R help - Jul 2009 - Continue to finish for loop even there is an error in one of rounds.

I am trying to fit a logistic model to my 10 year data (1999-2008) by year. 
Codes like below:

Year <- c(1999: 2008)
for(y in 1:length(year)) {
        file.input <- paste("C:\\", year[y],
"\\data.csv", sep="")
table <- read.csv(file=fileinput, header=TRUE, as.is=TRUE,
na.strings=c(""))
        initial <- getInitial(percent ~ SSlogis(age, Asym, xmid, scal), data
= table)
fm1 <- nls(percent ~ SSlogis(age, Asym, xmid, scal), data = table)
        summary <- summary(fm1)
        parameters <- summary$parameters
        file.output <- paste("C:\\", year[y],
"\\parameters.csv", sep="")
        write.csv(parameters, file=file.output, row.names=FALSE)
}

However, when one of 10 years can't be converged, such as 2000, the loop
stops in that year (2000) even though the rest years (2001 to 2008) can be
converged. I would really appreciate if someone helps me on how to force the
loop function to finish all 10 rounds even when errors occur due to no
convergences for some of years.


Hongsheng (Hank) Liao
Lab Manager
Center for Quantitative Fisheries Ecology
Old Dominion University
Phone: 757-683-4571




	[[alternative HTML version deleted]]

You probably want to wrap the nls(...) in a 'try' or 'tryCatch'
function.

Scott



Scott Sherrill-Mix
Department of Microbiology
University of Pennsylvania
402B Johnson Pavilion
3610 Hamilton Walk
Philadelphia, PA  19104-6076
Phone: 215-573-3141



On Thu, Jul 30, 2009 at 1:14 PM, Liao, Hongsheng<HLiao at odu.edu>
wrote:
> I am trying to fit a logistic model to my 10 year data (1999-2008) by year.
?Codes like below:
>
> Year <- c(1999: 2008)
> for(y in 1:length(year)) {
> ? ? ? ?file.input <- paste("C:\\", year[y],
"\\data.csv", sep="")
> table <- read.csv(file=fileinput, header=TRUE, as.is=TRUE,
na.strings=c(""))
> ? ? ? ?initial <- getInitial(percent ~ SSlogis(age, Asym, xmid, scal),
data = table)
> fm1 <- nls(percent ~ SSlogis(age, Asym, xmid, scal), data = table)
> ? ? ? ?summary <- summary(fm1)
> ? ? ? ?parameters <- summary$parameters
> ? ? ? ?file.output <- paste("C:\\", year[y],
"\\parameters.csv", sep="")
> ? ? ? ?write.csv(parameters, file=file.output, row.names=FALSE)
> }
>
> However, when one of 10 years can't be converged, such as 2000, the
loop stops in that year (2000) even though the rest years (2001 to 2008) can be
converged. I would really appreciate if someone helps me on how to force the
loop function to finish all 10 rounds even when errors occur due to no
convergences for some of years.
>
>
> Hongsheng (Hank) Liao
> Lab Manager
> Center for Quantitative Fisheries Ecology
> Old Dominion University
> Phone: 757-683-4571
>
>
>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>