[R] tryCatch - Continuing for/next loop after error
Dear all,
I am not sure I understand fully the functionality of tryCatch and
try commands and how these are used to continue a for/next loop if an
error occurs within the loop.
Can somebody point me to material (or share some code) with more
extensive examples than the ones in the help/FAQ pages?
Do explain my problem in more detail:
for (i in 100:1000)
{
## do some other stuff
dataset-head(data,i)
tryCatch(estimatemodel(dataset))
}
My for/next loop reads in data (increasing the dataset by one point at
every loop run) and then estimates a model. When the problem is
computationally singular, the loop exits. I want to continue the loop
and register an error estimation value for that step. However when I
use use the try tryCatch(estimatemodel(data)) (where estimatemodel() is
a wrapper function calling the model estimation and optimization
routines), the problem still persists.
Is this the correct way to use tryCatch (or try) or should these go
inside the actual code bits (i.e., in a more low level fashion) that
conduct the optimization and model estimation?
Apologies if this is not clear enough.
Best,
Costas
__
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] tryCatch - Continuing for/next loop after error
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
Dear all,
I am not sure I understand fully the functionality of tryCatch and
try commands and how these are used to continue a for/next loop if an
error occurs within the loop.
Can somebody point me to material (or share some code) with more
extensive examples than the ones in the help/FAQ pages?
Do explain my problem in more detail:
for (i in 100:1000)
{
## do some other stuff
dataset-head(data,i)
tryCatch(estimatemodel(dataset))
if estimatemodel returns an error (i.e. via a call to stop()), then this
should break out of the loop:
tryCatch(estimatemodel(dataset), error = function() break)
if you want to skip to the next iteration, use:
tryCatch(estimatemodel(dataset), error = function() next)
}
My for/next loop reads in data (increasing the dataset by one point at
every loop run) and then estimates a model. When the problem is
computationally singular, the loop exits. I want to continue the loop
and register an error estimation value for that step. However when I
use use the try tryCatch(estimatemodel(data)) (where estimatemodel() is
a wrapper function calling the model estimation and optimization
routines), the problem still persists.
Is this the correct way to use tryCatch (or try) or should these go
inside the actual code bits (i.e., in a more low level fashion) that
conduct the optimization and model estimation?
Apologies if this is not clear enough.
Best,
Costas
__
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.
__
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] tryCatch - Continuing for/next loop after error
Hi Jonathan, I was also trying to understand this tryCatch function on
my own problem. Here is mine:
fn1 - function(x) {
if(as.integer(x) == 5) {
stop(stop)
}
return(x+5)
}
res - matrix(NA, 5, 7)
for(i in 1:5) {
for(j in 1:7) {
res[i,j] - tryCatch(fn1(j), error = function()
next)
}
}
I was expecting while completion of these loops, the 5th column of
'res' will have NA values. However I got some error:
Error in value[[3L]](cond) : unused argument(s) (cond)
What is the actual problem here?
Thanks,
On Thu, Mar 10, 2011 at 7:19 PM, Jonathan P Daily jda...@usgs.gov wrote:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
Dear all,
I am not sure I understand fully the functionality of tryCatch and
try commands and how these are used to continue a for/next loop if an
error occurs within the loop.
Can somebody point me to material (or share some code) with more
extensive examples than the ones in the help/FAQ pages?
Do explain my problem in more detail:
for (i in 100:1000)
{
## do some other stuff
dataset-head(data,i)
tryCatch(estimatemodel(dataset))
if estimatemodel returns an error (i.e. via a call to stop()), then this
should break out of the loop:
tryCatch(estimatemodel(dataset), error = function() break)
if you want to skip to the next iteration, use:
tryCatch(estimatemodel(dataset), error = function() next)
}
My for/next loop reads in data (increasing the dataset by one point at
every loop run) and then estimates a model. When the problem is
computationally singular, the loop exits. I want to continue the loop
and register an error estimation value for that step. However when I
use use the try tryCatch(estimatemodel(data)) (where estimatemodel() is
a wrapper function calling the model estimation and optimization
routines), the problem still persists.
Is this the correct way to use tryCatch (or try) or should these go
inside the actual code bits (i.e., in a more low level fashion) that
conduct the optimization and model estimation?
Apologies if this is not clear enough.
Best,
Costas
__
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.
__
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.
