Using tryCatch in a for loop

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 at gmail.com>
Sent: May 22, 2018 2:13 PM
To: Bailey Hewitt
Cc: r-help at 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 at 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