R Catch Error And Continue
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R If Error Then
minute: Sign up R Script - How to Continue Code Execution on Error up vote 12 down vote favorite I have written an R script which includes a loop that retrieves external (web) data. The format of the data are most of the time the same, however sometimes the format changes in an unpredictable way and my loop is crashing (stops running). try function in r Is there a way to continue code execution regardless the error? I am looking for something similar to "On error Resume Next" from VBA. Thank you in advance. r share|improve this question asked Jan 13 '12 at 14:45 Financial Economist 153128 migrated from stats.stackexchange.com Jan 13 '12 at 14:54 This question came from our site for people interested in statistics, machine learning, data analysis, data mining, and data visualization. add a comment| 3 Answers 3 active oldest votes up vote 15 down vote Use try or tryCatch. for(i in something) { res <- try(expression_to_get_data) if(inherits(res, "try-error")) { #error handling code, maybe just skip this iteration using continue } #rest of iteration for case of no error } share|improve this answer answered Jan 13 '12 at 14:58 Richie Cotton 57.7k17127231 1 Use tryCatch instead of try, cleaner syntax and more control in my opinion. –Hansi Jan 13 '12 at 17:53 @Hansi: Agreed that tryCatch is cleaner once you know it, though it takes a bit longer to understand, so I figured try is more appropriate for a VBA programmer. <*ducks*> –Ri
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evaluation Expressions Domain specific languages Performant code Performance Profiling Memory Rcpp R's C interface Advanced R by Hadley Wickham Want to learn from me in person? I'm next teaching in DC, Sep 14-15. Want a http://adv-r.had.co.nz/Exceptions-Debugging.html physical copy of this material? Buy a book from amazon!. Contents How http://r.789695.n4.nabble.com/tryCatch-Continuing-for-next-loop-after-error-td3345408.html to contribute Edit this page Debugging, condition handling, and defensive programming What happens when something goes wrong with your R code? What do you do? What tools do you have to address the problem? This chapter will teach you how to fix unanticipated problems (debugging), show you how functions error in can communicate problems and how you can take action based on those communications (condition handling), and teach you how to avoid common problems before they occur (defensive programming). Debugging is the art and science of fixing unexpected problems in your code. In this section you’ll learn the tools and techniques that help you get to the root cause of an error. error in value[[3l]](cond) You’ll learn general strategies for debugging, useful R functions like traceback() and browser(), and interactive tools in RStudio. Not all problems are unexpected. When writing a function, you can often anticipate potential problems (like a non-existent file or the wrong type of input). Communicating these problems to the user is the job of conditions: errors, warnings, and messages. Fatal errors are raised by stop() and force all execution to terminate. Errors are used when there is no way for a function to continue. Warnings are generated by warning() and are used to display potential problems, such as when some elements of a vectorised input are invalid, like log(-1:2). Messages are generated by message() and are used to give informative output in a way that can easily be suppressed by the user (?suppressMessages()). I often use messages to let the user know what value the function has chosen for an important missing argument. Conditions are usually displayed prominently, in a bold font or coloured red depending on your R interface. You can tell them apart because errors always start with “Error” and
this post in threaded view ♦ ♦ | Report Content as Inappropriate ♦ ♦ 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. Jonathan P Daily Threaded Open this post in threaded view ♦ ♦ | Report Content as Inappropriate ♦ ♦ Re: 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 [hidden email] 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: > > [hidden email] > > 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 pag