__
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] tryCatch - Continuing for/next loop after error
Wow, I had a major brain fart there. The function after error was supposed
to accept an argument, and next won't do anything there because inside the
function there is no loop. Also, the first argument of tryCatch is an
expression, so do the assignment there. Corrections inline below:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
Nipesh Bajaj bajaj141...@gmail.com wrote on 03/10/2011 10:21:38 AM:
[image removed]
Re: [R] tryCatch - Continuing for/next loop after error
Nipesh Bajaj
to:
Jonathan P Daily
03/10/2011 10:21 AM
Cc:
r-help
Hi Jonathan, I was also trying to understand this tryCatch function on
my own problem. Here is mine:
fn1 - function(x) {
if(as.integer(x) == 5) {
stop(stop)
}
return(x+5)
}
res - matrix(NA, 5, 7)
for(i in 1:5) {
for(j in 1:7) {
res[i,j] - tryCatch(fn1(j), error = function() next)
}
}
for(i in 1:5) { for(j in 1:7) {
tryCatch(res[i,j] - fn1(j), error = function(x) x)
} }
I was expecting while completion of these loops, the 5th column of
'res' will have NA values. However I got some error:
Error in value[[3L]](cond) : unused argument(s) (cond)
What is the actual problem here?
Thanks,
On Thu, Mar 10, 2011 at 7:19 PM, Jonathan P Daily jda...@usgs.gov
wrote:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue
it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
Dear all,
I am not sure I understand fully the functionality of tryCatch and
try commands and how these are used to continue a for/next loop if
an
error occurs within the loop.
Can somebody point me to material (or share some code) with more
extensive examples than the ones in the help/FAQ pages?
Do explain my problem in more detail:
for (i in 100:1000)
{
## do some other stuff
dataset-head(data,i)
tryCatch(estimatemodel(dataset))
if estimatemodel returns an error (i.e. via a call to stop()), then
this
should break out of the loop:
tryCatch(estimatemodel(dataset), error = function() break)
if you want to skip to the next iteration, use:
tryCatch(estimatemodel(dataset), error = function() next)
}
My for/next loop reads in data (increasing the dataset by one point
at
every loop run) and then estimates a model. When the problem is
computationally singular, the loop exits. I want to continue the loop
and register an error estimation value for that step. However when
I
use use the try tryCatch(estimatemodel(data)) (where estimatemodel()
is
a wrapper function calling the model estimation and optimization
routines), the problem still persists.
Is this the correct way to use tryCatch (or try) or should these go
inside the actual code bits (i.e., in a more low level fashion) that
conduct the optimization and model estimation?
Apologies if this is not clear enough.
Best,
Costas
__
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.
__
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.
__
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] tryCatch - Continuing for/next loop after error
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Jonathan P Daily
Sent: Thursday, March 10, 2011 7:49 AM
To: Nipesh Bajaj
Cc: r-help@r-project.org
Subject: Re: [R] tryCatch - Continuing for/next loop after error
Wow, I had a major brain fart there. The function after error
was supposed
to accept an argument, and next won't do anything there
because inside the
function there is no loop. Also, the first argument of tryCatch is an
expression, so do the assignment there. Corrections inline below:
The stuff about the error handle requiring an argument and
not being able to call next() from outside of a loop is true,
but you do not need to do the assignment inside the main expression
of tryCatch(). I find it clearer if you do the assignment outside
of tryCatch() so the main expression can return one thing and the
error handler can return something else. You can use this in an
*apply() function or a for loop, while the assignment-in-tryCatch()
won't work in a *apply() call. E.g., suppose we have a function
that only works on positive odd integers:
o - function (x) {
stopifnot(x%%2 == 1, x0)
(x - 1)/2
}
Then you can use tryCatch to flag the bad inputs with a code
that tells you about the bad input:
sapply(1:5, function(i)tryCatch(o(i), error=function(e)-1000-i))
[1] 0 -1002 1 -1004 2
or with a for loop where you don't have to prefill the output
vector with any particular values:
value - numeric(5)
for(i in 1:5) value[i] - tryCatch(o(i), error=function(e)-1000-i)
value
[1] 0 -1002 1 -1004 2
To do that with with an assignment in the main expression of tryCatch
would require something like
value - -1000 -(1:5)
for(i in 1:5) tryCatch(value[i] - o(i), error=function(e)NULL)
value
[1] 0 -1002 1 -1004 2
which seems to me uglier and harder to follow since value's entries
are filled in different parts of the code.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word...
imbue it.
- Jubal Early, Firefly
Nipesh Bajaj bajaj141...@gmail.com wrote on 03/10/2011 10:21:38 AM:
[image removed]
Re: [R] tryCatch - Continuing for/next loop after error
Nipesh Bajaj
to:
Jonathan P Daily
03/10/2011 10:21 AM
Cc:
r-help
Hi Jonathan, I was also trying to understand this tryCatch
function on
my own problem. Here is mine:
fn1 - function(x) {
if(as.integer(x) == 5) {
stop(stop)
}
return(x+5)
}
res - matrix(NA, 5, 7)
for(i in 1:5) {
for(j in 1:7) {
res[i,j] - tryCatch(fn1(j), error = function() next)
}
}
for(i in 1:5) { for(j in 1:7) {
tryCatch(res[i,j] - fn1(j), error = function(x) x)
} }
I was expecting while completion of these loops, the 5th column of
'res' will have NA values. However I got some error:
Error in value[[3L]](cond) : unused argument(s) (cond)
What is the actual problem here?
