[R] Using tryCatch in a for loop

[Bert Gunter]

(practically) ALWAYS respond to the list. I have cc'ed them here.

Others may (almost always do!) have greater insight/better answers than I.

In this case, I have no clue, but presumably your call is wrong, but as I
have no experience with the segmented.lm function, I don't care to track
down how exactly. Your tryCatch call seems to be fine, however.

-- Bert





Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Tue, May 22, 2018 at 11:30 AM, Bailey Hewitt <bailster using hotmail.com>
wrote:

> Hi Bert,
>
>
> Thank you for the quick response!
>
>
> In its current state the code prints three lines that say "warning". What
> I was expecting is that I would get a matrix with 4 columns, 1. column
> names (from the original data, ex. Lake1) 2. breakpoint year 3. slope 4.
> slope difference from the first to the second segment of the segmented
> regression. Each row in the matrix would be the results of the segmented
> regression test for each lake in the original data frame, so Lake1 results
> would be in row 2 (row 1 would be titles) and so on. If any of this is
> confusing please let me know and I will clarify!
>
>
> Thanks!
>
>
> Bailey
>
>
> ------------------------------
> *From:* Bert Gunter <bgunter.4567 using gmail.com>
> *Sent:* May 22, 2018 2:13 PM
> *To:* Bailey Hewitt
> *Cc:* r-help using R-project.org
> *Subject:* Re: [R] Using tryCatch in a for loop
>
> Others may have greater insight, but my response is: Exactly what did or
> didn't happen that makes you say the code didn't work? That is, what did or
> didn't you get when you ran it compared to your expectations?
>
> Cheers,
> Bert
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Tue, May 22, 2018 at 10:55 AM, Bailey Hewitt <bailster using hotmail.com>
> wrote:
>
> Hello All,
>
> I have been trying to use a for loop to run segmented regressions (from R
> package segmented) on many columns  of data in a data frame with the end
> goal of writing a new file with the following columns: column title,
> breakpoint year, slope, and difference in slope. Unfortunately, when one of
> the columns doesn't have a breakpoint the code stops and provides an error
> or warning. I would like the loop to keep running regardless of the
> error/warning but I want it to write that it did encounter an error or
> warning. Based on my needs I found that tryCatch appears to do what I need.
> I have looked at multiple examples, blogs, etc. as well as gone over the
> documentation and Hadley Wickham's document in Advanced R but I am still a
> novice when it comes to coding and I am having a hard time getting the code
> to work properly. Below is the code I have developed thus far (with a test
> dataset as an example):
>
> #Creating a test dataset
> Year<- c(2000, 2001, 2002, 2003, 2004)
> Lake1<- c(2, 4, 5, 2, 1)
> Lake2<- c(1, 3, -1, 4, -2)
> Lake3<- c(1, 2, 5, -3, 1)
> mydata<- data.frame(Year, Lake1, Lake2, Lake3)
>
> #Running a for loop that indicates when an error or warning occurs
> y<- mydata[,2:4]
> year <- mydata$Year
> regimeshift <- data.frame()
> for (i in 1:3){
>   tryCatch({
>     y.val <- y[,i]
>     lin.reg <- lm(y.val~year, mydata)
>     seg.reg <- segmented.lm(lin.reg, seg.Z = ~ year, psi = NA, control =
> seg.control(stop.if.error = FALSE, n.boot = 0, it.max = 20))
>     RSyear <- summary(seg.reg)$psi [1,2]
>     SlopeRegime1 <- summary(seg.reg)$coefficients[2,1]
>     SlopeDiff <- summary(seg.reg)$coefficients[3,1]
>     new.regimeshift <- data.frame(RSyear=RSyear,
> SlopeRegime1=SlopeRegime1, SlopeDiff=SlopeDiff)
>     rownames(new.regimeshift) <- colnames(y)[i]
>     regimeshift <- rbind(regimeshift,new.regimeshift)
>     print(regimeshift)
>   }, error= function(e) {cat("Error", "\n")},
>     warning= function(w) {cat("Warning", "\n")})
> }
>
> Any ideas or suggestions you might have are greatly appreciated!
>
> Bailey Hewitt
> PhD Candidate
> York University
> Ontario, Canada
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posti
> ng-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>

	[[alternative HTML version deleted]]