avoid error within for loop, try, trycatch, while, move to next iteration, unlist

f <- function(x){ stopifnot(x>0.5) ; x }
o <- numeric(100); for(i in seq_along(o)) { while(inherits(try(tmp <- f(runif(1)), silent=TRUE), "try-error")) {} ; o[[i]] <- tmp }
range(o)

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
Of ?e???da? ?pa?t??
Sent: Saturday, May 26, 2012 6:15 AM
To: r-help at r-project.org
Subject: [R] avoid error within for loop, try, trycatch, while, move to next iteration, unlist




Hi there,

I would like to ask something about how to avoid a possible error message within a for
loop. I am running a simulation and in some repetitions there may be an error that will
cause a crash and stop the whole procedure, what I want is to simply move on to the
next iteration automatically and discard the "bad" repetitions from my results. I used the
"try" function to do this and it partially works.

Here is the thing:

logitsboots <- function(x,y,Jbh) {
logitseb=0;logitspb=0;
for (j in 1:1) {


#some code here that has to do with random numbers that may or may not produce an
error and calculates the values of two scalar quantities: spboots? and seboots,


? logitspb=log(spboots/(1-spboots))
? logitseb=log(seboots/(1-seboots))

#assume that I only care about logitseb for the moment
}
list(lse=logitseb)

}



# Now the following works just fine:


res=0
for(bb in 1:100) {
res[bb] <- try(logitsboots(x,y,Jbh), TRUE)
??? }
az=unlist(res[sapply(res, function(x) !inherits(x, "try-error"))])




#So far, so good and everything is working fine with "az" having the values of lse having
also discarded the "bad" iterations.


However I would like to store (as an output) both values (logitse AND logitsp) in the
function logitsboots, that is the list would be as :


list(lse=logitseb,lsp=logitspb).

This way the quantity "res" would have two arguments: res$lse and res$lsp each time it is
called. However when an error occures I just cannot seem to manage to "unlist" the "res"
properly since typing "res$lse" for example will warn me that the "$" operator will not
work (since it is not numeric anymore I guess). Something like the following would fail,
but I guess that clears what I want to do.


az1=unlist(res$lse[sapply(res$lse, function(x) !inherits(x, "try-error"))])

az2=unlist(res$lsp[sapply(res$lsp, function(x) !inherits(x, "try-error"))])

My final goal is to obtain 100 values of lse and 100 values of lsp. (Of course since the
iterations leading to an error would be discarded I will end up with less than 100
iterations. Any ideas of also using the "while" here in combination with the "try" to just
discard the bad iterations and replace them with new good ones would be great. This
way I would actually get exactly 100 values of lse and lsp).

Most important is to manage to keep both values in a two column matrix or something. I
hope I was clear enough..



Thanx in advance for any answers!

Leo.
	[[alternative HTML version deleted]]

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
Of William Dunlap
Sent: Saturday, May 26, 2012 9:20 AM
To: ???????? ???????; r-help at r-project.org
Subject: Re: [R] avoid error within for loop, try, trycatch, while, move to next iteration,
unlist

You could put the try() into a while loop, inside for for or lapply loop,
as in:

f <- function(x){ stopifnot(x>0.5) ; x }
o <- numeric(100); for(i in seq_along(o)) { while(inherits(try(tmp <- f(runif(1)),

silent=TRUE), "try-error")) {} ; o[[i]] <- tmp }

range(o)

[1] 0.5000588 0.9991261

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
Of ?e???da? ?pa?t??
Sent: Saturday, May 26, 2012 6:15 AM
To: r-help at r-project.org
Subject: [R] avoid error within for loop, try, trycatch, while, move to next iteration,

unlist

Hi there,

I would like to ask something about how to avoid a possible error message within a for
loop. I am running a simulation and in some repetitions there may be an error that will
cause a crash and stop the whole procedure, what I want is to simply move on to the
next iteration automatically and discard the "bad" repetitions from my results. I used

the

"try" function to do this and it partially works.

Here is the thing:

logitsboots <- function(x,y,Jbh) {
logitseb=0;logitspb=0;
for (j in 1:1) {


#some code here that has to do with random numbers that may or may not produce an
error and calculates the values of two scalar quantities: spboots? and seboots,


? logitspb=log(spboots/(1-spboots))
? logitseb=log(seboots/(1-seboots))

#assume that I only care about logitseb for the moment
}
list(lse=logitseb)

}



# Now the following works just fine:


res=0
for(bb in 1:100) {
res[bb] <- try(logitsboots(x,y,Jbh), TRUE)
??? }
az=unlist(res[sapply(res, function(x) !inherits(x, "try-error"))])




#So far, so good and everything is working fine with "az" having the values of lse having
also discarded the "bad" iterations.


However I would like to store (as an output) both values (logitse AND logitsp) in the
function logitsboots, that is the list would be as :


list(lse=logitseb,lsp=logitspb).

This way the quantity "res" would have two arguments: res$lse and res$lsp each time it

is

called. However when an error occures I just cannot seem to manage to "unlist" the

"res"

properly since typing "res$lse" for example will warn me that the "$" operator will not
work (since it is not numeric anymore I guess). Something like the following would fail,
but I guess that clears what I want to do.


az1=unlist(res$lse[sapply(res$lse, function(x) !inherits(x, "try-error"))])

az2=unlist(res$lsp[sapply(res$lsp, function(x) !inherits(x, "try-error"))])

My final goal is to obtain 100 values of lse and 100 values of lsp. (Of course since the
iterations leading to an error would be discarded I will end up with less than 100
iterations. Any ideas of also using the "while" here in combination with the "try" to just
discard the bad iterations and replace them with new good ones would be great. This
way I would actually get exactly 100 values of lse and lsp).

Most important is to manage to keep both values in a two column matrix or something.

I

hope I was clear enough..



Thanx in advance for any answers!

Leo.
	[[alternative HTML version deleted]]