Thanks,
On Thu, Mar 10, 2011 at 7:19 PM, Jonathan P Daily jda...@usgs.gov
wrote:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the
word... imbue
it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
Dear all,
I am not sure I understand fully the functionality of
tryCatch and
try commands and how these are used to continue a
for/next loop if
an
error occurs within the loop.
Can somebody point me to material (or share some code) with more
extensive examples than the ones in the help/FAQ pages?
Do explain my problem in more detail:
for (i in 100:1000)
{
## do some other stuff
dataset-head(data,i)
tryCatch(estimatemodel(dataset))
if estimatemodel returns an error (i.e. via a call to
stop()), then
this
should break out of the loop:
tryCatch(estimatemodel(dataset), error = function() break)
if you want to skip to the next iteration, use:
tryCatch(estimatemodel(dataset), error = function() next)
}
My for/next loop reads in data (increasing the dataset
by one point
at
every loop run
Re: [R] tryCatch - Continuing for/next loop after error
I did not know that. When reading the help topic for the first time
myself, I think I assumed that it returned no value since it had no Value
section, and I haven't used it in a way that it would return a value.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
William Dunlap wdun...@tibco.com wrote on 03/10/2011 11:29:59 AM:
[image removed]
RE: [R] tryCatch - Continuing for/next loop after error
William Dunlap
to:
Jonathan P Daily, Nipesh Bajaj
03/10/2011 11:30 AM
Cc:
r-help
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Jonathan P Daily
Sent: Thursday, March 10, 2011 7:49 AM
To: Nipesh Bajaj
Cc: r-help@r-project.org
Subject: Re: [R] tryCatch - Continuing for/next loop after error
Wow, I had a major brain fart there. The function after error
was supposed
to accept an argument, and next won't do anything there
because inside the
function there is no loop. Also, the first argument of tryCatch is an
expression, so do the assignment there. Corrections inline below:
The stuff about the error handle requiring an argument and
not being able to call next() from outside of a loop is true,
but you do not need to do the assignment inside the main expression
of tryCatch(). I find it clearer if you do the assignment outside
of tryCatch() so the main expression can return one thing and the
error handler can return something else. You can use this in an
*apply() function or a for loop, while the assignment-in-tryCatch()
won't work in a *apply() call. E.g., suppose we have a function
that only works on positive odd integers:
o - function (x) {
stopifnot(x%%2 == 1, x0)
(x - 1)/2
}
Then you can use tryCatch to flag the bad inputs with a code
that tells you about the bad input:
sapply(1:5, function(i)tryCatch(o(i), error=function(e)-1000-i))
[1] 0 -1002 1 -1004 2
or with a for loop where you don't have to prefill the output
vector with any particular values:
value - numeric(5)
for(i in 1:5) value[i] - tryCatch(o(i), error=function(e)-1000-i)
value
[1] 0 -1002 1 -1004 2
To do that with with an assignment in the main expression of tryCatch
would require something like
value - -1000 -(1:5)
for(i in 1:5) tryCatch(value[i] - o(i), error=function(e)NULL)
value
[1] 0 -1002 1 -1004 2
which seems to me uglier and harder to follow since value's entries
are filled in different parts of the code.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word...
imbue it.
- Jubal Early, Firefly
Nipesh Bajaj bajaj141...@gmail.com wrote on 03/10/2011 10:21:38 AM:
[image removed]
Re: [R] tryCatch - Continuing for/next loop after error
Nipesh Bajaj
to:
Jonathan P Daily
03/10/2011 10:21 AM
Cc:
r-help
Hi Jonathan, I was also trying to understand this tryCatch
function on
my own problem. Here is mine:
fn1 - function(x) {
if(as.integer(x) == 5) {
stop(stop)
}
return(x+5)
}
res - matrix(NA, 5, 7)
for(i in 1:5) {
for(j in 1:7) {
res[i,j] - tryCatch(fn1(j), error = function() next)
}
}
for(i in 1:5) { for(j in 1:7) {
tryCatch(res[i,j] - fn1(j), error = function(x) x)
} }
I was expecting while completion of these loops, the 5th column of
'res' will have NA values. However I got some error:
Error in value[[3L]](cond) : unused argument(s) (cond)
What is the actual problem here?
Thanks,
On Thu, Mar 10, 2011 at 7:19 PM, Jonathan P Daily jda...@usgs.gov
wrote:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the
word... imbue
it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
