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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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