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
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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.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, CanadaMy 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
Hi Dan, Thank you for trying this out! I have been able to use the segmented.lm code outside of the loop effectively. When it gave you the first warning: No breakpoint estimated, that is what I would expect it to do, and since there is no breakpoint there aren't any variables in seg.reg. What I would like to have happen is that when I get this warning, I want it to be caught by tryCatch and write "warning" in the matrix, and the loop should continue on. Is there a way to manipulate the code for this or something similar?to happen? Bert, you are right! My apologies, I did mean to reply all! Thanks! Bailey From: Daniel Nordlund <djnordlund at gmail.com> Sent: May 22, 2018 3:06 PM To: Bailey Hewitt; Bert Gunter Cc: r-help at R-project.org Subject: Re: [R] Using tryCatch in a for loop ? 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.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, CanadaMy 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
After Dan's suggestions I went back to testing the code outside the for loop again and realized I haven't included a lake that WILL have a breakpoint in my "test" dataset. Below I provide data where some of the lakes produce warnings and others produce results. The output is the matrix I want (as I described previously) but the "warning" is printed outside the final matrix. So I get results for lakes 2 and 4 but there isn't a warning written for Lake 1 and 3 in the final matrix. This is much closer so thank you Dan! Is there any way to get the final result with "warning" written in for lakes without breakpoints so that I can write it into a .csv? Bailey ________________________________ From: Daniel Nordlund <djnordlund at gmail.com> Sent: May 22, 2018 3:06 PM To: Bailey Hewitt; Bert Gunter Cc: r-help at R-project.org Subject: Re: [R] Using tryCatch in a for loop On 5/22/2018 11:32 AM, Bailey Hewitt wrote:> Hi Bert, >[[elided Hotmail spam]]> > 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 pleas[[elided Hotmail spam]] > > 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")}) > } >[[elided Hotmail spam]]> > Bailey Hewitt > PhD Candidate > York University > Ontario, CanadaMy 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 [[alternative HTML version deleted]]
Data and code as promised:
#Creating a test dataset
Year<- c(2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
2011, 2012, 2013, 2014)
Lake1<- c(2, 4, 5, 2, 1, 1, 2, 3, 4, 5, 6, 2, 3, 1, 2)
Lake2<- c(1, 3, -1, 4, -2, 1, 2, 3, 4, 5, 6, 2, 3, 1, 2)
Lake3<- c(1, 2, 5, -3, 1, 1, 2, 3, 4, 5, 6, 2, 3, 1, 2)
Lake4<- c(1, 1, 1, 1, 1, 1, 1, 250, 240, 240, 240, 240, 240, 239, 255)
mydata<- data.frame(Year, Lake1, Lake2, Lake3, Lake4)
#Running a for loop that indicates when an error or warning occurs
y<- mydata[,2:5]
year <- mydata$Year
regimeshift <- data.frame()
for (i in 1:4){
tryCatch({
y.val <- y[,i]
lin.reg <- lm(y.val~year, mydata)
seg.reg <- segmented.lm(lin.reg, seg.Z = ~ year, psi = NA, control =
seg.control(stop.if.error = FALSE, n.boot = 0, it.max = 20))
RSyear <- summary(seg.reg)$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")})
}
Bailey
From: Daniel Nordlund <djnordlund at gmail.com>
Sent: May 22, 2018 3:06 PM
To: Bailey Hewitt; Bert Gunter
Cc: r-help at R-project.org
Subject: Re: [R] Using tryCatch in a for loop
?
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.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
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