On 5/22/2018 11:32 AM, Bailey Hewitt 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.4...@gmail.com>
Sent: May 22, 2018 2:13 PM
To: Bailey Hewitt
Cc: r-help@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 <bails...@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
My suggestion is that you get your code to work on a single iteration
before running in a loop and wrapping the code in tryCatch
I ran your "set-up" code (before the loop). then extracted your code
from the loop, set i <- 1, and then ran the code. Here is what I got:
> i <- 1
> 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))
Warning message:
No breakpoint estimated
> RSyear <- summary(seg.reg)$psi [1,2]
> SlopeRegime1 <- summary(seg.reg)$coefficients[2,1]
> SlopeDiff <- summary(seg.reg)$coefficients[3,1]
Error in summary(seg.reg)$coefficients[3, 1] : subscript out of bounds
> new.regimeshift <- data.frame(RSyear=RSyear,
SlopeRegime1=SlopeRegime1, SlopeDiff=SlopeDiff)
Error in data.frame(RSyear = RSyear, SlopeRegime1 = SlopeRegime1,
SlopeDiff = SlopeDiff) :
object 'SlopeDiff' not found
> rownames(new.regimeshift) <- colnames(y)[i]
Error in rownames(new.regimeshift) <- colnames(y)[i] :
object 'new.regimeshift' not found
> regimeshift <- rbind(regimeshift,new.regimeshift)
Error in rbind(regimeshift, new.regimeshift) :
object 'new.regimeshift' not found
> print(regimeshift)
the immediate problems that show up are
1. there is no variable psi the summary(seg.reg) object (RSyear is NULL).
2. the coefficients[] matrix in the summary(seg.reg) object does not
have 3 rows, so you get an error and SlopeDiff is not created.
You need to correct these problems, and any others, so that your code
runs correctly when there are no data problems. Then you can worry
about trapping errors in the case where there are data problems.
Hope this is helpful,
Dan
--
Daniel Nordlund
Port Townsend, WA USA
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