise that and
then carry on in a loop
x<-rnorm(2);y<-c(1,0)
ff<-glm(y/23~x, family=binomial)
so this would be incorporated into a loop that might be
x<-rnorm(10);y<-rep(c(1,0),5)
for (i in 1:10)
{ee<-glm(y~x, family=binomial)
ff<-glm(y/23~x, family=binomial)}
from which I would recognise the warning in ff and not those in ee, saving
results from ee and not from ff. The last bit would be easy adding a line
if(there_is_a_warning_message) {newvector<-NA} else {use results} but how do
you detect the warning message?
Thanks all for your feedback so far,
Paul
--
View this message in context:
http://r.789695.n4.nabble.com/How-to-say-if-error-tp2266619p2267140.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] How to say "if error"
That's great. That solves it. I can work on eloquence later :) I just to
sort out that model problem:
dof<-numeric(10)
for (i in 1:10){
x<-rnorm(i-1);y<-rnorm(i-1)
cc <- try(lm(y~x), silent=T)
if(is(cc,"try-error")) {dof[i]<-NA}
else {dof[i]<-(summary(lm(rnorm(10)~rgamma(10,1,1)))$coef[1,1])}
}
Thank you!
Paul
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Re: [R] How to say "if error"
An old-fashioned and I guess also advised-against method would be to
use try() itself, eg :
set.seed(1)
x <- rnorm(1:10)
y <- letters[1:10]
z <- rnorm(1:10)
for (i in list(x,y,z)){
cc <- try(sum(i), silent=T)
if(is(cc,"try-error")) {next}
print(cc)
}
Put silent=F if you want to see the error methods. See also ?try (and ?is )
Cheers
Joris
On Thu, Jun 24, 2010 at 3:34 PM, Duncan Murdoch
wrote:
> On 24/06/2010 7:06 AM, Paul Chatfield wrote:
>>
>> I've had a look at the conditions in base and I can't get the ones to work
>> I've looked at but it is all new to me.
>> For example, I can work the examples for tryCatch, but it won't print a
>> finally message for me when I apply it to my model. Even if I could get
>> this to work, I think it would still cause a break e.g.
>> for (j in 1:10)
>> {tryCatch(ifelse(j==5, stop(j), j), finally=print("oh dear"))}
>>
>> Thanks for the suggestion though - any others?
>>
>
> I think you don't want to use finally, which is just code that's guaranteed
> to be executed at the end. You want to catch the errors and continue. For
> example,
>
> for (j in 1:10)
> { tryCatch(ifelse(j==5, stop(j), print(j)), error=function(e) {print("caught
> error"); print(e)}) }
>
> Duncan Murdoch
>
> __
> 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.
>
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
__
R-help@r-project.org mailing list
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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.
Re: [R] How to say "if error"
On 24/06/2010 7:06 AM, Paul Chatfield wrote:
I've had a look at the conditions in base and I can't get the ones to work
I've looked at but it is all new to me.
For example, I can work the examples for tryCatch, but it won't print a
finally message for me when I apply it to my model. Even if I could get
this to work, I think it would still cause a break e.g.
for (j in 1:10)
{tryCatch(ifelse(j==5, stop(j), j), finally=print("oh dear"))}
Thanks for the suggestion though - any others?
I think you don't want to use finally, which is just code that's
guaranteed to be executed at the end. You want to catch the errors and
continue. For example,
for (j in 1:10)
{ tryCatch(ifelse(j==5, stop(j), print(j)), error=function(e)
{print("caught error"); print(e)}) }
Duncan Murdoch
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Re: [R] How to say "if error"
Thanks Roman - you're right it can do more than I thought. We're close now to solving it I feel. Essentially I'm trying to get the code below to work. If the condition is satisfied, it prints 2, but it doesn't save it in z. I want it to save it even though there's an error. Perhaps you can easily see what I'm missing, x<-rnorm(0);y<-rnorm(0) z<-ifelse(tryCatch(lm(y~x), finally=print(2))==1, NA,lm(rnorm(10)~rnorm(10))) -- View this message in context: http://r.789695.n4.nabble.com/How-to-say-if-error-tp2266619p2266782.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] How to say "if error"
I've had a look at the conditions in base and I can't get the ones to work
I've looked at but it is all new to me.
For example, I can work the examples for tryCatch, but it won't print a
finally message for me when I apply it to my model. Even if I could get
this to work, I think it would still cause a break e.g.
for (j in 1:10)
{tryCatch(ifelse(j==5, stop(j), j), finally=print("oh dear"))}
Thanks for the suggestion though - any others?
--
View this message in context:
http://r.789695.n4.nabble.com/How-to-say-if-error-tp2266619p2266760.html
Sent from the R help mailing list archive at Nabble.com.
__
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Re: [R] How to say "if error"
Does ?tryCatch do what you want? -- View this message in context: http://r.789695.n4.nabble.com/How-to-say-if-error-tp2266619p2266749.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] How to say "if error"
I'm sorry, I don't understand your problem to the detail so my suggestion
may be waaay off, but how's this? You can see in vector vec - all ok values
except where there's an error.
n <- 10
vec <- rep(NA, n)
for (j in 1:n)
{tryCatch(ifelse(j==5, vec[j] <- j, j), finally=print("oh dear"))}
vec
Cheers,
Roman
On Thu, Jun 24, 2010 at 1:06 PM, Paul Chatfield [via R] <
ml-node+2266760-1183296220-76...@n4.nabble.com
> wrote:
> I've had a look at the conditions in base and I can't get the ones to work
> I've looked at but it is all new to me.
>
> For example, I can work the examples for tryCatch, but it won't print a
> finally message for me when I apply it to my model. Even if I could get
> this to work, I think it would still cause a break e.g.
> for (j in 1:10)
> {tryCatch(ifelse(j==5, stop(j), j), finally=print("oh dear"))}
>
> Thanks for the suggestion though - any others?
>
> --
> View message @
> http://r.789695.n4.nabble.com/How-to-say-if-error-tp2266619p2266760.html
> To unsubscribe from Re: How to say "if error", click here< (link removed) >.
>
>
>
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